Next Article in Journal
Establishment of a Cre-loxP System Based on a Leaky LAC4 Promoter and an Unstable panARS Element in Kluyveromyces marxianus
Next Article in Special Issue
Quorum Sensing and Quorum Quenching with a Focus on Cariogenic and Periodontopathic Oral Biofilms
Previous Article in Journal
Evaluation of Commercial Concentration Methods for Microscopic Diagnosis of Protozoa and Helminths in Human Stool Samples in a Non-Endemic Area
Previous Article in Special Issue
Anti-Virulence Properties of Plant Species: Correlation between In Vitro Activity and Efficacy in a Murine Model of Bacterial Infection
 
 
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Review

Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria

The Biofilm Research Laboratory, The Institute of Biomedical and Oral Research, The Faculty of Dental Medicine, Hadassah Medical School, The Hebrew University, Jerusalem 9112102, Israel
*
Author to whom correspondence should be addressed.
Microorganisms 2022, 10(6), 1239; https://doi.org/10.3390/microorganisms10061239
Submission received: 22 May 2022 / Revised: 12 June 2022 / Accepted: 14 June 2022 / Published: 16 June 2022

Abstract

:
Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections.

1. Introduction

The discovery of compounds with antibacterial activities has paved the way to rescue the lives of patients with serious infectious diseases. However, the rapid development of antibiotic-resistant bacterial strains has often led to treatment failure. Another medical challenge is biofilm-associated bacterial infections that are often difficult to treat due to the reduced antibiotic sensitivity of the sessile biofilm-embedded bacteria together with diminished penetrability of antibiotics through the extracellular matrix composed of extracellular polymeric substances (EPS) and other materials produced by the bacteria [1,2]. Biofilm-forming microorganisms are estimated to cause 65–80% of human infections [3,4]. Biofilms are communities of bacteria that are embedded in a hydrated, predominantly anionic matrix of bacterial exopolymers such as polysaccharides that have trapped other components from the bacteria or the surroundings including proteins, nucleic acids, lipids, teichoic acids, and various other organic molecules [1,2]. The production of EPS functions as an anchorage site for the adherence of additional bacteria. The microbes communicate with each other through quorum sensing (QS), which regulates the metabolic activity of the cells, promotes biofilm formation, and increases virulence [4]. Based on the central role of QS in the regulation of bacterial biofilm and virulence, several strategies have been developed to target this signaling system [4,5,6,7,8,9,10,11,12].
The biofilms can be formed on both biotic surfaces such as connective tissue, mucus, epithelium, endothelium, intestine, cardiac valves, bone marrow, and the skin [3,4,13,14], and abiotic surfaces such as prostheses, implants, stents, and catheters [4,14,15]. Biofilm-associated diseases include otitis media, chronic rhinosinusitis, pharyngitis, laryngitis, pneumonia, bacterial vaginosis, infective endocarditis, mastitis, atherosclerosis, osteomyelitis, meningitis, urinary tract infections, kidney infections, skin infections, and inflammatory bowel diseases [13,14,15]. Biofilms formed on biological tissues are a major etiological cause of chronic and recurrent infections. In addition, biofilm formation by oral cariogenic bacteria is associated with tooth decay and gingivitis [16]. The sessile biofilm-associated bacteria have been shown to be up to 100–1000 times more tolerant to antibiotics in comparison to the same bacteria in the planktonic state [15,17,18,19,20,21]. Thus, targeting biofilms would be a prominent approach to overcoming the antibiotic resistance of biofilm-associated infections.
Common bacteria involved in severe biofilm-associated infections include the pathogens of the “ESKAPE” group (Enterococcus spp., Staphylococcus aureus, Staphylococcus epidermidis, Klebsiella spp., Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.), which cause a variety of infections such as skin and soft tissue infections of wounds, bacteremia, urinary tract infections, meningitis, and pneumonia [22,23,24,25,26,27,28,29]. The “ESKAPE” acronym is derived from the ability of these pathogens to “escape” from antimicrobial therapy and the defense mechanisms of the immune system. These bacteria are common causes of life-threatening nosocomial infections, especially in cystic fibrosis patients, critically ill, and immunocompromised individuals [25,27]. The bacteria can adhere to both biotic and abiotic surfaces and form biofilms that are difficult to eradicate. In addition, the bacteria frequently develop resistance to existing antibiotics, which urges the development of new therapeutic strategies.
This review deals with various aspects of the interrelationship between antibiotic resistance, QS, and biofilms with a specific emphasis on pathogenic bacteria of the “ESKAPE” group. The first part describes various mechanisms involved in antibiotic resistance. The second part describes quorum sensing and various two-component systems (TCSs) affecting antibiotic resistance. The third part discusses various factors including TCSs that affect biofilm formation and the impact of biofilms on antibiotic resistance. In the last section of the review, some strategies that have been developed to break the vicious communication between quorum sensing, biofilm, and antibiotic resistance are described. Due to the enormous number of publications describing these issues, we have restricted our review to selected examples, and apologize for omitting others. The general concept is emphasized.

2. Antibiotic Resistance Mechanisms

Although the introduction of antibiotics into the clinics is indispensable for the medical treatment of severe infections, their frequent uses have led to the spread of antibiotic-resistant bacterial strains that lead to treatment failure. There are multiple mechanisms that are involved in the acquisition of antibiotic resistance. Among them, drug resistance can be caused by: (i) the acquisition of various antibiotic-resistant genes via horizontal gene transfer; (ii) decreased membrane permeability; (iii) increased production of degrading enzymes that cleave and thus inactivate the antibiotics; (iv) increased production of antibiotic modification enzymes that inactivate the antibiotics; (v) alterations of the target that disable the binding of the antibiotics; (vi) overexpression of efflux pumps that lead to rapid extrusion of the drugs with consequent low intracellular drug concentration; (vii) expression of regulatory small RNAs (sRNAs); (viii) methyltransferases that methylate 16S and 23S rRNA, thus altering the antibiotic binding site with reduced drug affinity; (ix) mutations in rRNAs; (x) ribosomal protection; (xi) changes in the metabolic state of the bacteria; (xii) biofilm formation; (xiii) elevated nutrient sequestering mechanisms; (xiv) induction of antibiotic tolerance; (xv) appearance of persister cells [20,25,28,30,31,32,33,34,35,36,37,38] (Table 1).
Some organisms show intrinsic resistance to given antibiotics, while in others the resistance mechanism can be acquired, and even induced by the antibiotic itself resulting in adaptive resistance [39,40]. The adaptive resistance is usually transient and reversed after the removal of the triggering environmental factors. Adaptive resistance is a major mechanism of how persister cells evade antibiotics [41]. Due to the high mechanistic versatility of antibiotic resistance, it is not possible to include all of them in this review, and the readers are referred to comprehensive reviews elsewhere [28,30,31,35,39,42]. We will below describe in brief the major antibiotic resistance mechanisms with selected examples. The involvement of biofilm in antibiotic resistance will be discussed in Section 4.2.
Table 1. Various antibiotic resistance mechanisms in Gram-positive and Gram-negative bacteria.
Table 1. Various antibiotic resistance mechanisms in Gram-positive and Gram-negative bacteria.
Resistance MechanismExamplesReferences
Reduced
drug uptake
-
Reduced expression of outer membrane porins (OMPs) in Gram-negative bacteria (e.g., Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii) causes resistance to β-lactams, sulbactam, imipenem, panipenem, and ertapenem.
[32,34,43,44,45]
Antibiotic
degrading
enzymes
-
Group 1 β-lactamases or cephalosporinases hydrolyze cephalosporins (e.g., Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa).
-
Group 2 β-lactamases or penicillinases cleave the β-lactam ring of penicillin (e.g., Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Staphylococcus aureus).
-
Group 3 metallo-β-lactamases or carbapenemases hydrolyze carbapenem antibiotics (e.g., Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii).
-
ereA-D erythromycin esterase genes mediate the enzymatic cleavage of the macrolactone ring of the macrolide antibiotics (e.g., Enterobacteriaceae, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella enterica, MRSA).
[25,28,34,46,47]
Antibiotic
modifying
enzymes
-
The aminoglycoside-modifying enzymes (e.g., phosphotransferases, acetyltransferases, and adenylyltransferases) inactivate gentamicin and other aminoglycoside antibiotics by catalyzing hydroxyl/amino group modifications (e.g., Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella typhimurium, Staphylococcus aureus).
-
Chloramphenicol acetyltransferase detoxifies chloramphenicol by adding an acetyl group thereby preventing its binding to ribosomes (e.g., Vibrio cholerae, Pseudomonas aeruginosa, Staphylococcus aureus, Enterococcus faecium).
-
Macrolide phosphotransferases inactivate erythromycin, azithromycin, and other macrolide antibiotics (e.g., Enterobacter, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa).
-
Tet(X)-mediated flavin-dependent monooxygenase inactivates tetracyclines including the last-resort antibiotic tigecycline by adding a hydroxyl group to the C-11a position, resulting in an unstable compound that undergoes auto-decomposition (e.g., Enterobacteriaceae, Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa).
[25,28,48,49,50]
Proteases and Peptidases
-
The protease SepA of Staphylococcus epidermidis degrades antimicrobial peptides produced by neutrophils.
-
Various membrane proteases (e.g., FtsH and HtpX) of Pseudomonas aeruginosa protect the bacteria from aminoglycoside antibiotics.
-
D-stereospecific peptidases (e.g., TriF and BogQ) lead to hydrolytic cleavage of the peptide antibiotics polymyxin, vancomycin, and teixobactin (e.g., Firmicutes, Bacillus, and Clostridium species).
-
The DD-peptidases VanX and VanY catalyze the removal of vancomycin target in peptidoglycans of Gram-positive bacteria (e.g., Staphylococcus aureus, Enterococcus faecium), resulting in resistance to this antibiotic.
[51,52,53,54]
Efflux pumps
-
AbcA, a type III ABC transporter in Staphylococcus aureus, confers resistance to β-lactams such as methicillin and cefotaxime; the phosphoglycolipid moenomycin; the lipopeptide antibiotic daptomycin.
-
AbeM in Acinetobacter baumannii extrudes fluoroquinolones.
-
AbeS in Acinetobacter baumannii confers resistance to chloramphenicol, ciprofloxacin, and erythromycin.
-
AcrAB-TolC in Enterobacter species confers resistance to β-lactams, fluoroquinolones, tigecycline, chloramphenicol, lincosamides, tetracyclines, fusidic acid, rifampin, and nalidixic acid.
-
AcrAD-TolC in Enterobacter species causes resistance to aminoglycosides, β-lactams, and quinolones.
-
AdeABC in Acinetobacter baumannii extrudes β-lactams, chloramphenicol, fluoroquinolones, tetracycline, tigecycline, macrolides, and aminoglycosides.
-
AdeFGH in Acinetobacter baumannii provides resistance to fluoroquinolones, chloramphenicol, trimethoprim, clindamycin, and to a lesser extent tetracyclines, tigecycline, and sulfamethoxazole.
-
AdeIJK in Acinetobacter baumannii provides resistance to β-lactams, fluoroquinolones, tetracyclines, tigecycline, lincosamides, rifampin, chloramphenicol, cotrimoxazole, novobiocin, and fusidic acid.
-
AmvA in Acinetobacter baumannii extrudes chlorhexidine, benzalkonium chloride, and polyamines.
-
EmrAB-TolC efflux pump of Enterobacter species confers resistance to nalidixic acid, thiolactomycin, nitroxoline, and hydrophobic proton uncouplers (e.g., carbonyl-cyanide m-chlorophenylhydrazone (CCCP)).
-
EmrD in Escherichia coli extrudes benzalkonium chloride and sodium dodecylsulfate.
-
KexD efflux pump of Klebsiella pneumoniae extrudes macrolides and tetracycline.
-
KpnEF efflux pump of Klebsiella pneumoniae provides resistance to several antimicrobial compounds including benzalkonium chloride, colistin, erythromycin, rifampin, tetracycline, chlorhexidine, triclosan, and bile salts.
-
KpnGH efflux pump of Klebsiella pneumoniae confers resistance not only to multiple antibiotics including azithromycin, ciprofloxacin, erythromycin, gentamicin, and chlorhexidine, but also protects the bacteria from oxidative and nitrosactive stress stimuli.
-
MacAB-TolC efflux pump of Klebsiella pneumoniae confers resistance to eravacycline.
-
MdfA in Acinetobacter baumannii extrudes ciprofloxacin and chloramphenicol.
-
MdtABC-TolC in Enterobacter species confers resistance to novobiocin and quinolones.
-
MdtEF-TolC in Enterobacter species causes resistance to erythromycin and bile acids.
-
Mef/Mel efflux pumps extrude macrolide antibiotics in Streptococcus pneumoniae.
-
MepA in Staphylococcus aureus pumps out fluoroquinolones, tetracyclines, and quaternary ammonium compounds (QACs).
-
MexAB-OprM in Pseudomonas aeruginosa is responsible for resistance to carbapenems, fluoroquinolones, and aminoglycosides. It is also involved in invasiveness and virulence.
-
MexCD-OprJ in Pseudomonas aeruginosa is responsible for the extrusion of quinolones, erythromycin, and cephalosporins.
-
MexEF-OprN in Pseudomonas aeruginosa confers resistance to chloramphenicol, fluoroquinolones, tetracyclines, and trimethoprim.
-
MexHI-OpmD in Pseudomonas aeruginosa confers resistance to vanadium, norfloxacin, and acriflavine.
-
MexXY-OprM in Pseudomonas aeruginosa confers resistance to aminoglycosides, fluoroquinolones and cefepime.
-
MsrA in Staphylococcus epidermidis extrudes macrolide antibiotics.
-
NorA-C in Staphylococcus aureus extrude fluoroquinolones (ciprofloxacin and norfloxacin).
-
OpxAB-TolC in Escherichia coli and Klebsiella pneumoniae is associated with resistance to olaquindox, chloramphenicol, quinolones, tigecycline, and nitrofurantoin.
-
PmrA in Streptococcus pneumoniae confers resistance to fluoroquinolones.
-
QacAB in Staphylococcus aureus extrudes quaternary ammonium compounds (QACs), biguanidines, and diamidines.
-
TetA and TetB efflux pumps extrude tetracyclines in several bacterial species.
-
YejABEF ABC transporter in Salmonella enterica serovar Typhimurium confers resistance to protamine, melittin, polymyxin B, and human defensin-1 and 2.
[55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77]
Reduced
affinity of
targets to the
antibiotics
-
The mobile genetic element staphylococcal chromosomal cassette (SCCmec) in MRSA carries the mecA and mecC genes encoding for the penicillin-binding protein (PBP) variant PBP2a with low affinity for β-lactams.
-
Mutations in 23S rRNA and ribosomal proteins L4 and L22 in Streptococcus pneumoniae confer resistance to macrolide antibiotics.
-
A mutation in S10 ribosomal in Klebsiella pneumoniae confers resistance to tigecycline.
-
Mutations in gyrase gyrA and topoisomerase IV subunit parC (e.g., Escherichia coli, Acinetobacter baumannii) cause resistance to quinolones such as ciprofloxacin, ofloxacin, levofloxacin, and norfloxacin.
[78,79,80,81,82,83,84,85]
Modification
of the targets
-
Mobile colistin resistance (mcr) (e.g., mcr-1) in Gram-negative bacteria (e.g., Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii) encodes for a phosphoethanolamine transferase that adds phosphoethanolamine to lipid A of LPS, thereby reducing the affinity of polymyxins to LPS.
-
The ArnT enzyme in Gram-negative bacteria (e.g., Escherichia coli, Pseudomonas aeruginosa, Salmonella spp.) adds 4-amino-4-deoxy-L-arabinose (L-Ara4N) to the phosphate group of lipid A, thus conferring resistance to polymyxin.
-
Erm genes methylate 23S ribosomal RNA, resulting in a decreased drug-binding affinity of macrolide antibiotics (e.g., Staphylococcus and Streptococcus spp., Escherichia coli). The ermB gene in Staphylococcus aureus product confers cross-resistance to lincosamides and streptogramin B.
-
Crf genes (e.g., Enterococcus faecalis, Staphylococcus aureus, Clostridium difficile) methylate 23S ribosomal RNA and confer resistance to chloramphenicol, clindamycin, linezolid, pleuromutilins, streptogramin A, and macrolide antibiotics.
-
PagP (e.g., Escherichia coli, Yersinia enterocolitica) transfers palmitate to lipid A, which contributes to resistance to antimicrobial peptides.
-
The vanHAX operon (e.g., Staphylococcus aureus, Enterococcus faecium) is responsible for the substitution of D-alanyl-D-lactate for the D-alanyl–D-alanine dipeptide, resulting in a 1000-fold lower affinity for vancomycin.
[79,86,87,88,89,90,91,92,93]
Target
protection
-
The quinolone resistance protein QnrA interacts with Escherichia coli topoisomerase IV and gyrase, thus conferring resistance to fluoroquinolones.
-
The mutant QnrB1 in Escherichia coli showed a 10-fold higher affinity to gyrase B (GyrB) than gyrase A (GyrA).
-
In Escherichia coli, sub-MICs of ciprofloxacin or nalidixic acid interfered with the interaction between QnrB1 and GyrA, while having no effect on the interaction between QnrB1 and GyrB.
-
QnrB19 interacts with Salmonella Typhimurium DNA gyrase and confers resistance to norfloxacin and ciprofloxacin.
[94,95,96,97]
Ribosomal
protection
-
Ribosomal protection proteins of the tet family dislodge tetracycline antibiotics from the 30S ribosomal unit, resulting in tetracycline resistance (both Gram-positive and Gram-negative bacteria).
-
The ABC-F proteins (e.g., MsrE of Pseudomonas aeruginosa; VgaA of Staphylococcus aureus and Staphylococcus heamolyticus; LsaA and OptrA of Enterococcus faecalis) confer resistance to ribosomal-acting antibiotics via a ribosomal protection mechanism by interacting with the ribosome and displacing the bound drug.
[98,99,100,101,102,103]
Biofilm-
embedded
bacteria
-
Reduced penetration of antibiotics.
-
Sequestration of tobramycin and other positive charged antibiotics by the negatively charged polysaccharides of the EPS.
-
Presence of sessile bacteria with low metabolic activity.
-
Presence of persister cells exhibiting antibiotic tolerance.
-
Increased expression of efflux pumps.
-
Increased horizontal transfer of antibiotic-resistant genes.
-
Sequestration of nutrients.
-
Increased mutation frequency.
-
Evasion of host defense mechanisms.
[1,13,14,20,104,105,106]

2.1. Acquisition of Various Antibiotic-Resistant Genes via Horizontal Gene Transfer

Bacteria show high genetic plasticity that enables the individual bacteria to develop different phenotypes in an ever-changing environment and to promote adaptive evolution, thus providing the bacteria with fitness traits and survival advantages [39]. The acquisition of antibiotic resistance-conferring genes can occur through horizontal gene transfer, including plasmids, gene cassettes in integrons, and transposons that can capture and disseminate genetic material across bacterial genomes.
The readiness for horizontal gene transfer of mobile genetic elements has led to the terminology “mobilome” [107]. Transposons are transposable elements capable of moving from one position to another within a given genome and are often associated with the dissemination of antimicrobial resistance determinants [42]. Integrons use site-specific recombination to move resistant genes between defined sites [42]. The mobile genetic elements are often present in multiple copies in different locations in the genome and can be transferred to other bacteria through intercellular mechanisms of genetic exchange such as conjugation, mobilization, bacteriophage-mediated transduction, and uptake of extracellular DNA by transformation [42]. For instance, Acinetobacter baumannii shows high genetic plasticity with a prominent ability to acquire plasmids [108], transposons [109], and integrons [110], conferring resistance against most classes of antibiotics.
A classic example of horizontal gene transfer resulting in antibiotic resistance is the plasmid-mediated colistin resistance by mobile colistin resistance (mcr) in Enterobacteriaceae that limits the clinical application of colistin as a last-line drug against bacterial infection [111,112]. Since its detection, several mcr genes have been characterized and they have been found in other bacterial species too [86]. Colistin (polymyxin E) acts by binding to negatively charged lipopolysaccharides (LPS) and phospholipids in the outer membrane of Gram-negative bacteria, resulting in increased permeability of the bacterial membrane, and consequent bacterial death [86]. The mcr genes encode for a phosphoethanolamine transferase that adds phosphoethanolamine to lipid A of LPS, thereby reducing the affinity of polymyxins to LPS [86].
Another example of horizontal gene transfer is the mobile genetic element staphylococcal chromosomal cassette (SCCmec) that carries the mecA and mecC genes encoding for the penicillin-binding protein (PBP) variant PBP2a with low affinity for β-lactams, and the site-specific recombinase genes ccrAB and ccrC that mediate the integration and excision of SCCmec into and from the chromosome [78]. After accurate excision and integration mediated by the site-specific recombinase genes ccrAB and ccrC, SCCmec is integrated into the staphylococcal chromosome, thus leading to the acquisition of β-lactam antibiotic resistance [78]. SCCmec is rapidly transferred between staphylococcal species and might be integrated several times within the same bacterial genome [113]. Various SCCmec elements are the underlying cause of the appearance of methicillin-resistant Staphylococcus aureus (MRSA) which poses a challenge to hospital infections [78].

2.2. Decreased Membrane Permeability

Since most antibiotics target intracellular processes, they need to penetrate the bacterial membrane. One mechanism of drug resistance can be achieved by preventing drug uptake. In Gram-negative bacteria, the outer membrane serves as a physical and functional barrier where lipid A modifications limit the interaction with drugs with a concomitant reduction in drug permeability [114]. The uptake of antibiotics in the Gram-negative bacteria requires, among others, the outer membrane porins (OMPs) which are transmembrane pore-forming proteins with a β-barrel structure that allows the passive transport of hydrophilic compounds including nutrients [32]. OPMs are also important for maintaining membrane integrity [32].
In Acinetobacter baumannii, the porin OmpAAb was found to be required for the uptake of β-lactams and sulbactam [115]. Reduced expression of some outer membrane proteins in Acinetobacter baumannii was associated with imipenem resistance [43,44]. Later studies showed that oprD and carO were downregulated in imipenem-resistant Acinetobacter baumannii in comparison to drug-sensitive species, together with an upregulation of an efflux pump [45]. Paradoxically, a ΔompA mutant of Acinetobacter baumannii was more sensitive to several antibiotics including aztreonam, nalidixic acid, chloramphenicol, and trimethoprim than the parental wild-type strain [116,117]. The increased susceptibility of the ΔompA mutant to antibiotics despite its involvement in antibiotic uptake might be explained by the increased outer membrane permeability to hydrophobic molecules when ompA is lacking [118], and the presence of other porins that contribute to the uptake of the antibiotics. Recently, the trimeric, porin-like DcaP was found to facilitate the permeation of the β-lactamase inhibitor sulbactam into these bacteria [119]. DcaP shows an abundance of positively charged residues which leads to a preferential transport of negatively charged substrates [119]. Besides the negatively charged β-lactamase inhibitors, this porin transports succinate and phthalates [119]. OmpA is also important for biofilm formation on both abiotic and biotic surfaces [120,121]. Compound 62520 inhibits ompA expression and prevents biofilm formation in Acinetobacter baumannii [122].
In Escherichia coli, the outer membrane expresses the two porins OmpF and OmpC [123]. An ompF-defective Escherichia coli mutant was resistant to several antibiotics including β-lactams, suggesting that OmpF functions as the main route of outer membrane penetration for many antibiotics [32,124]. Similar antibiotic resistance was observed in porin mutants of Klebsiella pneumoniaeompK35) [125], Serratia marcescensompF) [126], Pseudomonas aeruginosaoprD) [127], and Enterobacter aerogenes (omp36 Gly112Asp mutant) [128]. In Klebsiella pneumoniae, which has developed resistance to ertapenem, the non-selective porins OmpK36 and OmpK35 were found to be reduced, lost, mutated, or truncated [34,129,130,131]. OmpK35 of Klebsiella pneumoniae forms large permeable porins with high permeability toward lipophilic (e.g., benzylpenicillin) and large (e.g., cefepime) antibiotics [125]. OmpF of Serratia marcescens is important for the penetration of nitrofurantoin and the β-lactams ampicillin and cefoxitin [126]. The omp36 mutant of Enterobacter aerogenes that has a substitution of Gly112Asp in the conserved eyelet L3 region of the porin, confers resistance to β-lactams [128]. Reduced expression of the porin protein OprD in Pseudomonas aeruginosa led to reduced drug influx of panipenem [132]. This channel is used by the bacteria to take up basic amino acids. The addition of basic amino acids such as L-lysine reduced the response to panipenem, suggesting a competition for the OprD channel [132].
The major OprF porin of Pseudomonas aeruginosa, a homolog to the OmpA of Enterobacteriaceae, appears mainly in the closed state, which might explain the low outer membrane permeability of these bacteria in comparison to other bacteria [133]. OprF anchors the outer membrane to the peptidoglycan layer and allows the diffusion of small polar nutrients including polysaccharides [134]. Of note, the absence of OprF in Pseudomonas aeruginosa caused an increase in biofilm formation and production of the Pel exopolysaccharide through upregulation of the second messenger bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) [135]. These authors proposed that the absence of OprF leads to cell envelope stress that activates the SigX regulon that is involved in regulating c-di-GMP levels, which in turn regulates the pel and psl gene clusters. The PA1181 and adcA (PA4843) genes of the SigX regulon are involved in the increased c-di-GMP levels [135].

2.3. Increased Production of Antibiotic Degrading Enzymes

The classical examples of bacteria-produced enzymes that inactivate antibiotics are β-lactamases that cleave the β-lactam ring of penicillin [25,28] and carbapenemases that result in resistance to imipenem, ceftazidime, and ceftriaxone among others [25,28,34,136]. The β-lactam antibiotic methicillin was developed to resist β-lactam-mediated degradation, but rapidly after its introduction into the clinics, resistance to methicillin emerged in Staphylococcus aureus due to the SCCmec cassette carrying the mecA gene encoding for the low penicillin-binding protein PBP2a [78]. A different strategy to overcome resistance caused by β-lactamases is the use of β-lactamase inhibitors such as clavulanic acid, sulbactam, avibactam, and ETX2514 in combination with the β-lactam antibiotics [137].
Resistance to macrolide antibiotics such as erythromycin can emerge by the enzymatic cleavage of the macrolactone ring by erythromycin esterases encoded by the ereA-D genes [46,47]. The detoxification of macrolides adds to other mechanisms of macrolide resistance that include decreased intracellular concentration via the efflux pumps such as Mel and Mef [55], the expression of ermB gene product that methylates the peptidyl-transferase center of newly synthesized 23S rRNA conferring cross-resistance to lincosamides and streptogramin B (MLS phenotype) [79], mutations in 23S rRNA and ribosomal proteins L4 and L22 [79,80], ribosomal protection, e.g., by MsrE [98] and macrolide phosphotransferase mediated modification [49].
Enzymes of the Tet(X) family are flavin-dependent monooxygenases that inactivate tetracyclines including the last-resort antibiotic tigecycline by adding a hydroxyl group to the C-11a position, resulting in an unstable compound that undergoes auto-decomposition [50,138,139,140,141]. This has led to their nickname “tetracycline destructases” [142].

2.4. Increased Production of Antibiotic Modification Enzymes

The aminoglycoside-modifying enzymes (acetyltransferases, nucleotidyltranferases, and phosphotransferases) inactivate gentamicin and other aminoglycoside antibiotics by catalyzing hydroxyl/amino group modifications to the 2-deoxystreptamine nucleus of the sugar moieties [28,48]. Chloramphenicol acetyltransferase (CAT) detoxifies chloramphenicol by adding an acetyl group thereby preventing its binding to ribosomes [25,28].

2.5. Alterations of the Target That Disable the Binding of Antibiotics

Methicillin-resistant Staphylococcus aureus (MRSA) has acquired a PBP2 variant, PBP2a expressed on the SCCmec cassette [78]. This PBP2 variant shows low affinity to penicillin, thus enabling cell wall synthesis even in the presence of high concentrations of β-lactam drugs including methicillin [78]. Several variants of the SCCmec cassette have been observed [143].
Vancomycin, a glycopeptide antibiotic, acts by binding to the terminal D-alanyl–D-alanine dipeptide of peptidoglycan precursors, thereby interfering with bacterial wall synthesis. Acquired resistance to vancomycin is caused by the substitution of D-alanyl-D-lactate for the D-alanyl–D-alanine dipeptide, resulting in a 1000-fold lower affinity for vancomycin [87]. This modification is mediated by genes of the vanHAX operon. The vanHAX operon is regulated at the transcriptional level by the two-component VanR/VanS regulatory system in response to vancomycin [88]. In this case, vancomycin activates the membrane sensory kinase VanS, which, in turn, phosphorylates the transcription regulator VanR that drives the expression of the vanHAX operon [88,144] (Figure 1A). The van gene cluster has been found in human pathogens such as Enterococcus faecalis, Enterococcus faecium, and Staphylococcus aureus [88].
The zinc-dependent D, D-carboxypeptidases VanX, and VanY act by hydrolyzing the dipeptide (D-Ala-D-Ala) and pentapeptide (UDP-MurNac-L-Ala-D-Glu-L-Lys-D-Ala-D-Ala), respectively, and confer vancomycin resistance in Enterococci by eliminating the substrate D-Ala-D-Ala [54,145,146].

2.6. Overexpression of Efflux Pumps

A frequent reason for drug resistance is the elevated expression of various efflux pumps that extrude the drugs, thereby reducing the intracellular concentration of the antibiotics below the required minimum inhibitory concentration (MIC) [28]. Efflux pumps, in general, regulate the intracellular environment by extruding toxic substrates including secondary metabolites, QS molecules, dyes, biocides, bile acids, hormones, host defense molecules, fatty acids, detergents, heavy metals, organic pollutants, and antibiotics [31,77,147,148,149,150]. In addition, some efflux pumps have a role in the colonization and the persistence of bacteria in the host [151]. Efflux pumps may affect virulence and biofilm formation by excreting extracellular matrix proteins and QS molecules that coordinate biofilm formation, and by affecting surface adhesion [151,152,153,154,155,156,157,158].
The efflux pumps can be categorized into different families based on the amino acid sequence identity, the energy source required to drive export, and the substrate specificities. The major efflux pump families include the resistance-nodulation-cell division family (RND), the major facilitator superfamily (MFS), the multidrug and toxic compound extrusion family (MATE), the small multidrug resistance family (SMR), ATP-binding cassette family (ABC), and the proteobacterial antimicrobial compound efflux family (PACE) [77,152,159,160]. The ABC superfamily belongs to the primary active transporters that use ATP hydrolysis as the energy source, while the other efflux family members are secondary active transporters (symporters, antiporters, and uniporters) that use energy from proton and/or sodium gradient [77,161,162]. The RDN superfamily is only found in Gram-negative bacteria, while the other efflux pump families are found in both Gram-negative and Gram-positive bacteria [163]. Efflux pumps are either single-component transporters catalyzing the drug efflux across the inner cytoplasmic membrane, or multiple-component systems composed of an inner membrane transporter, periplasmic adaptor, and an outer membrane channel [163,164]. The three components in the latter type of efflux pumps (usually belonging to the RDN family) function together to promote the efflux across both the inner and outer membrane of Gram-negative bacteria [163]. Examples of RDN efflux pumps are the AcrAB-TolC of Escherichia coli and Salmonella typhimurium, and MexAB-OprM and MexXY-OprM of Pseudomonas aeruginosa [163]. EmrE of Escherichia coli and QacC of Staphylococcus aureus belong to the SMR family, while NorA and QacA of Staphylococcus aureus and PmrA of Streptococcus pneumoniae belong to the MFS family [163,165]. PmpM of Pseudomonas aeruginosa and MepA of Staphylococcus aureus are examples of efflux pumps belonging to the MATE family, and AbcA of Staphylococcus aureus and LmrA of Lactococcus lactis belong to the ABC superfamily [163,165].

2.6.1. Inducible Efflux Pumps

The activities of many regulators of the efflux pumps are frequently affected by the substrates that will be transported by the regulated efflux pump [166,167,168,169,170]. These regulators usually contain a drug-binding pocket within the ligand-binding domain, and the binding of the drug to these regulators modulates their transcriptional repressor/activator activities [171,172,173,174]. The best-understood example of the regulation of a gene encoding the regulation of a drug exporter is the control of tetA expression by the specific repressor protein TetR [172,175]. Tetracycline binds to TetR, resulting in the transcription of the tetA efflux pump [172,175]. The Staphylococcus aureus multidrug transporter QacA is transcriptionally repressed by QacR, which interacts with similar substrates as QacA including chlorhexidine digluconate, benzalkonium chloride, and cetylpyridinium chloride [176]. Upon exposure to these compounds, QacR is released from the qacA promoter, resulting in the upregulation of QacA [176]. In Escherichia coli, EmrR is a negative regulator of the gene encoding the macrolide efflux pump emrAB, the repression of which is relieved upon binding of substrates such as tetrachlorosalicylanilide to EmrR [177,178]. Mutations in emrR in Salmonella typhi and Salmonella enterica cause an upregulation of emrAB with consequently reduced susceptibility to ciprofloxacin and other antibiotics [179,180]. Norfloxacin induces the expression of the norA efflux pump in Staphylococcus aureus [181]. NorA expression is regulated by the ArlRS QS system [182], NorR [183], NorG [184], and MgrA [185] (Figure 1B). Mupirocin induces the expression of the efflux pumps NorA and MepA, resulting in resistance induction to norfloxacin and chlorhexidine [186].
The macrolide erythromycin induced the expression of the mefE-mel efflux pumps in Streptococcus pneumoniae by specific interactions of the macrolide C-5 saccharide with the ribosome that alleviate transcriptional attenuation of mefE-mel [61]. Transcriptional attenuation occurs when the secondary structure of the leader sequence of the transcript terminates transcription in a rho-independent manner [61]. Additionally, certain antimicrobial peptides such as LL-37 activate the transcription of mefE-mel, resulting in the resistance to erythromycin [187].
The MexXY-OprM efflux pump in Pseudomonas aeruginosa can be induced by ribosome-targeting antibiotics such as chloramphenicol, tetracycline, macrolides, and aminoglycosides [188,189,190] (Figure 2). Mutations in the fmt gene that encodes for methionyl-tRNA formyltransferase, or the folD gene, a component of the folate biosynthesis pathway, led to impaired protein synthesis and upregulation of mexXY [191]. Additionally, mutations in the ribosomal proteins L1 (encoded by rplA) and L25 (encoded by rplY) resulted in an upregulation of mexXY, further supporting a functional link between mexXY transcription and ribosome dysfunction [192,193]. Stalling of ribosomes at the PA5471 leader peptide (PA5471.1) leads to the transcription of PA5471 that upregulates the expression of mexXY through releasing the repressive action of MexZ [194,195]. mexXY expression is also regulated by MexR [196] and the QS systems ParRS [66] and AmgRS [197]. MexZ is frequently mutated in aminoglycoside-resistant Pseudomonas aeruginosa clinical isolates [198,199,200]. Calcium and magnesium ions could antagonize aminoglycoside efflux through MexXY-OprM [65].
Pathogens that survive in the intestine have often developed resistance mechanisms to the hazardous effects of bile acids [201] (Figure 3). One mechanism is the expression of the AcrAB efflux pump in the Enterobacteriaceae family including Escherichia coli, Salmonella, Shigella, and Klebsiella [202]. Other resistance mechanisms include the production of bile salt hydrolase that deconjugates bile acids and neutralizes its antimicrobial activity [203] and the expression of the signaling protein IreK (PrkC) that maintains cell wall integrity resulting in resistance to bile salts and cell wall active antibiotics such as cephalosporins [204,205]. Bile salts induce the expression of the efflux pumps emrB and qacA in Enterococcus faecalis, resulting in the simultaneous acquisition of resistance to various antibiotics [206]. In Pseudomonas aeruginosa, bile salts induced the expression of mexAB-oprM and some other efflux pumps, resulting in resistance to macrolide antibiotics and polymyxin [207]. Bile salts also activate various QS two-component systems (QS TCSs) resulting in increased bacterial virulence. In Lactobacillus rhamnosus GG, bile salts increased the expression of baeRS, phoRP3, and vraRS [208]. In Escherichia coli, bile salts led to the upregulation of the acrAB efflux pump, the TCSs basRS, and pmrAB, as well as lipid A modification genes (arnBCADTEF and ugd), resulting in cross-resistance to polymyxin [209]. The TCSs BcrXRS and LiaFSR were found to contribute to bile salt resistance in Enterococcus faecium [210]. The TCS CpxAR conferred bile acid resistance in Klebsiella pneumoniae [211].
The metabolite indole that is produced by the degradation of tryptophan by Escherichia coli and other gut bacteria was shown to induce the expression of the efflux pumps acdD and mdtABC in Escherichia coli through a mechanism involving the TCSs BaeSR and CpxAR [212] (Figure 4). In this study, the transcriptional induction by CpxAR required BaeSR, while BaeSR could act alone, suggesting that BaeR is the primary regulator, while CpxR enhances the effect of BaeR [212]. The induction of the efflux pump mdtE by indole in Escherichia coli was mediated by transcriptional regulator GadX [212]. Moreover, indole was shown to act as an intercellular signaling molecule that induces RamA-mediated upregulation of the acrAB multidrug efflux pump in Salmonella enterica, with the consequent acquisition of drug resistance [213,214]. Indole is excreted from Escherichia coli via the AcrEF-TolC efflux pump [215].

2.6.2. Mechanisms Resulting in Constitutive Overexpression of Efflux Pump

Besides being induced by antibiotics and various other toxic compounds for the bacteria, the expression of the efflux pump is regulated by QS (see Section 3), various stress stimuli (e.g., membrane disruption, protein misfolding), changes in metabolic state, and when the bacteria are embedded in a biofilm (see Section 4) [31,64,77,216]. Moreover, additional factors can result in the constitutive overexpression of efflux pumps, including (i) mutations in the local repressor gene; (ii) mutations in a global regulatory gene; (iii) mutations in the promoter region of the efflux gene; (iv) insertion elements upstream of the efflux pump gene [164,165]. Due to the multiple regulatory mechanisms, only selected examples will be highlighted here.
In Klebsiella pneumoniae, resistance to tigecycline can be caused by mutations in ramR, acrR, and rpsJ [217,218]. RamR represses the transcription of ramA [219], which regulates the multidrug efflux pump AcrAB-TolC [220]. Transformation of ramR mutant strains of Klebsiella pneumonia with the wild-type ramR gene restored susceptibility to tigecycline [219]. ramR mutations in a Salmonella enterica serovar Typhimurium strain led to overexpression of ramA and consequent overproduction of the AcrAB efflux pump [221]. A 2-nucleotide deletion in the putative RamR binding site of the ramA promoter was found to confer resistance to fluoroquinolones [221].
The AcrAB-TolC efflux pump is also regulated by the stress-response regulators MarA, RarA, SoxS, and RobA [149,222,223,224] (Figure 5). In tolC mutant bacteria, the two QS systems for sensing extracytoplasmic stress BaeRS and CpxARP were upregulated along with the upregulation of MarA, SoxS, and RobA [149]. RarA also regulates the expression of the oqxAB efflux genes and the porin ompF [222].
Insertion sequence (IS) elements that disrupt the function of regulatory proteins can upregulate the expression of acrAB, adeABC, and kpgABC efflux pump genes in Escherichia coli, Acinetobacter baumannii, and Klebsiella pneumoniae, respectively, resulting in tigecycline resistance [225,226,227]. IS1 elements were found to disrupt the function of AcrR, a repressor of acrAB in Escherichia coli [225]. Fluoroquinonolone resistance in a Salmonella enterica serovar Typhimurium strain was found to be due to an activation insertion sequence (IS1 or IS10) integrated upstream of the acrEF operon that encodes for the acrEF efflux pump [228].

2.6.3. Major Efflux Pumps in Pseudomonas aeruginosa

Pseudomonas aeruginosa contains a large number of efflux pumps, with four potent RND-type multidrug resistance efflux pumps (Mex) capable of eliminating toxic compounds from the periplasm and cytoplasm. These efflux pumps (MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY-OprM) have overlapping spectra of antibiotic substrates and confer resistance to carbapenems, fluoroquinolones, and/or aminoglycosides [25]. The MexAB and MexCD are located in the inner membrane, while the OprM and OprJ are in the outer membrane [64]. The mexAB-oprM operon is repressed by MexR [196] and NalD [229], while activated by BrlR [230] and CpxR [231] (Figure 6). The mexCD-oprJ operon is repressed by NfxB [232]; and the mexEF-oprN operon is repressed by NfxC, while activated by the MexT transcriptional activator [233]. Mutation in MexR or NalC results in upregulation of mexAB-oprM, and resistance to aztreonam [234,235,236].
The efflux pump MexHI-OpmD exports the toxic metabolite anthranilate that serves as a precursor of the autoinducer PQS [237]. Pseudomonas aeruginosa lacking a functional MexHI-OpmD pump showed impaired growth due to accumulation of the toxic anthranilate [237]. The MexHI-OpmD efflux pump confers resistance to vanadium, norfloxacin, and acriflavine [237]. However, mutants lacking MexHI-OpmD became less sensitive to tetracycline, chloramphenicol, and rifampicin, and resistant to kanamycin and spectinomycin [237]. Extracellular addition of the autoinducer PQS increased the susceptibility of both the mexI and opmD mutant strains as well as the wild-type strain to these antibiotics [237]. MexHI-OpmD is upregulated by the endogenous 5-methylphenazine-1-carboxylate which is a substrate of this efflux pump and required for normal Pseudomonas aeruginosa biofilm morphogenesis [238]. 5-methylphenazine-1-carboxylate is an intermediate metabolite formed during the conversion of phenazine-1-carboxylic acid to the virulence factor pyocyanin (5-N-methyl-1-hydroxyphenazine) [238]. Pyocyanin upregulates mexHI-opmD through activation of the redox-responding transcription factor SoxR [239].

2.6.4. Major Efflux Pumps in Enterobacter spp.

The AcrAB-TolC tripartite multidrug efflux pump of Enterobacter species belongs to the RND superfamily and forms a tripartite complex consisting of an inner membrane pump protein (AcrB) and an outer membrane channel protein (TolC) bridged by a periplasmic adaptor protein (AcrA) [77]. It utilizes the proton motive force as an energy source to extrude the various substrates [56]. This efflux pump is essential for bacterial survival, particularly in the presence of toxic agents. Subinhibitory concentrations of ertapenem induced the expression of the regulator of antibiotic resistance A (rarA) that upregulates the expression of acrAB-tolC [40]. The expression of the acrAB and tolC genes are upregulated by the AraC-type transcriptional activators MarA, RamA, and SoxS [224,240,241]. acrAB is also upregulated by the QS regulator SdiA [242], while repressed by the transcriptional regulators AcrR [243] and Rob [244]. Bile salts and fatty acids bind to the C-terminal part of Rob, inducing a conformational alteration that results in the transcriptional activation of acrAB [244] (Figure 5).
The multidrug-resistant operon marRAB encodes the repressor marR, the activator marA, and the repressor marB which reduces the rate of marA transcription [245,246]. The operon is activated by compounds such as salicylate, chloramphenicol, tetracycline, acetaminophen, and sodium benzoate [247,248]. marA was found to be upregulated by the TCS QseBC in Escherichia coli through directly binding of QseB to the marA promoter [249]. MarA causes a decreased production of the ompF porin in Escherichia coli by activating the transcription of micF, an antisense RNA that binds to ompF mRNA, preventing its translation [250]. The OqxAB efflux pump was shown to be regulated by the AraC multidrug-resistant regulators RamA and RarA [222,241,251]. The transcription factor SoxR is oxidized in response to oxidative stress stimuli resulting in the activation of SoxS [252,253,254]. The SoxRS response protects the cells against superoxide toxicity [252], among others by inducing sodA [255]. SoxA also induced the expression of the acrAB-tolC efflux pump in Klebsiella pneumoniae with concomitant resistance to tetracycline [255].

2.6.5. Major Efflux Pumps in Staphylococcus aureus Contributing to the MRSA and MDRSA Phenotypes

More than 30 efflux genes have been characterized in Staphylococcus aureus [57]. Among these, NorA-C, MepA, and MdeA pump out fluoroquinolones and quaternary ammonium compounds (QACs), and the efflux pumps SepA and QacA/B extrude QACs and biguanidines such as chlorhexidine [57]. The norA gene is overexpressed in around 50% of Staphylococcus aureus strains and contributes to antibiotic-resistant strains [256,257].
The multidrug efflux pump AbcA that confers resistance to β-lactam antibiotics, moenomycin, and daptomycin in Staphylococcus aureus, is regulated by the transcription factors NorG, Rot, SarA, SarZ, MgrA, and the QS system AgrBDCA [258,259,260] (Figure 1B). In addition, AbcA is involved in the secretion of the phenol-soluble modulins (PSMs) [71,72], which are cytolytic toxins that lyse erythrocytes and neutrophils and play important roles in Staphylococcus aureus infections [51,261,262]. AbcA also affects cell wall autolysis [260]. Subinhibitory concentrations of ampicillin increased the expression of abcA and the surface proteins clfB, isdA, and sasG with a concomitant increase in biofilm formation [263].

2.7. Involvement of rRNA Methyltransferase in Antibiotic Resistance

Dimethylation of a specific nucleotide residue in the 23S ribosomal RNA by erythromycin resistance methyltransferase (erm) protects bacteria from macrolide antibiotics [89]. The majority of the erm genes are induced by the macrolide antibiotics, which is likely due to the reduced fitness caused by the ribosomal modification [89,264]. The Cfr methyltransferases methylate 23S ribosomal RNA, thereby preventing the binding of antibiotics to the peptidyl-transferase center [92]. Crf genes have been shown to confer resistance to chloramphenicol, clindamycin, linezolid, pleuromutilins, streptogramin A, and macrolide antibiotics [92,93].

2.8. Involvement of DNA Methyltransferase in Antibiotic Resistance

The DNA methyltransferase VchM was found to be required for the sensitivity of Vibrio cholerae to aminoglycosides [265]. VchM is an m5C DNA methylase that methylates cytosine at 5′-RCCGGY-3′ motifs. The lack of VchM results in increased expression of groESL-2 chaperone genes and tolerance to aminoglycosides, likely by capturing aminoglycoside-induced misfolded proteins [265].

2.9. Involvement of Ribosomal Protection in Antibiotic Resistance

Ribosomal protection proteins (RPPs) are involved in conferring antibiotic resistance toward ribosome-targeting antibiotics [103,266]. The ribosomal protection proteins TetM, TetO, TetS, TetT, TetQ, TetB, and TetW confer resistance to tetracycline antibiotics by releasing the drugs from the 30S ribosomal subunit or by preventing their binding to the ribosome [103]. These RPPs exhibit GTPase activity, bind ribosomes analogously to elongation factors, and displace ribosomal-bound antibiotics [103]. The GTP hydrolysis depends on the binding of the RPP to the ribosome and occurs only after correct codon-anticodon interaction [103]. After the release of the drug, GTP is hydrolyzed and the Tet RRP dissociates from the ribosome, enabling the ribosome to continue the elongation cycle [103].
The ATP-binding cassette (ABC) proteins of the F-subtype (ABC-F) confer resistance to several antibiotics such as lincosamides, pleuromutilins, streptogramin A, and oxazolidinones that target the ribosome peptidyl-transferase center (PTC) of the 50S large ribosomal subunit, and antibiotics such as macrolides and streptogramin B that target the adjacent nascent peptide exit tunnel (NPET) region of the 50S large ribosomal subunit [100,102,267]. The ABC-F proteins are ATPases that confer antibiotic resistance via ribosomal protection mechanism by interacting with the ribosome and displacing the bound drug, thus alleviating the translational inhibition caused by the antibiotics [99,100,268]. Examples are the LsaA and OptrA of Enterococcus faecalis, VgaA of Staphylococcus aureus, and VgaL of Listeria monocytogenes that confer resistance to PTC-binding antibiotics, and the macrolide and streptogramin B resistance (Msr) proteins such as MsrE of Pseudomonas aeruginosa, that confer resistance to NPET-binding antibiotics [101,102,268,269].

2.10. Involvement of Non-Coding RNAs in Antibiotic Resistance

Bacterial non-coding RNAs (ncRNAs), although not translated into functional proteins, can regulate sensitivity to antibiotics [33,270] as well as biofilm formation [271,272,273,274,275,276], virulence [277,278,279,280,281], and stress responses [280,282,283,284] by modulating gene expression. Some regulatory ncRNAs (rRNAs) reside in the 5’UTR of the regulated gene and sense the presence of the antibiotics by recruiting translating ribosomes onto short upstream open reading frames embedded in the ncRNA. In the presence of translation-inhibiting antibiotics, ribosomes arrest over the upstream open reading frames, altering the RNA structure of the regulator and thus activating the transcription of the resistance gene [33]. The ciprofloxacin stress-induced ncRNA CsiR was found to regulate in a negative manner ciprofloxacin resistance in Proteus vulgaris by targeting the efflux pump emrB [285]. CsiR-deficient strains were less sensitive to ciprofloxacin than the wild-type strain [285].
A ribosome-dependent riboregulation is involved in controlling the expression of the Staphylococcus aureus macrolide resistance methyltransferase ermC gene [286]. In the absence of erythromycin, ermC expression is repressed because the ribosome-binding site and AUG start codon of the ermC mRNA are sequestered in a stem-loop structure [286]. However, in the presence of erythromycin, ribosomes translating the ErmCL leader peptide become stalled, leading to an alternative stem-loop structure in the ermC mRNA that exposes the ribosome-binding site and start codon of the ermC gene and thus allows ribosome binding and induction of ermC expression [286].
Overexpression of the small RNA SprX in Staphylococcus aureus increased the sensitivity of the bacteria to the glycopeptide antibiotics teichoplanin and vancomycin [270]. An spxR deletion mutant showed reduced sensitivity to these antibiotics [270]. SprX inhibits the expression of the RNA-binding protein SpoVG [270], which is involved in bacterial resistance to methicillin, oxacillin, and glycopeptide antibiotics, among others, through promoting cell wall synthesis and inhibiting cell wall degradation [287,288]. SpoVG positively regulates the two-component system LysSR resulting in the activation of the antiholin lrgA and repression of the murein hydrolase lytN [270]. Overexpression of LrgA inhibits murein hydrolase activity and reduces the sensitivity of Staphylococcus aureus to penicillin [289] (Figure 7).

2.11. Involvement of Bacterial Proteases in Antibiotic Resistance

Bacterial-produced proteases (e.g., SepA) can degrade and thus inactivate antimicrobial peptides [51]. Various membrane proteases in Pseudomonas aeruginosa could confer resistance to aminoglycoside antibiotics [52]. Deletion mutation of the ftsH gene or insertion inactivation of two FtsH protease accessory factors (HflK and HflC) and the cytoplasmic protease HslUV increased the bacterial sensitivity to tobramycin [52]. Additionally, YccA, a modulator of FtsH, and the membrane protease HtpX conferred resistance to aminoglycosides [52]. The expression of the two latter gene products is regulated by the AmgRS two-component system [52]. The authors proposed that the proteases conferred resistance to aminoglycosides through the elimination of membrane-disruptive mistranslation products [52].

3. Quorum Sensing

Quorum sensing (QS) is an intercellular signaling mechanism that allows the communication between bacteria in a cell density-dependent manner [290]. The QS signaling system enables the bacteria to modify their gene expression pattern in response to changes in the environmental conditions, such as nutrient starvation, alterations in temperature, pH and osmolarity, oxidative stress, membrane stresses, antibiotics, and other toxic substances. It provides the bacteria with a selective survival advantage under different harsh conditions. Among others, the QS signaling cascade modulates cellular functions such as metabolic activity, extracellular polymeric substance (EPS) production, nutrient acquisition, transfer of genetic material between the cells, motility, biofilm formation, antibiotic resistance, virulence, and the synthesis of secondary metabolites [4,5,290,291,292,293,294,295,296]. In Pseudomonas aeruginosa, QS may also increase the resistance to oxidative stress stimuli by increasing the expression of catalase and superoxide dismutase [297].
The QS system usually involves the secretion of small molecules (autoinducers) that act on surface receptors on adjacent bacteria resulting in the induction of signal transduction pathways regulating biofilm formation, virulence, competence, conjugation, antibiotic resistance, motility, and sporulation [290,298,299,300]. These sensor–regulator pairs are called two-component systems (TCS) and involve phosphotransfer and phosphorelay that activates specific transcriptional regulators [290]. Usually, one of the TCS components encodes the autoinducer, while the other is the receptor that responds to the autoinducer. The sensor receptor is often membrane-bound and consists of an N-terminal sensor domain linked to a C-terminal cytoplasmic histidine kinase that autophosphorylates a conserved histidine residue in its own domain upon receptor activation. The sensor domains can, among others, detect changes in pH, temperature, and osmolarity. To ensure the transfer of the phosphoryl group from the sensor receptor kinase to the response regulator, an intermediate histidine phosphotransfer module (Hpt) is often required [290,301,302]. Phosphorylation of the response regulator leads to conformational changes resulting in altered affinity of the effector domain for its target DNA. As a result, the activation of TCS results in extensive alterations in gene expression. To emphasize the complexity of the bacterial QS system, more than 127 TCS members have been identified in Pseudomonas aeruginosa [303,304,305], versus 62 in Escherichia coli [306], 70 in Bacillus subtilis [307], 17 in Staphylococcus aureus [308,309,310,311], 15 in Enterococcus faecalis [312], and more than 20 in Acinetobacter baumannii [313].
Usually, the QS molecules in Gram-positive bacteria are oligopeptides such as autoinducing peptides (AIP), while in Gram-negative bacteria they belong to the family of N-acyl-L-homoserine lactones (AHL) [290,314,315,316,317,318]. The activation of the QS signaling system is usually induced when the autoinducer concentrations reach a threshold level, which occurs at higher cell densities. When activated, the QS leads to the large transcriptional alterations of hundreds of genes in the bacterial genome [290].
The transportation of autoinducers into the extracellular space is essential for their function as ligands for the respective receptors. Some autoinducers such as 3-oxohexanoyl homoserine lactone (3-Oxo-C6-HSL) from Vibrio fischeri and N-butyryl homoserine lactone (PAI-2) of Pseudomonas aeruginosa, are freely diffusible across the bacterial membranes [319,320]. However, other autoinducers, e.g., N-(3-oxododecanoyl) homoserine lactone (3-Oxo-C12-HSL, PAI-1) and 2-heptyl-3-hydroxy-4-quinolone (PQS) of Pseudomonas aeruginosa require a trafficking system [320,321]. One trafficking mechanism is the packaging of the autoinducers into membrane vesicles that are released from the bacteria [321]. The autoinducer PAI-1 of Pseudomonas aeruginosa is exported by the MexAB-OprM efflux system [320,322,323], while the autoinducers C4-homoserine lactone (C4-HSL) and 2-heptyl-3-hydroxy-4-quinolone (Pseudomonas quinolone signal, PQS), as well as the precursor 4-hydroxy-2-heptylquinoline (HHQ), are extruded by the MexEF-OprN efflux pump [324,325]. The overexpression of these efflux pumps in Pseudomonas aeruginosa reduces the intracellular autoinducer levels with concomitant diminished QS signaling [322,324]. Loss of MexAB-OprM caused increased QS responses [323].

3.1. TCSs in Vibrio Strains

The QS in various Vibrio strains including Vibrio fischeri, Vibrio harveyi, and Vibrio cholerae has been extensively studied [290,326,327,328]. The two major autoinducers in Vibrio cholerae are (S)-3-hydroxytridecan-4-one (cholera autoinducer-1; CAI-1) produced by CqsA and 4,5-dihydroxy-2,3-pentanedione (autoinducer-2; AI-2) synthesized by LuxS [327,329,330]. CAI-1 and AI-2 act on the membrane-bound receptors CqsR and LuxPQ, respectively, resulting in the dephosphorylation of LuxO, with concomitant reduced expression of the regulatory small RNAs qrr1-4, reduced expression of the AphA regulator, but increased expression of the HapR regulator [331,332,333]. AphA activates genes required for biofilm formation and pathogenicity [334], while HapR prevents biofilm formation by repressing the transcriptional activator vpsT [335]. HapR induces the expression of genes encoding proteases that promote Vibrio cholerae dispersion [336]. A third QS system of Vibrio cholerae is mediated by the autoinducer 3,5-dimethylpyrazin-2-ol (DPO), which activates the transcription factor VqmA, resulting in the expression of the small regulatory RNA vqmR [328]. VqmR, in turn, represses genes required for biofilm formation [328]. In Vibrio harveyi and Vibrio fischeri, the autoinducers activate a signal transduction pathway that leads to the activation of the master regulator LuxR that induces bioluminescence and biofilm formation [337,338,339,340].
Homologs of LuxS have been found in many different Gram-positive and Gram-negative bacterial species, suggesting interbacterial communication [341,342,343,344,345]. Moreover, bacteria can respond to autoinducers produced by other bacteria. For instance, Escherichia coli and Salmonella enterica serovar Typhimurium detect autoinducers produced by other bacteria through the orphan receptor SdiA which is a homolog to LuxR [346,347]. In addition, the dCACHE-domain proteins PctA/TlpQ in Pseudomonas aeruginosa function as a receptor for AI-2 [348]. The AI-2 (R-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran) produced by LuxS in Escherichia coli interacts with its receptor LsrB that regulates the cognate signal kinase LsrK and the activity of the transcriptional repressor LsrR [349,350].
Besides function as an AI-2 synthase, LuxS plays a central role in the metabolic activated methyl cycle (AMC), which is involved in the recycling of S-adenosylmethionine (SAM), a major methyl donor of the cell [341]. Thus, inactivation of luxS could result in changes in gene expression due to defective signaling, methionine metabolism, or accumulation of intermediates of S-adenosylmethionine metabolism [341].

3.2. TCSs in Pseudomonas aeruginosa

The rapid adaption of Pseudomonas aeruginosa to environmental stress conditions has been attributed to the high percentage of the genome encoding TCS elements (64 genes encoding response regulators and 63 histidine kinases) as well as 16 atypical kinases [305]. The major QS systems of Pseudomonas aeruginosa rely on the LasI/LasR, RhlI/RhlR, PqsABCDE/PqsR (MvfR), and the AmbBCDE/IqsR TCSs involved in the communal response to extracellular signaling autoinducer molecules, such as N-(3-oxododecanoyl) homoserine lactone (3-Oxo-C12-HSL) encoded by LasI, N-butyryl-L-homoserine lactone (C4-HSL) encoded by RhlI, 2-heptyl-3-hydroxy-4-quinolone (PQS) by PqsABCD and PqsH, and 2-(2-hydroxyphenyl)-thiazole-4-carbaldehyde (IQS) by AmbBCDE [296,351,352]. In the Las system, the transcription factor LasR is activated by the autoinducer 3OH-C12-HSL, and then LasR drives LasI expression and triggers the production of exotoxin A, the LasA protease, and the LasB elastase. In the Rhl TCS, the autoinducer C4-HSL increases RhlI expression by the binding and interaction of C4-HSL with RhlR and induces controlled production of the LasB elastase, rhamnolipids, pyocyanin, and cytotoxic lectins that play crucial roles in virulence and biofilm formation and development. The Las, Rhl, Pqs, and Iqs QS systems are hierarchically connected [296,353,354] (Figure 8). The Rhl and Pqs systems are regulated by the LasR/C12-HSL complex at the transcriptional and posttranscriptional levels [353,355,356]. The genes regulated by LasR and RhlR are involved in biofilm formation, bacterial motility, virulence, and antibiotic resistance. PqsE regulates a range of genes involved in biofilm formation, virulence, and antioxidative processes by serving as a link between the Las and Rhl QS systems [357,358,359,360,361]. Under conditions of low phosphate concentrations, the IQS QS system is activated and promotes biofilm formation through the Rhl and Pqs QS systems [362].
A regulatory network between β-lactam resistance, alginate production, QS, and virulence factors has been shown to exist in Pseudomonas aeruginosa [363]. In the presence of β-lactam antibiotics and the β-lactam antibiotic resistance master regulator AmpR, the sigma factor AlgT/U upregulates ampR gene expression, while AmpR represses algT/U gene expression, generating a negative regulatory feedback loop [363]. In the absence of ampR, there is an increase in the transcription of the QS components lasI and lasR, with a concomitant increase in alginate and pyocyanin production, increased LasA staphylolytic protease activity, and elevated expression levels of the two inducible β-lactamase genes, ampC and poxB [363,364]. AmpR also modulates antibiotic resistance to other antibiotics by regulating the expression of the MexEF-OprN efflux pump [365].

3.3. TCSs in Staphylococcus aureus

Virulence factor production in Staphylococcus aureus is largely under the control of the accessory gene regulator (agr) QS system (agrBDCA), the SaeRS and ArlRS QS systems, as well as the transcriptional regulators SarA and MgrA [308,366,367,368,369,370] (Figure 9). There are four agr groups, all of which exhibit bacterial interference [366,370,371]. Each agr type synthesizes a cyclic autoinducing peptide (AIP) with a distinct sequence that activates its cognate AgrC receptor and inhibits the activation of others [366,370]. The four Staphylococcus aureus AIPs are seven to nine amino acids long and all contain a thiolactone macrocycle, involving a conserved cysteine sulfhydryl group and R-carboxylate, and an N-terminal tail region [366,370].
The P2 operon in the agr locus encodes a polycistronic mRNA termed RNAII which is translated into four Agr proteins (AgrA-D) involved in the autoinduction circuit [370]. AgrD is the precursor of AIP which is proteolytically processed by the AgrB peptidase to generate a thiolactone intermediate. The intermediate is exported and further processed into mature AIP pheromone that activates the membrane-bound AgrC receptor histidine kinase, resulting in the phosphorylation and activation of the response regulator AgrA [366,370]. The phosphorylated AgrA activates the P2 promoter resulting in the upregulation of RNAII, thereby providing a feed-forward QS signaling circuit. In addition, ArgA activates the P3 operon encoding RNAIII, which is a pleiotropic regulator factor. RNAIII functions by base-pairing to the 5’-ends of virulence factor mRNAs, suppressing the synthesis of proteins involved in adhesion, while increasing those involved in invasion [372]. A portion of RNAIII is translated into δ-toxin. RNAIII upregulates the expression of alpha-hemolysin [373] and the global regulator mgrA [374], while represses the expression of coa (coagulase), spa (protein A), and the pleiotropic transcription factor rot (repressor of toxin), which is responsible for the repression of toxins [375,376].
AgrCA positively regulates various virulence factors such as hemolysins, proteases, nucleases, phenol-soluble modulins (PSMs), leukocidins, toxins, and capsular polysaccharides, that contribute to the invasive phenotype [308]. In addition, AgrCA upregulates the TCSs arlRS and saePQRS [308]. The activity of AgrA can be modulated by SarA and SarR [377]. SaeRS regulates the expression of various virulence factors including fibronectin-binding proteins, hemolysins, leukocidins, and coagulase that are important for the pathogenicity of Staphylococcus aureus [378,379].
Agr also represses the expression of apsRS which confers resistance to antimicrobial peptides such as human β-defensin-3, LL37, and bacteriocins (nisin A, nukacin ISK-1) [380]. ApsR regulates the dlt operon that adds alanine to teichoic acid in the cell wall and mprF (fmtC), which adds lysine to phosphatidylglycerol in cell membranes [381,382,383]. This leads to a reduced negative charge of the bacterial surface, and a consequently reduced binding of the positively charged antimicrobial peptides [381,382,383]. Since Agr expression is low during the early phase of bacterial growth, while high in the stationary phase, the susceptibility to antimicrobial peptides changes during cell growth with low susceptibility during the exponential phase and high susceptibility in the stationary phase [380,384].

3.4. Involvement of Two-Component Systems in Promoting Antibiotic Resistance

QS may affect antibiotic resistance by altering the expression of efflux pumps and β-lactamases, modulating the membrane structure, and promoting biofilm formation [31,302,385,386,387] (Table 2 and Section 4.1). Vice versa, efflux pumps may be important for QS and biofilm formation. For instance, the QS-regulated biofilm formation in Burkholderia pseudomallei was found to rely on the BpeAB-OprB efflux pump [388]. The autoinducers N-octanoyl-homoserine lactone (C8-HSL) and N-decanoyl-homoserine lactone (C10-HSL) of Burkholderia pseudomallei induced the expression of BpeAB-OprB, and BpeAB was required for acyl-homoserine lactone (acyl-HSL) production and optimal production of quorum sensing-controlled virulence factors such as siderophore and phospholipase C [388]. In analogy, reduced biofilm formation was observed in Escherichia coli mutants that do not express various genes associated with efflux pumps including emrD, emrE, emrK, acrD, acrE, and mftE [158].
The envelope stress responsive AmgRS TCS of Pseudomonas aeruginosa is activated following membrane damage caused by Zn ions and aminoglycosides [197,396]. The aminoglycoside-mediated activation of AmgRS results in the induction of mexXY and mexAB-oprM multidrug efflux operons, which confer aminoglycoside resistance [197,397]. The Zn-induced mexXY expression relies on the TCS ParRS [396]. Zinc also activates the TCS ColSR that promotes cell envelope-protective modifications, contributing to Zn tolerance [415].
Gram-negative bacteria survive harmful environmental stressors by modifying their outer membrane. This protection is often achieved by modifying the lipid A moiety of LPS. Various environmental stress stimuli can induce the addition of cationic components, such as 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine (pEtN) at the lipid A phosphate groups, which contribute to the stabilization of the outer membrane.
The TCS CprRS of Pseudomonas aeruginosa triggers the expression of the LPS modification arnBCADTEF operon upon exposure to cationic antimicrobial peptides [418]. The arnBCADTEF operon mediates the addition of the positively charged arabinosamine to the negatively charged lipopolysaccharides, thereby preventing the binding of cationic antimicrobial peptides to the lipopolysaccharides [418]. Since the membrane permeabilization activity caused by the antimicrobial peptides relay on their binding to LPS, the arabinosamine modification of LPS leads to drug resistance [418]. The arn operon is also induced by low Mg2+ concentration detected by the TCSs PhoPQ and PmrAB [452], and by cationic peptides that activate the TCS ParRS [449]. Extracellular DNA present in biofilms activates PhoPQ and PmrAB through chelating metal ions, thus inducing antimicrobial peptide resistance [471]. The activation of PhoPQ and PmrAB is also caused by extracellular DNA-mediated acidification of the biofilms [454]. The activation of PhoPQ and PmrAB resulted in resistance to aminoglycoside antibiotics which is caused by both aminoarabinose modification of lipid A and production of spermidine on the bacterial outer membrane which interacts electrostatically with the negative charges of the O-antigen [454,471]. Both modifications likely reduce the entry of the aminoglycoside into the bacteria [454,471]. DNA-enriched biofilms were 8-fold more tolerant to the antimicrobial peptides polymyxin B and colistin, and 64- to 128-fold more tolerant to the aminoglycosides gentamicin and tobramycin [472].
In Pseudomonas aeruginosa, the phosphoethanolamine modification is mediated by a pEtN transferase that is regulated by zinc ions via the ColRS TCS [415]. In Escherichia coli and Salmonella enterica, the pEtN transferase eptA is regulated by the PmrAB TCS [473]. Mutation in PmrAB in Acinetobacter baumannii showed a 30-fold increase in the transcription of pmrC, which encodes the lipid A phosphoethanolamine transferase [474]. In Salmonella, PhoP can activate pagB, which encodes a palmitoyltransferase that adds palmitic acid to lipid A [475]. In Salmonella enterica, the knockout of PhoPQ made the bacteria more susceptible to antimicrobial peptides by making their surface less rigid and more polarized [476].
The Cpx stress response mediated by the two-component sensor histidine kinase CpxA and the cytoplasmic response regulator CpxR confers resistance to aminoglycoside antibiotics [477], hydroxyurea [477], cationic antimicrobial peptides [420,423], β-lactams [211,403], and chlorhexidine [478], besides being implicated in virulence [479] and biofilm formation [480,481] (Figure 10). The Cpx TCS senses periplasmic or inner membrane protein misfolding and accumulation resulting in the upregulation of the periplasmic protease DegP and degradation of the misfolded proteins [482]. In addition, Cpx induces the expression of the protein folding factors dsbA, ppiA, cpxP, and spy [482]. The expression of Cpx-regulated genes was shown to be upregulated upon initial adhesion of Escherichia coli to abiotic surfaces, a response requiring the outer membrane lipoprotein NlpE [483]. The Cpx regulon is also upregulated by cell wall-acting antibiotics such as β-lactams [484] and cationic antimicrobial peptides [420] besides its induction by copper ions [485] and alterations in pH and osmolarity [211]. Activation of CpxRA by the aromatic metabolite indole stimulates mar transcription [423], which subsequently triggers the multidrug resistance cascade. The CpxRA TCS controls the expression of proteoglycan-modifying enzymes such as the LdtD (YcbB) transpeptidase which catalyzes unusual diaminopimelic acid (DAP)-DAP crosslinks [486] and mediates resistance to β-lactams [487]. In Salmonella, CpxRA upregulates the expression of the two N-acetylmuramoyl-L-alanine amidases encoded by amiA and amiC, resulting in bacterial resistance to protamine and the α-helical peptides magainin 2 and melittin [424]. CpxRA, together with the TCS EnvZ/OmpR, regulates the expression of the porins ompF and ompC in Escherichia coli [211,425].
In Staphylococcus aureus, the TCS GraRS was found to regulate resistance to cationic antimicrobial peptides and vancomycin [439]. The membranal receptor GraS senses cationic antimicrobial peptides, resulting in its autophosphorylation on histidine [439]. The GraS then phosphorylates the GraR regulator that upregulates the efflux pump vraFG that can pump out cationic antimicrobial peptides as well as vancomycin [439,442]. VraFG can also affect the expression of mprF, which attaches lysine to membrane phospholipids and dltABCD which adds D-alanine to cell wall teichoic acids, two processes that result in an increase in the net surface positive charges [439,488].

4. Biofilms

Biofilm formation is one of the main causes of the persistence of pathogenic bacteria associated with severe infections and outbreaks in hospitals. It is a universal phenomenon among microorganisms and is an important virulence factor that is responsible for the colonization of living tissues or medical devices and causes treatment failure due to decreased susceptibility to antimicrobial drugs and resistance to host defense mechanisms. The biofilms appear as complex three-dimensional structures where the bacteria are embedded in a network of extracellular polymeric matrices (EPS) composed of proteins, polysaccharides, alginates, lipids, teichoic acids, extracellular DNA (eDNA), and other organic compounds secreted by the bacteria or absorbed from the surrounding environment. The EPS can account for over 90% of the biofilm biomass [2,489]. The EPS functions as a barrier and boundary between the microbial community and the external environment, and it plays a central role in bacterial attachment. Additionally, eDNA released from the lysis of a subpopulation of bacterial cells is involved in the attachment, aggregation, and stabilization of the biofilms [490]. eDNA may even facilitate adhesion to highly hydrophobic surfaces [491]. Some autolysins are important for the release of eDNA and the consequent biofilm formation [490,492,493,494,495]. The biofilms have a high water content that allows the flow of nutrients required for bacterial survival within the biofilms [4].
Biofilm formation is characterized by four major stages that act in a cyclic mode [2,8,496,497,498]: (1) an initial reversible attachment to a biotic or abiotic surface, followed by an irreversible binding to the surface; (2) maturation stage where replication of the bacteria forms a microcolony, accompanied by the production of EPS and other components of the extracellular matrix surrounding the microcolony; (3) adhesion of other bacteria to the glycocalyx composed of EPS and other components, thus increasing the complexity and depth of the biofilm that can reach multiple layers of more than 100 μm; (4) release of some of the bacteria from the mature biofilm, leading to the dispersion of the bacteria to other locations thus generating infection with potentially new biofilm formation. During biofilm maturation, canals are formed in the biofilm structure. These allow gradient-based passage of nutrients and signaling molecules, favoring organized agglomeration and differentiation of cells based on their metabolic state [2].
The initial attachment can be active or passive depending on microbial factors such as motility and expression of adhesins and is affected by the kind of surface [499]. The glycocalyx, which is composed of glycoproteins and polysaccharides, contributes to the maturation of the biofilms through electrostatic and hydrogen bonds between the EPS and the surface [499]. Not only the complex polysaccharides but also extracellular DNA contribute to the structure of the matrix and enable cell–cell and cell–surface interactions [500]. The bacteria might also produce factors that induce tissue damage, thereby favoring their subsequent adhesion [501]. The EPS is important for the development of a microenvironment that allows microbial cell–cell interactions and communication, and some of its components may serve as a reservoir of metabolic substances, nutrients, and energy for the biofilm-embedded microbes [2]. Enzymes that can degrade the EPS polymers play an important role in the biofilm life cycle. They provide carbon and energy during starvation and cause biofilm degradation during detachment and dispersal [496,502]. The bacteria in the outer biofilm layers display active metabolism, while those in the deeper layers of the biofilm where hypoxia prevails, show reduced metabolism and have entered a sessile, dormant state [4].

4.1. Regulation of Biofilm Formation

Biofilm formation is induced by different factors including changes in the environmental conditions including oxidative stress, alterations in nutritional and metabolic cues, low pH, starvation, heavy metals, host-derived signals, toxic compounds, QS signals, and subinhibitory concentrations of antimicrobials [20,503,504,505,506,507,508,509,510,511,512]. For instance, biofilm formation of Salmonella typhimurium is induced by acidic stress and bile salts under oxygen-limiting conditions in the stomach and the small intestine [513]. Biofilm formation is affected by the properties of the biotic or abiotic surfaces [4,499]. Within the biofilms, the microbes coordinate their behavior for promoting growth and producing EPS [489,514].

4.1.1. Induction of Biofilm Formation by Low Antibiotic Concentrations

Various antibiotics at subinhibitory concentrations can induce biofilm formation [263,510,512,515,516,517,518,519,520]. The cell wall antibiotic-induced biofilm formation of Enterococcus faecalis was associated with increased cell lysis, increased extracellular DNA levels, and an increased density of bacteria within the biofilm [510]. In Staphylococcus aureus, the β-lactam antibiotics induce extracellular DNA release that was dependent on the autolysin Atl [515]. The mupirocin-induced biofilm formation of Staphylococcus aureus was dependent on the upregulation of the CidA holin that was associated with the increased production of extracellular DNA [520]. Hoffman et al. [516] observed that aminoglycoside antibiotics could induce biofilm formation of Pseudomonas aeruginosa through a mechanism that depends on the aminoglycoside response regulator (arr). The arr gene encodes for an inner membrane phosphodiesterase whose substrate is cyclic di-guanosine monophosphate (c-di-GMP), a second messenger that regulates cell-surface adhesiveness [516,517] (see Section 4.1.3). Chloramphenicol and erythromycin induce the expression of the capsular exopolysaccharide in Acinetobacter baumannii through a mechanism that depends on the TCS BfmRS [518].
Azithromycin, on the other hand, reduces biofilm formation of Pseudomonas aeruginosa and inhibits QS-regulated virulence factors such as autoinducer production, pyocyanin production, and swarming [521,522,523]. Azithromycin downregulates the expression of gacA [521], which mediates the switch between the motile and biofilm lifestyles of Pseudomonas aeruginosa [524]. The involvement of GacA in biofilm formation will be further discussed in Section 4.4.

4.1.2. Involvement of Two-Component Systems in Biofilm Formation

The QS cell-to-cell communication among bacteria facilitates the formation of specialized biofilm structures and causes alterations in the expression of surface molecules such as adhesins that promote adhesion [4,5,301,335,503,507,525,526,527,528,529] (Table 3). The QS-regulated biofilm formation affects both bacterial pathogenesis and resistance to antibiotics [526,527,530,531]. The dependency of biofilm induction on cell density varies between the bacterial species. For instance, in Vibrio cholerae, the biofilm-related genes are induced at low cell density, whereas biofilm-related genes in Pseudomonas aeruginosa are expressed at high cell density [326,505,532].
LuxS, which is responsible for AI-2 synthesis, is one of the first autoinducer synthetases that was demonstrated to affect biofilm formation [530]. It might either reduce or promote biofilm formation depending on the bacterial species [344,530,533,534,535,536,537] (Table 3). For instance, in Vibrio strains AI-2 increases biofilm formation and motility [290,338]. In Staphylococcus epidermidis, the luxS mutant formed a thicker and more compact biofilm compared to the wild-type strain [533]. LuxS appears to repress biofilm formation in these bacteria through transcriptional regulation of the ica gene locus that is responsible for PIA exopolysaccharide production [533]. Similarly, in Staphylococcus aureus, LuxS seems to prevent biofilm formation by activating the transcription of icaR, a repressor of the ica operon [538]. In Salmonella typhimurium, AI-2 induces the transcription of the lsrACDBFGE operon which, among others, encodes for the lsr ATP-binding (ABC) transport system involved in the uptake of AI-2 [539]. LuxS is also responsible for virulence gene expression in Salmonella typhimurium [540], and in the absence of luxS and AI-2, biofilm formation was impaired in these bacteria [536]. Exogenously added AI-2 increased Escherichia coli biofilm formation among others by upregulating adhesin antigen 43 and curli fibers [537,541,542].
Table 3. Examples of regulatory factors including two-component systems (TCSs) affecting biofilm formation.
Table 3. Examples of regulatory factors including two-component systems (TCSs) affecting biofilm formation.
Biofilm
Formation
Regulating
Factors
FunctionSpeciesReference
Agr
-
Agr is a QS TCS of Staphylococcus species that leads to the spread of infection by dispersion of the biofilm and increased production of exoproteins and murein hydrolases at high cell density.
-
Loss of agr activity is associated with enhanced biofilm formation and decreased autolysis rates.
Staphylococcus aureus[370]
AlgD-A
-
AlgD-A is responsible for alginate synthesis, which is involved in adherence and early biofilm formation.
Pseudomonas aeruginosa[509,543,544]
AlsSD
-
AlsSD is an α-acetolactate synthase/decarboxylase that is active during staphylococcal biofilm development.
-
AlsSD prevents cell death by antagonizing CidABC, thus affecting the biofilm biomass. The cidC-encoded pyruvate:menaquinone oxidoreductase contributes to cell death through acetate-mediated acidification of the bacterial cytoplasm, while AlsSD involved in acetoin biosynthesis, promotes cell survival by consuming protons, thereby increasing cytoplasmic pH.
Staphylococcus aureus[545,546]
ArgR
-
Deletion of ArgR reduces biofilm formation of MRSA through the arginine catabolic pathway.
-
argR is upregulated 3.9-fold in a biofilm compared to exponential-phase planktonic cells.
Staphylococcus aureus[547,548]
ArlRS
-
ArlRS is important for ica-dependent biofilm formation.
-
ArlRS regulates PNAG synthesis by relieving IcaR-mediated repression of the icaADBC operon.
-
An arl mutant showed deficient PNAG production and reduced capacity to colonize implanted catheters.
-
ArlRS represses the expression of rbf, a positive regulator of biofilm formation.
-
ArlRS promotes the expression of aur, thereby inhibiting protein-mediated, ica-independent, biofilm formation.
Staphylococcus aureus[549,550,551,552]
AtlA/AtlE
-
AtlA is important for the initial adhesion to a surface.
-
AtlE is an autolysin gene involved in bacterial lysis resulting in the release of eDNA important for biofilm formation.
Staphylococcus aureus,
Staphylococcus epidermidis
[492,493,553]
BasSR
-
BasSR is a TCS important for biofilm formation.
-
BasSR is involved in the expression of biofilm-related genes including the glucan biosynthesis protein opgC, the cellulose synthase subunit bcsA, the major subunit of curli fibers csgA, the basic unit of flagellar filament structural protein fliC, the flagellar motor complex unit motA, and the type-1 fimbrial subunit fimA.
-
BasSR is induced by Fe and Zn ions.
Escherichia coli[554]
BfiRS
-
Inactivation of bfiS arrests biofilm formation at the irreversible attachment stage and reduces virulence.
-
Deletion of bfiS results in elevated rsmYZ levels in biofilm cells.
-
BfiSR regulates biofilm formation via transcription of cafA (RNase G). Inactivation of cafA results in increased rsmZ levels and arrested biofilm formation.
Pseudomonas aeruginosa[555,556,557]
BfmRS (RtsAB)
-
BfmS is the sensor kinase that acts on the transcriptional regulator BfmR.
-
BfmRS increases the expression of capsular exopolysaccharides in Acinetobacter baumannii, resulting in enhanced biofilm formation and resistance to killing by host complement.
-
Sublethal concentrations of the antibiotics chloramphenicol and erythromycin enhance capsular exopolysaccharide production in Acinetobacter baumannii, which depends on BfmRS.
-
BmfRS regulates biofilm maturation of Pseudomonas aeruginosa.
Acinetobacter baumannii, Pseudomonas aeruginosa[518,558,559,560,561]
cAMP-CRP
-
cAMP-CRP is stimulated by reduced metabolic energy.
-
In the absence of cAMP, cAMP receptor protein (CRP) is in an “off” state, which binds DNA nonspecifically and weakly. Upon cAMP binding, CRP undergoes an allosteric transition and is activated to the “on” state, which binds DNA specifically and strongly via its C-terminal domain.
-
cAMP is produced by adenylate cyclase (CyaA) in Escherichia coli and deletion of cyaA results in reduced extracellular matrix production and biofilm formation.
-
CRP positively regulates csgD transcription, leading to curli and cellulose production in Escherichia coli.
-
cAMP-CRP in Klebsiella pneumoniae is required for fimbria production and biofilm formation, but it inhibits the capsular polysaccharide biosynthesis.
-
crp mutant Klebsiella pneumoniae strains could not express MrkA, the major subunit of the type 3 fimbrial shaft.
Escherichia coli,
Klebsiella pneumoniae
[562,563,564,565]
CidABC
-
CidABC enhances murein hydrolase activity with pro-death functions.
-
CidABC facilitates DNA release and biofilm formation.
Staphylococcus aureus[495,546,566]
c-di-GMP
-
High concentrations of c-di-GMP promote alginate and Pel polysaccharide production and biofilm formation in Pseudomonas aeruginosa.
-
A high level of c-di-GMP is associated with reduced OprD expression in the presence of imipenem.
-
c-di-GMP contributes to biofilm-associated antimicrobial resistance via upregulation of the transcriptional regulator BrlR.
-
The diguanylate cyclase YdeH is involved in c-di-GMP production.
Pseudomonas aeruginosa[508,517,567,568,569,570,571]
CodY
-
CodY is a transcriptional repressor that is activated by binding GTP. Depletion of GTP during stringent responses causes de-repression of CodY-regulated genes.
-
codY mutants showed reduced biofilm formation and increased protease activity.
Staphylococcus aureus[572,573,574]
CqsA
-
CqsA is an autoinducer synthase that reduces biofilm formation through HapR-mediated repression of the Vibrio polysaccharide synthesis (vps) operon.
Vibrio harveyi[336]
CpxRA
-
CpxRA responds to extracellular stress stimuli.
-
CpxA is the membrane sensor kinase/phosphatase and CpxR is the response regulator.
-
CpxR plays a role in biofilm formation via induction of curli csgAB and fimbrial stdAC, and repression of sdiA transcription.
Escherichia coli,
Salmonellaenteritidis
[575]
CreBC (BlrAB)
-
CreBC is a TCS activated by the β-lactam cefoxitin that inhibits PBP4, and when PBP4 is mutated.
-
CreBC promotes biofilm formation, among others through its effector CreD.
-
The cefoxitin-mediated inhibition of biofilm formation is enhanced in creD and creBC mutants.
Pseudomonas aeruginosa[426,576]
CsgD
-
CsgD is a master regulator of biofilm formation that activates the production of curli fimbriae, EPS, and several genes including adrA encoding a diguanylate cyclase involved in the synthesis of cyclic di-GMP.
-
csgD translation is negatively controlled by the RprA sRNA in Escherichia coli.
-
CsgD of Salmonella enterica serovar Typhimurium is required for the expression of csgBA, which encodes curli fimbriae.
Escherichia coli,
Salmonella enterica
[577,578,579,580]
DltA
-
A dltA mutant that leads to a lack of D-alanine modification of the cell wall teichoic acid, shows impaired biofilm formation.
Staphylococcus aureus[581]
FsrBDC
-
FsrBDC is a QS-dependent regulatory system involved in biofilm formation through the production of gelatinase. Gelatinase is essential for the release of extracellular DNA required for biofilm formation.
Enterococcus faecalis[582,583,584]
GacSA
-
The histidine kinase GacS and its cognate response regulator GacA regulate the expression of the two small RNAs rsmY and rsmZ that antagonize RsmA, thereby promoting biofilm formation in Pseudomonas aeruginosa.
-
The GacSA TCS is regulated by RetS, LadS, and PA1611 in Pseudomonas aeruginosa.
-
Disruption of gacA caused a 10-fold reduction in biofilm formation by Pseudomonas aeruginosa.
-
GacSA increases biofilm formation in Acinetobacter baumannii by regulating the csu operon involved in pilus biosynthesis.
Pseudomonas aeruginosa,
Acinetobacter baumannii
[507,559,585,586,587,588]
GraRS
-
A ΔgraRS mutant showed reduced staphyloxanthin production, retarded coagulation, weaker hemolysis on blood agar plates, and a decreased biofilm formation.
-
Expression of the virulence-associated genes coa, hla, hlb, agrA, and mgrA were downregulated in a ΔgraRS mutant.
-
A CA-MRSA with a transposon insertion in graS showed increased autolysis and defective biofilm formation.
-
GraRS activates the dlt operon responsible for the D-alanylation of teichoic acid.
-
GraRS induces the expression of the autolysin gene atlA.
Staphylococcus aureus[441,589]
HapR
-
HapR, a major regulator of QS, represses biofilm formation by regulating the transcription of a series of genes that ultimately causes a reduction in cellular c-di-GMP levels.
-
HapR represses the expression of the biofilm transcriptional activator vpsT.
-
HapR activates hapA, which encodes for a hemagglutinin/protease that promotes detachment of Vibrio cholerae from epithelial cells.
Vibrio cholerae[335,504]
LadS
-
LadS is a calcium-responsive kinase that stimulates GacA activity, thereby promoting biofilm formation by GacA-mediated upregulation of the two small non-coding RNAs rsmY and rsmZ.
Pseudomonas aeruginosa[507,585,590]
LasR/LasI
-
LasR/LasI is a TCS system involved in virulence and biofilm formation.
-
LasI produces the autoinducer 3OC12-HSL that binds to LasR activating several genes including the TCS component rhlR.
-
A lasI mutant formed flat, undifferentiated biofilms that were sensitive to the biocide sodium dodecyl sulfate.
-
LasR regulates the expression of more than 300 genes, including the psl exopolysaccharide.
Pseudomonas aeruginosa[296,505,509,591]
LecA
-
LecA is a cytotoxic lectin and adhesin that binds to hydrophobic galactosides and contributes to biofilm formation.
Pseudomonas aeruginosa[592]
LrgAB
-
LrgAB inhibits murein hydrolase activity and promotes penicillin tolerance.
-
A lrgAB mutant exhibited increased biofilm formation and matrix-associated extracellular DNA.
Staphylococcus aureus[289,593]
LuxS
-
LuxS is involved in the synthesis of the QS autoinducer-2 (AI-2).
-
In Escherichia coli, AI-2 stimulates biofilm formation and affects biofilm architecture through activating the quorum sensing regulators mqsR and B3022. B3022 positively regulates the expression of qseBC, flhD, fliA, and motA.
-
In Staphylococcus aureus, the LuxS/AI-2 system inhibits PIA-dependent biofilm formation by repressing the expression of rbf and activation of icaR.
-
In Streptococcus pneumoniae, LuxS is important for early biofilm formation. LuxS induces the expression of the autolysin lytA that is implicated in biofilm formation.
-
LuxS promotes iron-dependent biofilm formation in Streptococcus pneumoniae.
-
A luxS mutant of Klebsiella pneumoniae was able to form mature biofilms in the intestine but showed reduced capacity in developing microcolonies.
-
A luxS mutant of a Salmonella serovar produced thinner biofilms.
Salmonella species,
Vibrio species,
Escherichia coli,
Staphylococcus aureus,
Streptococcus pneumoniae,
Klebsiella pneumoniae
[525,530,538,541,594,595,596]
LytA
-
The lack of the autolysin gene lytA resulted in impaired biofilm formation.
Streptococcus pneumoniae[597]
LytSR
-
LytSR senses decreases in membrane potential.
-
LytSR induces the expression of lrgAB that inhibits murein hydrolase activity.
-
A lytS mutant formed a more adherent biofilm.
Staphylococcus aureus[598,599]
MgrA
-
MgrA acts downstream to ArlRS to control the expression of various virulence genes.
-
MgrA regulates PNAG synthesis.
-
MgrA can directly bind to the promoter of the ica operon, enhancing the expression of icaA and PIA.
-
A mgrA mutant was deficient in PNAG production and showed reduced capacity to colonize catheters.
-
MgrA represses the expression of rbf, a positive regulator of biofilm formation.
-
MgrA promotes the expression of aur, thereby inhibiting protein-mediated biofilm formation.
-
The mgrA mRNA is stabilized by RNAIII of the arg QS system.
Staphylococcus aureus[374,398,549,550,552,600]
MifRS
-
MifR is involved in regulating the maturation stage of biofilm formation.
-
mifR deficient mutants fail to form microcolonies.
Pseudomonas aeruginosa[557,601]
QseBC
-
The QseC sensor kinase—QseB response regulator TCS affects carbon metabolism, flagellar motion, and promotes biofilm formation by upregulating the biofilm-associated genes bcsA, csgA, fliC, motA, wcaF, and fimA.
-
QseBC confers antibiotic resistance by upregulating the transcription of the efflux pump-associated genes marA, acrA, acrB, acrD, emrD, and mdtH.
-
The QseCB TCS is regulated by MqsR.
Escherichia coli,
Salmonella Typhimurium
[249,541,602,603,604]
PA1161
-
PA1161 is a hybrid sensor kinase that promotes biofilm formation by increasing rmsY and rmsZ expression, and by interacting with RetS, resulting in its inactivation.
-
PA1161 represses T3SS genes and swarming motility.
Pseudomonas aeruginosa[605]
PilSR
-
PilSR, which is composed of the PilS sensor and the PilR regulator, controls the expression of pilA, the major subunit of type IV pilus.
-
PilSR regulates the transcription of fleSR, and thus positively affects twitching and swimming motilities.
Pseudomonas aeruginosa[606,607]
(p)ppGpp
-
(p)ppGpp is induced by amino acid starvation.
-
RelA is involved in the synthesis of ppGpp, while the SpoT hydrolase reduces the ppGpp levels.
-
ppGpp positively regulates the ribosome modulation factor rmf in Escherichia coli.
-
SpoT-mediated reduction of ppGpp levels results in derepression of the poly-GlcNAc biosynthesis machinery PgaA in Escherichia coli.
-
A ppGpp-deficient strain of Acinetobacter baumannii showed a significant reduction in csu operon expression, which is important for pilus biosynthesis during early biofilm formation.
-
In Staphylococcus aureus, (p)ppGpp can be synthesized by Rel upon amino acid deprivation or by the two alarmone synthetases RelP and RelQ under cell wall stress. RelP and RelQ increase biofilm formation in response to subinhibitory concentrations of vancomycin.
-
(p)ppGpp contributes to antibiotic tolerance in Staphylococcus aureus where it activates ROS-detoxifying systems.
Escherichia coli,
Acinetobacter baumannii,
Staphylococcus aureus
[570,608,609,610,611,612,613]
PprAB
-
PprAB regulates the expression of the cupE1 gene involved in fimbria assembly.
-
Activation of PprAB triggers a hyper-biofilm phenotype characterized by the expression of BapA adhesin, a type 1 secretion system (T1SS) substrate, CupE CU fimbriae, Flp type IVb pili, and eDNA.
Pseudomonas aeruginosa[614,615]
Rbf
-
Rbf promotes biofilm formation.
-
Rbf induces the expression of sarX that negatively regulates the expression of icaR, thereby activating the icaADBC operon.
-
Rbf represses sarR transcription, resulting in activation of the icaADBC operon.
Staphylococcus aureus,
Staphylococcus epidermidis
[616,617,618]
RcsCDB
-
RcsC is a hybrid sensor kinase that upon activation undergoes autophosphorylation, then transfers the phosphoryl group to the histidine phosphotransferase RcsD, which, in turn, transfers the phosphoryl group to the response regulator RcsB.
-
The RcsC sensor kinase is required for induction of pgaABCD and normal biofilm development in Escherichia coli.
-
RcsC is activated during growth on a solid surface, by zinc ions and by osmotic shock in Escherichia coli.
-
The Rcs phosphorelay is activated by β-lactam antibiotics in Escherichia coli, resulting in the survival of the bacteria in the presence of the antibiotics.
-
In Salmonella enterica serovar Typhimurium, phosphorylated RcsB inhibits biofilm development by repressing csgD, which is mediated by the accumulation of the small non-coding RNA rprA. The RcsCDB phosphorelay is negatively regulated by IgaA, which interacts with RcsD.
-
RcsB positively regulates the cupD gene involved in cell-surface fimbria assembly that is required for biofilm formation in Pseudomonas aeruginosa.
Escherichia coli,
Salmonella enterica serovar
Typhimurium,
Pseudomonas aeruginosa
[484,619,620,621,622,623,624]
RetS
-
The RetS sensor inhibits biofilm formation by repressing GacA activity.
-
RetS is required for type III secretion system (T3SS) activation and represses exopolysaccharide production and biofilm formation.
-
A retS mutant expresses high levels of c-di-GMP and forms biofilms.
-
The retS mutation led to repression of the type III secretion system, while upregulation of the type VI secretion system was mediated by the diguanylate cyclase WspR.
Pseudomonas aeruginosa[524,625]
RhlR/RhlI
-
RhlR/RhlI is a TCS system that regulates virulence and biofilm formation.
-
RhlR binds the autoinducer C4-HSL and an alternative autoinducer to activate genes involved in the synthesis of virulence-associated QS factors and biofilm formation.
Pseudomonas aeruginosa[509,626,627]
RocS1A1R
-
RocS1A1R is a TCS that consists of two response regulators RocA1 and RocR, and the sensor RocS1.
-
RocA1 positively regulates the expression of the cupB and cupD genes involved in the assembly of cell-surface fimbriae required for biofilm formation.
-
RocR downregulates the expression of cupB and cupD, resulting in reduced biofilm formation.
-
RocR is a phosphodiesterase that leads to the hydrolysis of c-di-GMP into 5’pGpG.
Pseudomonas aeruginosa[628,629]
Rot
-
Rot is a DNA-binding transcriptional regulator that represses the transcription of secreted proteases, thus increasing biofilm mass.
Staphylococcus aureus[630]
RpoS
-
The expression of the RpoS/σS sigma subunit of RNA polymerase (RNAP) is induced during entry into the stationary phase and in response to stress conditions.
-
During rapid growth, the translation of RpoS is inhibited and the RpoS protein is degraded by the ClpXP protease.
-
RpoS regulates biofilm formation both in a positive and negative manner.
-
At low temperatures, RpoS contributes to the expression of the exopolysaccharide colanic acid.
-
An Escherichia coli rpoS mutant was defective in the formation of mature biofilms, while another rpoS mutant showed increased biofilm formation during the exponential growth phase.
-
RpoS together with the transcription factor MlrA induce the transcription of csgD. CsgD promotes biofilm formation by controlling the expression of curli fibers and the diguanylate cyclase adrA, which indirectly activates cellulose production.
-
rpoS transcription is negatively regulated by ArcBA, but positively by (p)ppGpp and cAMP.
-
The three sRNAs ArcZ, DsrA, and RprA activate the translation of rpoS mRNA by enabling ribosome entry to the Shine-Dalgarno sequence. The sRNA/rpoS mRNA complexes are stabilized by the RNA chaperone Hfq.
-
RpoS induces antibiotic tolerance in Pseudomonas aeruginosa, especially during the stationary phase.
Escherichia coli,
Pseudomonas aeruginosa
[578,631,632,633,634,635,636,637]
SadARS
-
SadARS is a three-component system that consists of a histidine kinase and two response regulators.
-
Nonpolar mutations in any of the sadARS genes result in biofilms with an altered mature structure without affecting growth, early biofilm formation, swimming, or twitching motility.
-
The mutant biofilms show reduced formation of water channels.
Pseudomonas aeruginosa[638]
SaeRS
-
SaeRS is a TCS that cooperates with Rot to activate the expression of the staphylococcal superantigen-like exoproteins.
-
A ΔsaeRS strain exhibited enhanced biofilm formation that was related to increased autolysis and consequent increased extracellular DNA production. The ΔsaeRS mutant showed increased expression of the autolysins atlE and aae, without any alterations in icaA expression.
Staphylococcus aureus[639,640]
SagS
-
SagS is a sensor regulator that contains a periplasmic sensory HmsP, and phosphorelay HisKA and Rec domains.
-
SagS promotes biofilm formation and drug tolerance.
-
SagS mediates the switch between the planktonic to the biofilm mode of growth.
-
A ΔsagS mutant showed unstructured biofilms and was more sensitive to antimicrobial drugs such as tobramycin.
-
SagS contributes to biofilm formation via hierarchical phosphotransfer-based signaling to the TCS BfiSR which is required for biofilm formation.
-
SagS activates the c-di-GMP-responsive transcriptional regulator BrlR, which mediates biofilm tolerance to antimicrobial agents by upregulating the efflux pumps MexAB-OprM, MexEF-OprN, and the ABC transport system PA1874-77.
Pseudomonas aeruginosa[230,555,568,641,642,643,644]
SarA
-
SarA is a transcription factor that influences virulence, metabolism, biofilm formation, and resistance to some antibiotics.
-
SarA upregulates the synthesis of fibronectin- and fibrinogen-binding proteins, hemolysins, enterotoxins, toxic shock syndrome toxin 1, oxidative stresses (sodM and trxB), and genes involved in biofilm formation (e.g., icaRA and bap), and represses expression of proteases (ssp and aur), protein A (spa), and collagen-binding proteins (cna).
-
The reduced capacity of a sarA mutant to form a biofilm involves increased expression of extracellular proteases.
Staphylococcus aureus[645,646,647,648]
SarX
-
SarX is a SarA homolog that activates spa transcription.
-
SarX promotes biofilm formation by regulating icaADBC transcription and PIA production.
-
sarX transcription is upregulated in the stationary phase.
-
sarX is upregulated by MgrA and Rbf.
Staphylococcus aureus,
Staphylococcus epidermidis
[616,649,650,651]
SdiA
-
SdiA is a QS receptor that detects acyl homoserine lactone (AHL) type autoinducers.
-
SdiA inhibits biofilm formation and adhesion to epithelial cells.
-
SdiA activates cell division by activating the ftsQAZ operon.
-
A sdiA Escherichia coli mutant formed thicker biofilms compared to the wild-type strain.
-
The addition of AHL to Escherichia coli reduces biofilm formation and represses the expression of csgD, csgA, and fimA.
-
The two-component systems ArcA, CpxR, OmpR, RcsB, and TorR repress sdiA transcription.
Escherichia coli,
Salmonella spp.
[652,653,654]
SigB
-
SigB is a sigma factor that inhibits the agr system, thus increasing biofilm formation.
-
A sigB mutant showed elevated RNAIII levels and increased protease activity.
Staphylococcus aureus[655]
SrrAB
-
An srr mutant showed reduced ability to colonize catheters.
Staphylococcus aureus[549]
TcaR/IcaR
-
TcaR and IcaR are negative regulators of the ica operon, thus preventing ica-dependent biofilm formation.
-
IcaR is the dominant repressor of the ica operon, and TcaR enhances the IcaR-mediated repression.
-
A ΔtcaRAB strain shows increased resistance to teicoplanin and methicillin.
Staphylococcus aureus[656,657,658]
VraSR
-
VraSR is a TCS that responds to cell wall stress.
-
A ΔvraSR mutant showed impaired biofilm formation with a higher ratio of dead cells within the biofilm.
Staphylococcus epidermidis[467]

4.1.3. Role of Cyclic di-GMP (c-di-GMP) in Biofilm Formation

Various bacterial species, especially Gram-negative bacteria such as Pseudomonas aeruginosa, Salmonella enterica, Escherichia coli, and Vibrio cholerae, use the secondary metabolite c-di-GMP signaling to regulate biofilm formation [659,660,661,662]. c-di-GMP regulates the transition from planktonic to biofilm state [662]. In general, low intracellular c-di-GMP levels are associated with motility and a planktonic lifestyle, whereas high c-di-GMP levels are associated with biofilm formation and sessility [507,517].
c-di-GMP modulates several aspects of biofilm formation, including flagella rotation, type IV pili retraction, EPS production, surface adhesin expression, resistance to antimicrobial drugs and other stress responses, secondary metabolite production, and biofilm dispersion [517,659] (Figure 11; and Section 4.4). In addition, c-di-GMP affects many other bacterial functions such as cell division, type III secretion, RNA modulation, stress responses, and virulence [663]. Changes in c-di-GMP levels are sensed by c-di-GMP receptor proteins and riboswitch RNAs which propagate the downstream signaling cascade [664,665]. In Pseudomonas aeruginosa, c-di-GMP is required for the synthesis of the extracellular polysaccharides Psl and Pel [666], affects the expression of the extracellular matrix adhesion protein CdrA that interacts with Psl and Pel [666,667], and modulates the production of alginate [668].
The c-di-GMP level is controlled by enzymes that synthesize c-di-GMP (e.g., diguanylate cyclases (DGCs) carrying a GGDEF active site motif) and enzymes that degrade the molecule (e.g., c-di-GMP phosphodiesterases (PDEs) carrying either EAL or HD-GP domains) [662]. The Pseudomonas aeruginosa genome encodes one of the highest numbers of DGCs and PDEs: 18 GGDEF, 5 EAL, 16 GGDEF/EAL, and 3 HD-GYP predicted proteins [517]. Upon contact of Pseudomonas aeruginosa with a surface, the membrane-bound receptor, WspA, becomes activated and triggers c-di-GMP production by the DGC WspR [669]. c-di-GMP, in turn, downregulates the flagellum motility machinery, thereby forcing the bacteria into a sessile growth mode [669].

4.1.4. Role of Non-Coding RNAs (ncRNAs) or Small Regulatory RNA (sRNA) in Regulating Biofilm Formation

The multicellular adhesive McaS sRNA of Escherichia coli interacts with mRNAs encoding master transcription regulators of curli and flagella synthesis, resulting in their respective downregulation and upregulation [276]. In Escherichia coli, McaS activates the synthesis of the exopolysaccharide β-1,6 N-acetyl-D-glucosamine (PGA) by binding and blocking the global RNA-binding protein CsrA, which negatively regulates pgaA translation and positively controls the flagellar master flhDC operon expression [276,578]. Ectopic McaS expression leads to the induction of diguanylate cyclases that are repressed by CsrA [276].
The bacterial 3’UTR-derived non-coding RNA RibS was found to affect the biofilm formation of Salmonella enterica serovar Typhi [271]. RibS is formed by RNase III-mediated cleavage of the 3’UTR of riboflavin synthase subunit alpha mRNA RibE [271]. Overexpression of RibS promotes biofilm formation by increasing the expression of the cyclopropane fatty acid synthase gene cfa [271]. The expression of cfa is also regulated by the sRNAs RydC, ArrS, and CpxQ [670]. Both RydC and ArrS mask the RNaseE cleavage site in the cfa mRNA 5’-UTR, resulting in the upregulation of cfa [670]. CpxQ binds to a different site of the cfa mRNA 5’UTR, resulting in the repression of cfa [670].
The σS-dependent sRNA SdsR was shown to regulate biofilm formation in Salmonella by activating csgD and curli expression and downregulating the ompD porin [578]. In Escherichia coli, SdsR inhibits flhDC expression [578].
The small non-coding RNA RsaE affects extracellular matrix composition in Staphylococcus epidermidis biofilm [671]. RsaE interacts with the antiholin lrgA mRNA, thereby facilitating bacterial lysis and eDNA release [671]. Moreover, RsaE augments PIA-mediated biofilm matrix production [671]. The long non-coding RNA IcaZ prevents icaR translation, thereby relieving the repression of icaADBC transcription with a consequent increase in PIA production [672].
The small non-coding RsmW RNA in Pseudomonas aeruginosa upregulates biofilm formation by binding to the RNA-binding regulator RsmA [673]. RsmA represses the type VI secretion system, exopolysaccharide production, and biofilm formation [674,675]. The involvement of RsmY and RmsZ in regulating RsmA will be discussed in Section 4.4.

4.2. Biofilm Formation by Vibrio cholerae

The extracellular matrix of Vibrio cholerae, the causative agent of cholera, is composed of Vibrio polysaccharides (VPS) and three major matrix proteins, RbmA, RbmC, and Bap1 involved in cell–cell and cell–surface adhesion [676]. Several transcriptional regulators and alternative sigma factors control the biofilm formation in Vibrio cholerae. Among them, VpsR and VpsT are considered master regulators of biofilm formation which positively regulate VPS production [677,678]. Both VpsR and VpsT respond to c-di-GMP by inducing the transcriptional switch toward biofilm-regulated genes [678,679,680].

4.3. Biofilm Formation by Escherichia coli

The QseBC TCS of Escherichia coli was found to promote biofilm formation in dairy cows that suffered from mastitis by upregulating the transcription of the biofilm-associated genes bcsA, csgA, fliC, motA, wcaF, and fimA, and conferred antibiotic resistance by upregulating the transcription of the efflux pump-associated genes marA, acrA, acrB, acrD, emrD, and mdtH [249]. The BasSR TCS promotes biofilm formation in avian pathogenic Escherichia coli by upregulating the expression of biofilm- and virulence-related genes, including ais, entC, opgC, gtcE, and fepA [554]. Moreover, the CpxRA TCS, which senses membrane stress and recognizes misfolded proteins, is required for proper biofilm formation, adherence, motility, and the production of type 1 fimbriae [681].

4.4. Biofilm Formation by Pseudomonas aeruginosa

The biofilms of Pseudomonas aeruginosa are characterized by exopolysaccharides (EPS) such as Psl, Pel, and alginate intermingled with proteins, rhamnolipids, membrane vesicles, and eDNA [682,683]. The rhamnolipid biosurfactants are required for the initial stage of microcolony formation, the formation of the mushroom-shaped microcolonies, the maintenance of channels between multicellular structures, and contribute to biofilm dispersal [682,683]. The intercalation of the redox active virulence factor pyocyanin with eDNA contributes to the stabilization of the Pseudomonas aeruginosa biofilm architecture [684]. Moreover, the flagellum is considered a central component of the biofilm formation of Pseudomonas aeruginosa since it provides the mobility needed to actively approach a surface [301]. The type IV pili play a role in surface attachment and colonization [301]. The Cup fimbriae were also found to contribute to the attachment to both abiotic and biotic surfaces, besides providing protection against the recognition by the immune system [301].
The production of the virulence factors rhamnolipids and pyocyanin, and the release of eDNA and membrane vesicles, as well as biofilm development, are controlled by the QS two-component system [296,514]. The QS also elicits a global metabolic rewiring in Pseudomonas aeruginosa which is caused by a combination of direct transcriptional alteration of metabolism-associated genes mediated by the QS system and indirectly by global metabolic readjustment as a result of the general and QS-dependent stress responses [685].
In Pseudomonas aeruginosa, small cationic polyamines such as putrescine as well as its biosynthetic precursors L-arginine and agmatine ((4-aminobutyl)guanidine), promote biofilm formation and confer resistance to environmental stress stimuli [508,517,686]. Both putrescine and L-arginine increase the intracellular c-di-GMP levels [686]. One of the diguanylate cyclases in Pseudomonas aeruginosa is SiaD which is co-transcribed with siaA/siaB/siaC from the siaABCD operon. The siaABCD encodes a signaling network regulating biofilm and aggregate formation by modulating the enzymatic activity of SiaD [687]. SiaC interacts with SiaD to promote its diguanylate cyclase activity, thus promoting c-di-GMP synthesis [687]. The interaction of SiaC with SiaD is facilitated by dephosphorylation mediated by the inner membrane-associated Ser/Thr SiaA phosphatase, while it is prevented when phosphorylated by the SiaB protein kinase [687]. SiaA is activated by external stress stimuli such as sodium dodecyl sulfate [687].
Biofilm formation in Pseudomonas aeruginosa is, among others, regulated by the two QS systems LasI/LasR and RhlR/RhlI that are expressed at both early and late biofilm phases [688,689]. A lasI mutant forms flat and undifferentiated biofilms that were sensitive to sodium dodecyl sulfate [505]. Pseudomonas aeruginosa rhlA mutants that are deficient in the synthesis of biosurfactants were not capable of forming microcolonies in the initial phase of biofilm formation and were defective in migration-dependent development of mushroom-shaped multicellular structures in the later phase of biofilm formation [682]. The Rhl system regulates the expression of pyocyanin and rhamnolipids that are responsible for the deposition of extracellular DNA which is an important component in the early and late biofilm developmental stages. Additionally, the PqsE thioesterase, which is part of the 2-alkyl-4-quinolone biosynthesis gene cluster pqsABCDE, plays a role in the production of pyocyanin, rhamnolipids, and lectin A [690].
The GacSA TCS in Pseudomonas aeruginosa increases the expression of the exopolysaccharides Pel and Psl by upregulating the expression of two small regulatory RNAs, rsmY and rsmZ [301]. RsmY and RsmZ sequester the translational repressor RsmA thus allowing translation of target mRNAs such as the exopolysaccharides pel and psl, required for biofilm formation [301,691] (Figure 12A). RsmA increases the expression of the type III secretion system (T3SS) while repressing the expression of the type VI secretion system (T6SS) [625,692]. The activity of GacS is activated by the hybrid histidine kinase LadS [585], while antagonized by the hybrid sensor kinase RetS [524]. The activity of RetS is repressed by the hybrid sensor kinase PA1611, which positively regulates biofilm formation by upregulating rsmY and rsmZ [605]. The expression level of PA1611 is increased during the transition between acute and chronic infection and mediates the transition to the biofilm state [605]. A retS mutant showed elevated levels of c-di-GMP, increased biofilm formation, and a shift in type III and type VI secretion systems that were dependent on c-di-GMP [625]. The siaABCD responsible for c-di-GMP production is repressed by RsmA [693], thereby generating a feedback loop (Figure 12A). GacSA also positively regulates the transcription of the QS components lasR and rhlR in Pseudomonas aeruginosa [296]. A ΔgacA mutant showed a 10-fold reduction in the ability to form biofilms [588]. The ΔgacS strain was hypermotile, produced a reduced amount of acyl-homoserine lactones, showed impaired biofilm maturation, and was more sensitive to certain antibiotics (e.g., tobramycin, ceftriaxone, oxacillin, piperacillin, and rifampicin) in comparison to the parental strain [694].
Other TCSs involved in the biofilm formation of Pseudomonas aeruginosa include SagS, BfiRS, BfmRS, and MifRS [301,556,557]. SagS, BfiRS, BfmRS, and MifRS are sequentially phosphorylated during biofilm formation [557] (Figure 12B). Inactivation of either of these components arrests biofilm formation at distinct developmental stages [502,555,556,557]. Biofilms formed by ΔsagS and ΔbfiS mutants are arrested at the irreversible attachment stage, while biofilms formed by ΔbfmR and ΔmifR mutants are arrested at the maturation-1 and maturation-2 stages of biofilm development, respectively [502,555,556,557]. SagS enables the switch from the planktonic state to the sessile, biofilm state, through activation of the TCS BfiRS [555,556,641]. BfiRS represses the rsmYZ expression levels which seem to be a necessary step for future maturation of Pseudomonas aeruginosa biofilm [556]. SagS is also required for the biofilm-associated resistance to antibiotics through BrlR-mediated upregulation of efflux pumps such as mexAB-oprM and mexEF-oprN [569,644]. The BrlR expression was dependent on sufficient levels of c-di-GMP [569]. BmfRS regulates biofilm maturation [561], while MifRS modulates microcolony formation [695]. The loss of biofilm biomass in the ΔbmfR mutant might be related to increased cell death [696].
The fimbrial cupB and cupC genes are regulated by the roc1 locus that encodes one sensor kinase (RocS1) and two response regulators (RocA1 and RocR) [301]. This cluster has also been termed sadARS and has been documented to positively regulate biofilm formation while repressing type III secretion genes [638]. Nonpolar mutations in any of the sadARS genes result in biofilms with an altered mature structure, but without defects in growth or early biofilm formation, swimming, or twitching motility [638]. Mutations in type III secretion genes resulted in strains with enhanced biofilm formation [638]. Type III secretion genes including pcrV are negatively regulated by c-di-GMP [697]. Of note, RocR contains an EAL motif with a phosphodiesterase activity that degrades c-di-GMP [629]. RocA2 was found to repress the expression of the mexAB-oprM efflux pump [698]. The RocS1A1R system seems to be counterintuitive by providing a signal cascade that promotes biofilm formation via Cup fimbriae and simultaneously increases the sensitivity to antibiotics by repressing a multidrug efflux pump. This could be associated with the fitness cost of this efflux pump in a biofilm environment [301].

4.5. Biofilm Formation by Staphylococcus Species

The biofilms of Staphylococcus aureus can be classified into ica-dependent and ica-independent biofilms. The ica-dependent biofilms are associated with exopolysaccharide intercellular adhesin/poly-N-acetylglucosamine (PIA/PNAG; product of the ica operon) involved in intercellular adhesion [699]. These polysaccharides are encoded by the icaADBC operon. The ArcC-type transcriptional regulator Rbf activates the icaADBC operon and PIA production in Staphylococcus epidermidis by preventing the transcription of the SarR repressor [617]. The ArlRS TCS regulates PNAG synthesis in Staphylococcus aureus by repressing icaR, a transcriptional repressor of the icaADBC operon [549]. The arl mutant of Staphylococcus aureus showed reduced catheter colonization [549].
The ica-independent biofilms have a proteinaceous matrix and are more frequently found in MRSA isolates [700,701]. These biofilms involve fibrinogen and fibronectin-binding proteins FnBPA and FnBPB, which are LPXTG-containing proteins anchored to peptidoglycan [700,702,703]. Loss of sortase (sarA), which anchors LPXTG-containing proteins to peptidoglycan, reduced the MRSA biofilm phenotype [700]. Other proteins involved in ica-independent biofilm formation include Staphylococcus aureus surface proteins C and G (SasC and SasG), extracellular adherence protein (Eap), biofilm-associated protein (Bap), fibronectin-binding proteins (FnBPs), clumping factor B (ClfB), and Staphylococcus protein A (Spa) [704,705,706,707,708,709].
In Staphylococcus aureus, the accessory gene regulator (arg) QS system is involved in regulating biofilm formation [370]. Silencing the agr system strengthens biofilm formation [533]. The increased biofilm thickness of the agr mutant is thought to be due to the inability of the cells to detach from the mature biofilm [533]. AgrB, which is associated with the secretion of virulence factors, promotes biofilm dispersion through increased production of the Aur metalloproteinase and the SplABCDEF serine proteases [528,710]. The Arg-mediated detachment of bacteria from the biofilm restored sensitivity to rifampicin [710]. Another reason for the increased biofilm formation of agr mutants might be the AgrA-mediated regulation of the phenol-soluble modulin (PSM) operon. PSMs have surfactant-like properties that are involved in biofilm dispersion [711]. Other systems in Staphylococcus aureus regulating virulence genes and biofilm formation include the TCSs ArlRS, SaeRS, SrrAB, and GraRS [367,368,441,549,712] (Table 3).
During the biofilm formation of Staphylococcus aureus, a small subpopulation undergoes lysis to provide extracellular DNA that glues together the extracellular matrix [593,713,714]. This process is regulated by the holin-like CidABC and the anti-holin-like LrgAB systems [495,593,715]. CidA, which regulates the activities of murein hydrolases, promotes genomic DNA release and biofilm formation [495,715]. LrgAB, which is regulated by the LytSR TCS [289], inhibits CidA-mediated lysis [593]. CidA and LrgA are membrane-associated proteins that form heteromers with disulfide bonds formed between cysteine residues [716]. An lrgAB mutant exhibited increased biofilm formation and matrix-associated extracellular DNA [593]. The murein hydrolase AtlA is important for the initial adhesion of Staphylococcus aureus to a surface [553]. AtlA is also required for cell division, cell wall turnover, and bacterial lysis [553].

4.6. Biofilm Formation by Klebsiella pneumoniae

In Klebsiella pneumoniae, some virulence-related genes are involved in biofilm formation. These include the cps gene cluster responsible for capsule formation [717], the fimA and mrkA genes involved in type 1 and type 3 fimbriae formations [718], wbbM, which encodes an enzyme involved in the biosynthesis of the O-antigen of LPS [719], wzm involved in the transport of LPS [719], luxS of the type 2 QS regulatory system [525], and the pgaABCD operon responsible for the synthesis and translocation of the poly-β-1,6-N-acetyl-D-glucosamine (PGA) adhesin [720]. The RcsAB TCS regulates the biosynthesis of capsular polysaccharides by upregulating the gene galF [721]. Type 1 fimbriae mediate adherence to many types of epithelial cells, while type 3 fimbriae can bind to the extracellular matrix of urinary and respiratory tissues [722]. The luxS mutant could form mature biofilms but had a reduced ability to develop microcolonies, especially during the early stages of biofilm formation [525]. PgaC is involved in bile salt-induced biofilm formation [720]. The OxyR transcription factor upregulates the defense mechanisms against oxidative stress, bile salt, and acid stresses, and is important for biofilm formation and the production of types 1 and 3 fimbriae [723].

4.7. Antibiotic Resistance of Biofilm-Embedded Bacteria

Biofilm formation by pathogens is a major contributor to antibiotic resistance and treatment failure [20,724,725,726,727,728]. The EPS surrounding the biofilm-embedded bacteria protects the cells from adverse and disruptive environmental conditions. The biofilms can increase microbial tolerance to dehydration [729], radiation [729], extreme temperature and pH [729], osmotic stress, nutrient deficiency, metal toxicity, and antibiotics [8,724,730,731,732].
Bacteria embedded in biofilms are often more resistant to antimicrobial agents than planktonic growing cells [153,503,724,727,731,732,733,734]. There are several explanations for this phenomenon. The biofilms are highly persistent and protected from the immune system as well as adverse conditions such as antibiotics owing to their specialized structures [13,14,104]. Within the biofilm, the bacteria adapt to environmental anoxia and nutrient limitations, showing an altered metabolism and altered gene expression profile, concomitant with lower metabolic activity, reduced cell proliferation, and increased nutrient sequestration [1,13,14]. In addition, biofilm growth is associated with an increased level of mutations [14], and the proximity of the biofilm-embedded cells facilitates the horizontal transfer of resistance genes between the bacteria [20,727,735]. The secretion of β-lactamase from a biofilm-embedded bacteria into the biofilm matrix can prevent the β-lactam antibiotics to act on a neighboring cell even if the latter does not produce the enzyme [727]. Thus, antibiotic resistance can be passively conferred.
Bacterial metabolites can also affect the response to antibiotics [727]. For instance, indole produced by the metabolism of tryptophan can shift the antibiotic sensitivity profiles of neighboring organisms [727]. Indole induces the expression of drug transporters such as acrD, acrE, cusB, emrK, mdtA, mdtE, and yceL in Escherichia coli [212]. The induction of acrD, and mdtA by indole is mediated by the BaeSR and CpxAR TCSs [212]. Escherichia coli-produced indole protects Salmonella Typhimurium from ciprofloxacin by activating OxyR-regulated genes that confer protection from oxidative stress [736]. Another example of cross-species adaptive resistance is the interaction between Staphylococcus aureus and Candida albicans hyphae, which leads to resistance of Staphylococcus aureus to miconazole and vancomycin [737,738].

4.7.1. Prevention of Antibiotic Penetration through the Biofilm

The EPS enwrapping the bacteria in the biofilm are less penetrable for many antibiotic drugs (e.g., ampicillin), although some can diffuse through the biofilm matrix (e.g., ciprofloxacin) [733,739]. The negatively charged polysaccharides (especially the Pel polysaccharide and alginate of Pseudomonas aeruginosa) can effectively sequestrate the positively charged aminoglycoside-class of antibiotics such as tobramycin, thus preventing them from penetrating the deeper layers of the biofilm [739,740]. This property of EPS also makes the biofilm-embedded bacteria tolerant to metals such as zinc, copper, and lead [741].
Additionally, the extracellular DNA (eDNA) released to the extracellular matrix of the biofilms has been shown to neutralize the activity of antimicrobial drugs such as tobramycin and antimicrobial peptides, through its cationic chelating properties [454,742]. The eDNA through chelating cations such as magnesium ions forms a cation-limited environment that results in the induction of the PhoPQ and PmrAB TCSs in Pseudomonas aeruginosa [472]. These TCSs regulate cationic antimicrobial peptide resistance by upregulating the PA3552-PA3559 operon [472]. The DNA-induced expression of PA3552-PA3559 results in up to a 2560-fold increase in the resistance to cationic antimicrobial peptides and a 640-fold increase in the resistance to aminoglycosides [472]. Wilton et al. [454] observed that the aminoglycoside resistance is caused by aminoarabinose modification of lipid A and the production of spermidine on the outer membrane of the bacteria, both contributing to reduced uptake of aminoglycosides by the bacteria. The addition of L-arginine or sodium bicarbonate that neutralizes the acidic environment caused by eDNA could sensitize Pseudomonas aeruginosa to aminoglycosides [454].
The release of eDNA was found to be mediated by the Twin-arginine translocation Tat factor, which acts downstream to the PQS TCS in Pseudomonas aeruginosa [743]. tat mutants of Pseudomonas aeruginosa exhibit reduced eDNA release, defective biofilm architecture, and enhanced susceptibility to tobramycin [743]. In addition, the tat mutants showed reduced production of pyocyanin, rhamnolipid, and membrane vesicles that were associated with deficient expression of Rieske iron-sulfur subunit of the cytochrome bc1 complex involved in electron transfer and energy transduction [743].

4.7.2. Antibiotic Tolerance Due to Low Metabolic State of Biofilm-Associated Bacteria

Since the biofilm is a multilayered community of bacteria, nutrient and oxygen gradients are formed from the outer part to the inner part of the biofilms, resulting in metabolically versatile bacterial communities [2,744]. Different bacterial subpopulations showing distinct metabolic activities evolve within the biofilm depending on their spatial localization [745]. Both nutrient sparsity and hypoxia result in a decreased metabolic activity and growth rate of the bacteria in the biofilm core [746]. The low metabolic activities and slow growth rates of the sessile biofilm-associated bacteria and persister cells make them tolerant to antibiotics that rely on cell division (e.g., ciprofloxacin, tobramycin, tetracycline, penicillin) [610,747,748,749,750,751]. Additionally, conditions with nutrient limitations induce antibiotic tolerance in bacteria, which is associated with reduced levels of oxidative stress and depends on the SOS response [752,753]. Some of the dormant bacterial variants develop into antibiotic-tolerant persister cells that can regain cell proliferation when the therapy is withdrawn [41]. The persister subpopulation is, among others, controlled by stress signaling pathways such as the general stress response or the SOS response, in conjunction with the second messenger (p)ppGpp and the toxin–antitoxin modules [41]. The MazEF toxin–antitoxin system is thought to be responsible for biofilm-associated antibiotic resistance and the reduced metabolism resulting in the appearance of persister cells [754,755]. MazF is an endoribonuclease that cleaves single-stranded ACA sequences with consequent translational inhibition, and MazE is an antitoxin that antagonizes MazF [756]. The persistent cells are responsible for chronic infections as they tolerate antibiotics and escape the immune system.

4.7.3. Antibiotic Tolerance Due to Altered Chemical Microenvironment within the Biofilm

The high-affinity quinol oxidase cytochrome bd encoded by the cydABX operon which is induced under hypoxic conditions and exhibits high oxygen affinity is expressed at elevated levels within Escherichia coli biofilms and plays a role in maintaining the biofilm structure [744]. It is required for aerobic respiration under hypoxic conditions [744], and bacteria lacking cytochrome bd showed reduced expression of EPS and increased sensitivity to exogenous stress stimuli such as oxidative and nitrosactive stress [744]. The latter protection might be related to its quinol peroxidase activity [757]. Further studies show that cytochrome bd promotes antibiotic tolerance in Escherichia coli biofilms by promoting the proton-mediated efflux of noxious chemicals through the RND tripartite export proteins [758]. Deletion of cytochrome bd increased the susceptibility of biofilm-embedded Escherichia coli to several antibiotics including aminoglycosides, β-lactams, and fluoroquinolones [758].

4.7.4. Activation of Protective Stress Responses

Environmental stress stimuli such as decreased nutrition, lack of oxygen, and lower pH induce stress-response genes including sigma factors that protect the bacteria from antibiotics, host immune factors, and environmental toxins [14,15,759]. For instance, biofilm-associated Pseudomonas aeruginosa expresses the gene ndvB which encodes a glycosyltransferase that catalyzes the synthesis of periplasmic β-(1→3)-cyclic glucans. The glucans are thought to promote aminoglycoside resistance by sequestering the antibiotics (e.g., tobramycin) in the periplasm away from their cellular target [18]. The expression of ndvB in biofilms is dependent on the stationary-phase sigma factor RpoS [759] which is the master regulator of general stress responses [760]. Blocking the alternative sigma factor RpoN (σ54), which regulates many virulence factors, increased the susceptibility of Pseudomonas aeruginosa to β-lactam antibiotics [761].

4.7.5. Altered Expression of Antibiotic-Resistant Genes in Biofilm-Embedded Bacteria

When Pseudomonas aeruginosa biofilms are exposed to β-lactam antibiotics or colistin, various resistance mechanisms are induced such as increased expression of β-lactamase [762,763] and the production of modified lipopolysaccharides that make the bacteria resistant to colistin and other polymyxin antibiotics [764]. Polymyxins are cationic antimicrobial peptides that target Gram-negative bacteria through electrostatic interactions with lipid A and core phosphates of LPS. The resistance to these antibiotics is caused by modification of the lipopolysaccharides through the addition of L-4-aminoarabinose (L-Ara4N) and phosphoethanolamine (PEtN) [764]. These modification systems are regulated by complex networks of two-component systems that sense magnesium, iron, zinc, cationic antimicrobial peptides, and pH [765] (Table 2).
Zhang et al. [766] observed that tssC1, which is implicated in type VI secretion (T6S), is upregulated in Pseudomonas aeruginosa biofilms. The upregulation of tssC1 was important for the induction of biofilm-associated antibiotic resistance to tobramycin, gentamicin, and ciprofloxacin [766].
Dale et al. [767] studied genetic determinants that are responsible for biofilm-associated antibiotic resistance in Enterococcus faecalis and observed a role for components of the quorum-sensing system (fsrA, fsrC), the virulence-associated protease gelE, and two glycosyltransferase (GTF) genes (epaI, epaOX). FsrC is a QS histidine kinase that phosphorylates the response regulator FsrA, resulting in the expression of gelE [582]. The polysaccharide production by EpaI and EpaOX is thought to make the biofilm less penetrable for antibiotics [767].
Acinetobacter baumannii biofilms often show high antibiotic resistance [768,769]. Proteomic analysis of the biofilm-embedded Acinetobacter baumannii in comparison to those in the planktonic state showed, among others, upregulation of a membrane Fe transport protein, a sensor histidine/response regulator, diguanylate cyclase, and bacterial antibiotic resistance-related proteins such as β-lactamase PER-1 and aminoglycoside acetyltransferase type I [770].

4.7.6. Increased Efflux Pump Expression in Biofilm-Embedded Bacteria

Another reason for biofilm-associated drug resistance is the increased expression of various efflux pumps in biofilm-associated bacteria [734,771,772]. Bacteria in biofilms show higher horizontal gene transmission than planktonic bacteria [773]. The gene transfer of antibiotic-resistant genes from resistant to susceptible bacterial species within the biofilms leads to antibiotic resistance.
In Escherichia coli biofilm, RapA was found to cause antibiotic resistance to β-lactams, norfloxacin, chloramphenicol, and gentamicin through upregulating the yhcQ multidrug resistance pump [734]. A rapA mutant formed biofilms with reduced content of polysaccharides [734]. These biofilms showed better penetration of antibiotics which may explain the increased sensitivity to antibiotics [734].
The expression of RND efflux pumps and genes involved in type III secretion were upregulated in antibiotic-resistant biofilms of Pseudomonas aeruginosa that have developed in the presence of azithromycin [771]. The MexAB-OprM and MexCD-OprJ efflux pumps, but not the type III secretion system, appeared to be integral to biofilm formation in the presence of azithromycin [771].
The PA1874-1877 cluster of genes in Pseudomonas aeruginosa encodes for an efflux pump of the ATP-binding cassette (ABC) transporter complex family that is involved in the biofilm-specific antibiotic resistance [772]. Deletion of the genes encoding this pump, resulted in an increase in sensitivity to tobramycin, gentamicin, and ciprofloxacin, especially when the mutant strain was growing in a biofilm [772]. This efflux pump is expressed at a higher level in biofilm cells in comparison to planktonic cells [772].

4.8. The Relationship between Biofilm Formation and Efflux Pumps

There are several lines of evidence that efflux pumps can affect biofilm formation and contribute to bacterial colonization and persistence [151,152,719,728,774,775,776]. Efflux pumps can affect biofilm formation directly by mediating the efflux of molecules required for biofilm formation (e.g., EPS) and biofilm-regulatory QS molecules, and indirectly by regulation of transcription factors involved in biofilm formation and bacterial adhesin expression [775].
Efflux pumps are frequently upregulated in biofilms [153,734,771,772,777,778], and deletion of efflux pumps might impair biofilm formation [153,155,158,779,780]. The expression of the norB, norC, and mdeA efflux pump genes were upregulated in Staphylococcus aureus during biofilm growth [777]. Deletion of acrB and tolC in Salmonella Typhimurium impaired avian gut colonization [780]. Impaired biofilm formation was observed in Escherichia coli upon deletion of acrB, acrD, acrE, emrD, emrE, emrK, or mdtE [153,158]. The reduced biofilm formation of an AcrAB-TolC defective Salmonella Typhimurium strain was related to the repression of curli biosynthesis [774].
The MexAB-OprM efflux pump of Pseudomonas aeruginosa was shown to play an important role in biofilm formation [779]. A ΔmexAB-oprM deletion strain was compromised in its capacity to invade and transmigrate across a monolayer of Madin–Darby canine kidney (MDCK) epithelial cells and could not kill mice, in contrast to wild-type bacteria which were highly invasive and caused fatal infection [779]. The defect in the ΔmexAB-oprM strain could be complemented by the addition of culture supernatant from MDCK cells infected with wild-type bacteria, suggesting that the efflux pump exports virulence determinants that contribute to bacterial virulence [779]. Another study showed that the MexAB-OprM efflux pump is involved in the secretion of AHL autoinducers [322]. Similarly, the AdeFGH and AcrAB efflux pumps of Acinetobacter baumannii have been shown to affect biofilm and pellicle formation [781,782].
A positive correlation has been observed between the expression of the AcrAB efflux pump in drug-resistant Klebsiella pneumoniae clinical isolates and biofilm formation [719]. Other studies have found a positive correlation between the AcrAB efflux channel and Klebsiella pneumoniae virulence [783,784]. The EefABXC efflux pump of Klebsiella pneumoniae contributes to the colonization of the bacteria in the digestive tract [785]. In addition to contributing to antibiotic resistance, this efflux pump confers acid tolerance to inorganic acids [785]. The eef promoter can be induced by an acidic environment and by hyperosmolarity [785]. An AcrB knockout strain of Klebsiella pneumoniae showed a reduced capacity to cause pneumonia in a murine model [783].
Studies using efflux pump inhibitors (EPIs) showed that these compounds not only sensitize bacteria to antibiotics but also impact biofilm formation [153,154,774,786,787]. The EPIs thioridazine and Phe-Arg-βNaphtylamide (PAβN) reduced biofilm formation in Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus [153]. The MexAB-OprM-specific EPI D13-9001 reduced the invasiveness of Pseudomonas aeruginosa [788]. These findings support a role for efflux pumps in biofilm formation. Alternatively, it could be that the EPIs affect a common nodule of both processes. For instance, the endocannabinoid anandamide inhibits both drug efflux and biofilm formation of antibiotic-sensitive and antibiotic-resistant Staphylococcus aureus species [789]. Anandamide induces immediate membrane depolarization [789], an effect that has implications on both drug export and biofilm formation.

5. Targeting Quorum Sensing and Biofilms as a Strategy to Overcome Antibiotic Resistance

The multiple resistance mechanisms that have evolved in the bacteria to protect them from commonly used antibiotics have urged the need for alternative treatment therapies and the development of drugs that act on new scaffolds of targets, with the hope that these approaches could hit the Achilles’ heel of the microorganisms. These drugs can be used as a single agent or in combination with other drugs including antibiotics. The multi-purposing drug therapy aims to target different nodal points, that together will eliminate the bacteria prior to the development of resistance mechanisms. For instance, the β-lactamase inhibitor tazobactam enhanced the synergy between the β-lactam antibiotic piperacillin and daptomycin [790].
Several strategies have been developed to overcome drug resistance. These include (i) use of multiple antibiotics to overcome drug resistance [791]. This approach has the advantages of targeting multiple targets in the same bacteria, increasing drug potency by synergistic effects, and suppressing resistance evolution. (ii) Use of drugs that target the resistance mechanism(s), thus sensitizing the bacteria to the respective antibiotics [791,792]. (iii) Use of drugs that target QS [10,531,793,794]. This approach aims to reduce bacterial virulence, diminish biofilm formation, and increase the susceptibility of the bacteria to antibiotics and human defense mechanisms. (iv) Use of drugs with anti-biofilm properties [795]. These drugs should preferentially also disrupt preformed biofilms. The release of bacteria from the biofilms will make them prone to both antibiotics and human immune defense mechanisms. (v) Use of drugs that target essential cell division mechanisms such as the Z-ring division protein FtsZ, which will increase the susceptibility to antibiotics [796]. (vi) Use of drugs that target cell wall teichoic acid that will interfere with biofilm formation and increase the response to antibiotics [797,798].
Anti-virulence agents represent a promising alternative to the use of antibiotics, as these compounds suppress the production of factors involved in bacterial pathogenicity, without affecting their replication. Thus, it is less likely that therapy resistance might occur. When reducing the ability of the pathogens to colonize and invade host tissue, the drugs will enable the host immune defense mechanisms to eradicate the infection [799].

5.1. Antibiotic Adjuvants

Drugs that can sensitize resistant bacteria to antibiotics are termed antibiotic adjuvants [800]. An adjuvant is a compound that usually does not exert an antimicrobial activity by itself but can potentiate the antibiotic activity. Such adjuvants include antibiotic resistance enzyme inhibitors, efflux pump inhibitors, membrane permeabilizers, compounds leading to outer membrane disruption or inner membrane depolarization, anti-virulence compounds, QS, and biofilm inhibitors [10,531,791,792,793,794,800,801,802]. Classical examples of inhibitors of enzymes that cause antibiotic resistance are the FDA-approved β-lactamase inhibitors clavulanic acid, sulbactam, tazobactam, avibactam, and vaborbactam, which sensitize β-lactamase-expressing bacteria to penicillin antibiotics such as amoxicillin [792]. Membrane permeabilizers include polymyxin B, colistin, cationic antimicrobial peptides, glycine peptides, and caragenins [792]. The non-psychotropic phytocannabinoid cannabidiol (CBD) was found to be highly potent against Gram-positive bacteria through disruption of the bacterial membrane [803,804,805]. Interestingly, the combined treatment of CBD with polymyxin B showed a synergistic effect against some Gram-negative bacteria including Acinetobacter baumannii, Klebsiella pneumoniae, and Escherichia coli [804,806,807].

Repurposing Clinically Approved Drugs as Antibiotic Adjuvants

Many efforts have been invested in finding clinically approved drugs that can function as antibiotic adjuvants. The advantage of this approach is the well-established knowledge of the pharmacokinetics and toxicology of these compounds [808]. Ejim et al. [809] screened a collection of 1057 FDA-approved drugs to identify compounds that could augment the activity of the antibiotic minocycline. Among these, 69 non-antibiotic compounds including anti-inflammatory, anti-histamine, anti-spasmodic, psychotropic, and anti-hypertensive drugs, exhibited synergy with minocycline against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa [809]. Among them, the acetaldehyde dehydrogenase inhibitor disulfiram synergized with minocycline to inhibit the growth of Staphylococcus aureus. Additionally, the DOPA decarboxylase inhibitor benserazide used for Parkinson’s disease, the serotonin 5-HT receptor antagonist tegaserod used for irritable bowel disease, and the opoid receptor agonist loperamide (Imodium) used to treat diarrhea were found to sensitize Pseudomonas aeruginosa to minocycline [809]. Of note, minocycline has been found to act as an inhibitor of the AcrAB-TolC efflux pump expressed in Enterobacter species [810].
Other studies have shown that the antiretroviral zidovudine in combination with carbapenems had a synergistic activity against New Delhi Metallo-β-lactamase (NDM-1) Enterobacteriaceae strains [811] and the anti-helminthic niclosamine had anti-biofilm and antibacterial activities against Staphylococcus aureus [812,813]. Niclosamine has also been shown to have a synergistic effect with colistin on colistin-resistant Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, Escherichia coli, and Enterobacter cloacae [814,815]. Similarly, the related anti-helminthic drug oxyclozanide could restore colistin sensitivity in drug-resistant Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, and Enterobacter cloacae [816,817].

5.2. Quorum Sensing Inhibitors and Quenchers

Due to the tight regulation of biofilm and antibiotic resistance by the QS system, efforts have been made to find QS inhibitors or quenchers that can overcome antibiotic resistance and combat biofilm formation [5,7,8,9,10,11,12,818,819,820,821] (Table 4). QS inhibitors interfere with the action of one or more of the components of the QS system, thereby reducing the virulence and biofilm formation of the bacteria with consequently increased sensitivity to antibiotics. The concept quorum quenchers are often used for enzymes that promote the degradation of the autoinducers, thereby interrupting the QS cascade at the autoinducer receptor interaction. Histidine kinase inhibitors that target TCSs are attractive since these systems are unique to bacteria [822]. Additionally, the catalytic ATP domain of the kinases is highly conserved among the different TCSs and across bacterial species, thereby broadening the spectrum of responsive bacteria [822].
The idea of using QS inhibitors in treating biofilm-associated infections came from the observation that certain sea-weed plants (e.g., the Australian macroalga Delisea pulchra) never become covered with bacteria, which was found to be due to the production of halogenated furanones which have QS inhibition activities [925,926].
Many secondary plant metabolites have been shown to have anti-quorum and anti-biofilm activity, which may increase the sensitivity of bacteria to antibiotics [509,927,928]. These compounds are part of the plant defense system to avoid microbial infections. These metabolites usually do not have a direct antibacterial activity, but through targeting biofilm formation and QS, they are involved in protecting the plants from infective diseases through mechanisms that act in synergy with antimicrobials [927]. Halogenated thiophenones are examples of QS inhibitors that can control biofilm formation [875]. Baicalin hydrate and cinnamaldehyde target the acyl-homoserine lactone-based QS system present in Pseudomonas aeruginosa [531], and hamamelitannin targets the peptide-based system of Staphylococcus aureus [531]. Baicalin increased the susceptibility of Pseudomonas aeruginosa to tobramycin [531].
Inhibition of the alkyl-quinolone (AQ)-responding PqsR QS component of Pseudomonas aeruginosa has been attractive since PqsR activates the pqsABCDE operon encoding the autoinducer enzymes PqsABCD and PqsE, which regulates the expression of the cytotoxic galactophilic lectin protein LecA [361,929,930,931] involved in biofilm development [592], and the PhzA1 enzyme involved in the biosynthesis of the virulence factor pyocyanin [743]. Ilangovan et al. [351] developed 2-alkyl-4(3H)-quinazolinone analogs with C7 or C9 alkyl side chains (e.g., 3-NH2-7Cl-C9-QZN) that bind to PqsR and antagonize the PqsR-mediated QS signaling cascade. These inhibitors were found to inhibit Pseudomonas aeruginosa virulence at microMolar concentrations [351].
Another approach to attenuate the QS signaling and Pseudomonas aeruginosa virulence is to use enzymes (e.g., the Hod 2,4-dioxygenase) that inactivate PQS [932]. Treating Pseudomonas aeruginosa with the Hod enzyme reduced the expression of pqsA and the virulence determinants lectin A, pyocyanin, and rhamnolipids [932]. However, the proteolytic cleavage of Hod by extracellular proteases together with the competitive inhibition by the PQS precursor 2-heptyl-4(1H)-quinolone reduced the efficiency of Hod as a QS quenching agent [932].
Researchers have also developed methylated or halogenated derivates of the QS precursor anthranilate (e.g., methyl anthranilate and 2-amino-4-chlorobenzoic acid) which inhibit PQS biosynthesis probably by competing with anthranilate for the active site of the PqsA enzyme [882,933]. Methyl anthranilate inhibited the production of PQS and reduced elastase production [882]. However, high concentrations (milliMolars) are required for therapeutic effect [882]. 2-amino-4-chlorobenzoic acid and 2-amino-6-fluorobenzoic acid inhibited HAQ biosynthesis, disrupted PqsR (MvfR)-dependent gene expression, and inhibited osmoprotection [933]. Small molecule inhibitors of PqsD have also been developed [934]. PqsD is a key enzyme in the biosynthesis of 2-heptyl-4-hydroxyquinoline (HHQ) and PQS. The use of the PqsD inhibitor (2-nitrophenyl)(phenyl)-methanol reduced biofilm formation by Pseudomonas aeruginosa [934]. Grossman et al. [896] have synthesized a new series of thiazole-containing quinazolinones (e.g., 6-chloro-3((2-pentylthiazol-4-yl)methyl)quinazolin-4(3H)-one) capable of binding to PqsR and inhibiting the production of pyocyanin.
In a Pseudomonas aeruginosa infection model in Caenorhabditis elegans, the lignans Sesamin and Sesamolin isolated from the Sesamum indicum (L.) plant were found to prevent the infection of pre-infected worms through attenuation of QS-regulated virulence factors of the bacteria [818]. Both the lignans exerted anti-QS activity at 75 μg/mL without affecting the bacterial growth. Sesamin and Sesamolin decreased the production of virulence factors such as pyocyanin, proteases, elastase, and chitinase [818]. Additionally, the biofilm constituents of Pseudomonas aeruginosa including alginate, exopolysaccharides, and rhamnolipids were affected by the lignans [818]. The lignans acted on the LasR QS system, with minimum effect on the Rhl system [818].
Tryptophan-containing peptides with antibacterial activities impaired QS and biofilm development in multidrug-resistant Pseudomonas aeruginosa and increased the susceptibility to ceftazidime and piperacillin [820]. The tryptophan-containing peptides reduced the production of QS-regulated virulence factors by downregulating the gene expression of both the Las and Rhl QS systems [820]. Biofilm formation was inhibited by the tryptophan-containing peptides that were associated with extracellular polysaccharide production inhibition by downregulating pelA, algD, and pslA transcription [820]. In addition, the peptides reduced the expression of the efflux pump genes oprM, mexX, and mexA [820].
Garlic extracts have been shown to block QS in Pseudomonas aeruginosa [935] and sensitize the biofilm-embedded bacteria to tobramycin [936]. The garlic extract also provoked a higher degree of inflammation and improved the clearance of the bacteria in an infection model in mice [936]. Olive (Olea europaea) leaf extract reduced the expression of lasI, lasR, rhlI, and rhlR, with concomitant suppression of virulence and biofilm formation by Pseudomonas aeruginosa [937]. Additionally, ginseng (Panax ginseng) extract was found to have anti-infective activity against Pseudomonas aeruginosa by inhibiting QS [938]. The ginseng extract did not affect bacterial viability and even enhanced the extracellular protein and alginate production [938]. However, it suppressed the production of LasA and LasB and downregulated the synthesis of the AHL molecules [938]. The anti-inflammatory agent itaconic acid (methylenesuccinic acid), which is a metabolite induced during the activation of immune cells [939], increased the anti-biofilm activity of tobramycin on Pseudomonas aeruginosa, likely by facilitating the transport of tobramycin through the biofilm [940].

5.3. Inhibition of Biofilm Formation

Inhibition of biofilm formation and eradication of established biofilms are major goals to overcome antibiotic resistance and infectious diseases [795,941]. In the previous section, we discussed the inhibition of biofilm formation and sensitization to antibiotics by using QS inhibitors or QS quenchers. However, there are also compounds that prevent biofilm formation whose action mechanisms do not involve the QS system (Table 5). They may act by preventing the production of EPS, adhesion molecules, or pili formation. Efflux pump inhibitors, which will be discussed in Section 5.4, might affect biofilm formation through simultaneous inhibition of other membrane transport systems. Compounds affecting the biosynthesis of cell wall teichoic acid and lipoteichoic acid will be discussed in Section 5.5. Another approach is the inhibition of the transpeptidase Sortase A (SrtA), which is involved in the covalent attachment of adhesive matrix molecules to the peptidoglycan cell wall in Gram-positive bacteria [942], resulting in the inhibition of biofilm formation [858,943,944,945,946,947,948,949].

5.4. Inhibition of Efflux Pumps

Another approach to restore the antibacterial activity of antibiotics is to use efflux pump inhibitors (EPIs) that increase the intracellular level of the drugs [162,801,991,992,993,994] (Table 6). Different mechanisms are involved in this activity. Some efflux pump inhibitors (e.g., IITR08027 and anandamide) dispatch the protein gradient required for efflux pump activities [789,995], while others (Phe-Arg-β-naphthylamide (PAβN), phenothiazines, and 1-(1-naphthylmethyl)-piperazine) bind to an efflux pump component such as AcrB [810,996]. Many of the efflux pump inhibitors also prevent biofilm formation as discussed in Section 4.8. Many of the efflux inhibitors have not been approved for clinical uses due to their cytotoxicity, which is seemingly caused by the simultaneous targeting of various membrane-spanning transporters in humans and the need for relatively high doses to achieve the effect [792]. For instance, reserpine causes neurotoxicity via the inhibition of the mammalian ABC-system P-glycoprotein [792]. MP-601205 is an EPI that has been used in clinical trials. It was delivered as an aerosol in patients with ventilation-associated pneumonia or respiratory infections in patients with cystic fibrosis [997]. However, due to tolerability issues, these trials were discontinued [998].
Thiazolidinedione derivatives that target NorA in Staphylococcus aureus and sensitize the bacteria to fluoroquinolones [1034] have also been shown to prevent biofilm formation in mixed Streptococcus mutans-Candida albicans cultures and Candida albicans monocultures [982,1035]. Additionally, these compounds exert anti-QS activity against Vibrio harveyi by decreasing the DNA-binding activity of LuxR [984]. Additionally, these compounds exerted anti-QS activities against Pseudomonas aeruginosa by targeting the LasI quorum-sensing signal synthase [981] and PhsZ, a key enzyme in the biosynthesis of the virulent factor pyocyanin [1036].
The antipsychotic phenothiazine drug chlorpromazine has been shown to potentiate the activities of many antibiotics at subinhibitory concentrations including nalidixic acid, norfloxacin, ciprofloxacin, chloramphenicol, tetracycline, rifampicin, and streptomycin [1019,1040]. Prochlorperazine and trans(E)-flupentixol prevent drug efflux in Staphylococcus aureus species by reducing the proton motive force with a concomitant reduction in the transmembrane potential [1041]. Chlorpromazine and amitriptyline were found to be substrates and inhibitors of the AcrB multidrug efflux pump of Salmonella typhimurium and Escherichia coli [996]. Some clinically approved antimicrobial drugs have been shown to inhibit efflux pumps, including ketoconazole and minocycline [787,810]. Additionally, raloxifene used for treating osteoporosis and pyrvinium used as an anthelmintics were shown to inhibit the NorA efflux pump of Staphylococcus aureus and sensitize the bacteria to ciprofloxacin [1024]. The antidiabetic drug metformin prevents drug efflux in Staphylococcus aureus and increases their susceptibility to various antibiotics [1015]. These drugs are potential antibiotic adjuvants for the treatment of drug-resistant bacteria.

5.5. Targeting Cell Wall Teichoic Acid Synthesis

There are several lines of evidence that the presence of wall teichoic acid (WTA) in the Gram-positive Staphylococcus aureus contributes to β-lactam resistance [798,1042,1043,1044]. Moreover, WTA has been shown to protect Staphylococcus aureus against the cytotoxic effects of some unsaturated fatty acids [921,1045]. WTA plays an important role in bacterial cell wall processes and integrity and is required for proper cell division, biofilm formation, host colonization, and endovascular infection [1043,1046,1047,1048,1049]. WTA acts as a scaffold for PBP2a and is required for the proper localization of PBP4, thereby contributing to β-lactam resistance [1042]. WTA is also involved in keeping the autolysins/cell wall amidases Sle1, Atl, and LytN in the cross-wall region of the cell wall during cell division of Staphylococcus aureus [1050,1051,1052,1053]. Since Sle1 confers β-lactam resistance and promotes biofilm formation in MRSA [1054,1055], WTA may indirectly contribute to β-lactam resistance and biofilm formation via its action on the autolysin.
WTA are anionic polymers composed of repeating units of N-acetylglucosaminyl-ribitol phosphate that are modified by D-alanylation, α-O-GlcNAcylation, and β-O-GlcNAcylation [1056]. WTA are synthesized on a bactoprenol lipid carrier inside the bacterial cell before being transported to the cell surface where they are covalently linked to proteoglycans [1049,1057]. Deletion of tarO, which catalyzes the first step of WTA synthesis, or deletion of tarS, which attaches β-O-GlcNAc (β-O-N-acetyl-D-glucosamine) residues to WTA, sensitized MRSA to β-lactam antibiotics [798,1042]. Deletion of the 2-epimerase mnaA, which interconverts UDP-GlcNAc and UDP-ManNAc to modulate substrate levels of TarO and TarA, caused complete loss of WTA synthesis and β-lactam hypersensitivity in MRSA and methicillin-resistant Staphylococcus epidermidis [1058]. Furthermore, alanine-modified teichoic acids contribute to antimicrobial peptide resistance [1059]. The four proteins DltA-D are essential for the incorporation of D-alanine residues into WTA [1059]. Genetic inactivation of the Dlt system or chemical inhibition (D-alanylacyl-sulfamoyl-adenosine) of D-alanylation of teichoic acid sensitized MRSA to the β-lactams oxacillin and imiprenem [1060] and the cationic antimicrobial peptides nisin and gallidermin [1061]. Upregulation of the dlt operon in a Staphylococcus aureus pitA6 mutant led to daptomycin tolerance [1062].
Several compounds have been tested for their ability to interfere with WTA synthesis and the consequences on antibiotic susceptibility (Table 7). Blocking the synthesis of WTA by inhibiting the first enzyme of the pathway, TarO, by tunicamycin, sensitized MRSA to β-lactams, even in the presence of PBP2a [1043]. The blockage of WTA synthesis led to defects in septation and cell separation [1043]. Ticlopidine, which targets the N-acetylglucosamine-1-phosphate transferase encoded by tarO, increased the sensitivity of MRSA to cefuroxime [798].
The small molecule 1835F03, which inhibits WTA biosynthesis by targeting the TarGH ABC transporter involved in the translocation of WTA across the cell membrane, showed potent antibacterial activity towards several Staphylococcus aureus stains including the Newman MRSA strain [1063]. On the basis of this compound, the TarG inhibitor targocil was developed [1044,1063,1064]. Targocil treatment inhibited bacterial growth, induced osmotic stress with subsequent swelling of the cells, and downregulated the expression of numerous virulence factors [1065]. Targocil was also found to block the translocation of the major autolysin Atl across the membrane, resulting in a significant decrease in autolysis [1053]. Compounds targeting TarG could increase the susceptibility of MRSA to β-lactams such as imipenem and oxacillin [1044]. Subinhibitory concentrations of beta-lactam antibiotics could suppress the development of targocil-resistant mutants [1043].
Table 7. Examples of compounds targeting wall teichoic acid (WTA) synthesis.
Table 7. Examples of compounds targeting wall teichoic acid (WTA) synthesis.
CompoundEffects on BacteriaReferences
Clomiphene
-
Clomiphene is a fertility drug that was shown to target the undecaprenyl diphosphate synthase (UppS). Undecaprenyl diphosphate synthase catalyzes the synthesis of a polyisoprenoid essential for peptidoglycan and WTA synthesis.
-
Clomiphene sensitizes MRSA to various β-lactam antibiotics (e.g., ampicillin, cloxacillin, piperacillin, cefuroxime), as well as bacitracin, which inhibits the dephosphorylation of undecaprenyl diphosphate.
[1066]
HSGN-94 and HSGN-189
-
HSGN-94 and HSGN-189 inhibit lipoteichoic acid synthesis and prevent biofilm formation by MRSA and vancomycin-resistant Enterococcus faecalis.
[1067]
Targocil
-
Targocil targets TarG, which together with TarH forms the WTA flippase involved in the export of WTA through the membrane to the cell wall.
-
Targocil inhibits bacterial growth, induces cell wall stress, and downregulates virulence factors in Staphylococcus aureus.
-
Targocil does not sensitize MRSA strains to beta-lactams; but subinhibitory concentrations of beta-lactams suppress the development of targocil-resistant mutants.
[1065]
Tarocin A and Tarocin B
-
The two tarocins inhibit TarO, the first step in WTA biosynthesis.
-
The tarocins increase the susceptibility of MRSA to β-lactam antibiotics.
[1068]
Ticlopidine
-
Ticlopidine is an antiplatelet drug that was found to inhibit WTA synthesis supposedly through inhibition of the TarO enzyme.
-
Ticlopidine sensitizes MRSA to cefuroxime.
[798]
Tunicamycin
-
The WTA synthesis inhibitor tunicamycin increases the susceptibility of MRSA to various β-lactam antibiotics but did not affect the susceptibility to vancomycin cycloserine, ciprofloxacin, chloramphenicol, or moenomycin.
-
Tunicamycin inhibits biofilm formation of Staphylococcus aureus and Listeria monocytogenes.
[1043,1058,1069]

5.6. Inactivation of PBP2a as an Approach to Sensitize MRSA to β-Lactams

The penicillin-binding proteins (PBPs) catalyze in separate domains the transglycosylase and transpeptidase activities involved in the biosynthesis of the cell wall peptidoglycans. β-lactam antibiotics inactivate the transpeptidase activity through irreversible acylation of an active site serine [62]. The PBP2a variant shows low affinity to β-lactams, and therefore continues to catalyze the DD-transpeptidation reaction necessary to complete the cell wall in the presence of these antibiotics [62,1070]. Since PBP2a lacks transglycosylase activity, intact cell wall synthesis requires the presence of the regular PBP2 [62,1070]. β-Lactam resistance is also achieved by elevated expression of PBP4 [1071] and the cell-division proteins FtsA, FtsW, and FtsZ [1072]. FtsZ is required for the proper localization of PBP2 to the division site where it mediates localized peptidoglycan synthesis prior to daughter cell separation [1073].
Otero et al. [1074] identified an allosteric binding domain 60 Å from the DD-transpeptidase active site of PBP2a. The binding of the β-lactam ceftaroline to the allosteric binding domain stimulated the allosteric opening of the active site, enabling a second β-lactam molecule to inactivate the PBP2a [1074]. The ability of compounds to inactivate PBP2a by allostery and thus sensitize the bacteria to antibiotics makes this protein the Achilles’ heel of MRSA [1075].
García-Fernández et al. [1076] observed that the scaffold protein flotillin facilitates oligomerization of PBP2a in functional membrane microdomains (FMMs) and drugs such as the cholesterol-lowering statin zaragozic acid, that disrupt the FMMs, prevent PBP2a oligomerization and sensitize MRSA to β-lactam antibiotics such as methicillin, oxacillin, flucoxacillin, nafcillin, and dicloxacillin. This finding can explain the observed beneficial clinical effects of statins in microbial infections [1077,1078,1079,1080]. Thus, repurposing the cholesterol-reducing drugs of the statin family can be used for overcoming β-lactam resistance to MRSA [1076].

5.7. Targeting Cell Division Proteins to Sensitize MRSA to β-Lactams

There are several lines of evidence that targeting bacteria cell division components could sensitize drug-resistant bacteria (e.g., MRSA) to antibiotics (e.g., β-lactams) [796,1081,1082,1083]. In particular, inhibition of the FtsZ cell division protein that forms a contractile ring structure termed the Z-ring at the future division sites has attracted attention [1081,1082,1084]. FtsZ mutant MRSA strains and an MRSA strain treated with FtsZ antisense displayed attenuated virulence and increased susceptibility to β-lactam antibiotics [1072,1083].
Several compounds have been developed to target FtsZ (Table 8). The FtsZ inhibitor PC190723 increases the susceptibility of MRSA to β-lactams [1083]. The effect of FtsZ inhibition is likely due to the delocalization of both FtsZ and PBP2 [1083]. Similarly, Ferrer-González et al. [1085] observed that the FtsZ inhibitor TXA707 leads to disruption of septum formation concomitant with mislocalization of PBPs from midcell to nonproductive peripheral sites [1085]. TXA707 acts synergistically with β-lactam antibiotics with a high affinity for PBP2 [1085]. This research group further observed that in the absence of TXA707, PBP1, PBP2, PBP3, and PBP4 colocalize with FtsZ at the septum of MRSA, while PBP2a localizes to distinct foci at the cell periphery [1086]. TXA707 disrupts septum formation resulting in FtsZ relocalization away from the midcell still interacting with PBP1 and PBP3 [1086]. The interaction of FtsZ with PBP2 and PBP4 was disrupted by TXA707 [1086]. When oxacillin was combined with TXA707, both PBP2 and PBP2a localized to malformed septum-like structures, which might be one mechanism how TXA707 renders MRSA susceptible to β-lactams [1086]. The combined treatment of the TXA707 prodrug TXA709 with the third-generation cephalosporine cefdinir could cure systemic and tissue infections in mice [1087].

6. Conclusions

In this review, we have presented data showing various mechanisms involved in antibiotic resistance of various ESKAPE pathogens with a specific emphasis on the triangle interconnection between quorum sensing, biofilm formation, and antibiotic resistance. A myriad of synthetic and natural compounds has been studied for their ability to interfere with one or more of these processes with the aim to eradicate biofilm and sensitize the bacteria to antibiotics. Altogether, these studies show that it is sufficient to target one or few nodal processes to overcome antibiotic resistance. A combination of these adjunctive compounds together with conventional antibiotics might be necessary to optimize their efficacy which is expected to improve the treatment regime against drug-resistant bacterial infections.

Author Contributions

Conceptualization, R.V.S.; writing—original draft preparation, R.V.S.; writing—review and editing, R.V.S. and D.S. All authors have read and agreed to the published version of the manuscript.

Funding

This research received no external funding.

Data Availability Statement

Not applicable.

Conflicts of Interest

The authors declare no conflict of interest.

Abbreviations

ABC—ATP-binding cassette; AHL—N-Acyl-L-homoserine lactone; AI-1—Autoinducer 1; AI-2—Autoinducer 2; AIP—Autoinducing peptide; c-di-GMP—bis-(3′-5′)-cyclic dimeric guanosine monophosphate; ECM—Extracellular matrix; eDNA—Extracellular DNA; EPI—Efflux pump inhibitor; EPS—Extracellular polymeric substances or exopolysaccharides; L-Ara4N—4-Amino-4-deoxy-L-arabinose; LPS—Lipopolysaccharides; MATE—Multidrug and toxic compound extrusion; MFS—Major facilitator superfamily; NPET—Nascent peptide exit tunnel; OMP—Outer membrane porin; QAC—Quaternary ammonium compounds; QS—Quorum sensing; QSI—Quorum sensing inhibitor; PACE—Proteobacterial antimicrobial compound efflux; PSM—Phenol-soluble modulin; PBP—Penicillin-binding protein; pEtN—Phosphoethanolamine; PTC—Peptidyl-transferase center; RND—Resistance-nodulation-cell division; RPP—Ribosomal protection proteins; SCC—Staphylococcal chromosomal cassette; SMR—Small multidrug resistance; TCS—Two-component system.

References

  1. Gebreyohannes, G.; Nyerere, A.; Bii, C.; Sbhatu, D.B. Challenges of intervention, treatment, and antibiotic resistance of biofilm-forming microorganisms. Heliyon 2019, 5, e02192. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  2. Flemming, H.C.; Wingender, J.; Szewzyk, U.; Steinberg, P.; Rice, S.A.; Kjelleberg, S. Biofilms: An emergent form of bacterial life. Nat. Rev. Microbiol. 2016, 14, 563–575. [Google Scholar] [CrossRef] [PubMed]
  3. Jamal, M.; Ahmad, W.; Andleeb, S.; Jalil, F.; Imran, M.; Nawaz, M.A.; Hussain, T.; Ali, M.; Rafiq, M.; Kamil, M.A. Bacterial biofilm and associated infections. J. Chin. Med. Assoc. 2018, 81, 7–11. [Google Scholar] [CrossRef] [PubMed]
  4. Preda, V.G.; Săndulescu, O. Communication is the key: Biofilms, quorum sensing, formation and prevention. Discoveries 2019, 7, e100. [Google Scholar] [CrossRef] [PubMed]
  5. Brackman, G.; Coenye, T. Quorum sensing inhibitors as anti-biofilm agents. Curr. Pharm. Des. 2015, 21, 5–11. [Google Scholar] [CrossRef]
  6. Jiang, Q.; Chen, J.; Yang, C.; Yin, Y.; Yao, K. Quorum sensing: A prospective therapeutic target for bacterial diseases. BioMed. Res. Int. 2019, 2019, 2015978. [Google Scholar] [CrossRef] [Green Version]
  7. Paluch, E.; Rewak-Soroczyńska, J.; Jędrusik, I.; Mazurkiewicz, E.; Jermakow, K. Prevention of biofilm formation by quorum quenching. Appl. Microbiol. Biotechnol. 2020, 104, 1871–1881. [Google Scholar] [CrossRef] [Green Version]
  8. Roy, R.; Tiwari, M.; Donelli, G.; Tiwari, V. Strategies for combating bacterial biofilms: A focus on anti-biofilm agents and their mechanisms of action. Virulence 2018, 9, 522–554. [Google Scholar] [CrossRef]
  9. Sikdar, R.; Elias, M. Quorum quenching enzymes and their effects on virulence, biofilm, and microbiomes: A review of recent advances. Expert Rev. Anti-Infect. Ther. 2020, 18, 1221–1233. [Google Scholar] [CrossRef]
  10. Tonkin, M.; Khan, S.; Wani, M.Y.; Ahmad, A. Quorum sensing—A stratagem for conquering multi-drug resistant pathogens. Curr. Pharm. Des. 2020, 27, 2835–2847. [Google Scholar] [CrossRef]
  11. Xiang, Y.; Ding, Y.; Cao, J.; Sun, Y.; Wang, F.; Ju, S.; Yu, J. Non-antibiotic methods against Pseudomonas aeruginosa include QS inhibitors: A narrative review. Ann. Palliat. Med. 2021, 10, 6926–6935. [Google Scholar] [CrossRef] [PubMed]
  12. Zhong, S.; He, S. Quorum Sensing inhibition or quenching in Acinetobacter baumannii: The novel therapeutic strategies for new drug development. Front. Microbiol. 2021, 12, 558003. [Google Scholar] [CrossRef] [PubMed]
  13. Vestby, L.K.; Grønseth, T.; Simm, R.; Nesse, L.L. Bacterial biofilm and its role in the pathogenesis of disease. Antibiotics 2020, 9, 59. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  14. Høiby, N.; Ciofu, O.; Johansen, H.K.; Song, Z.J.; Moser, C.; Jensen, P.; Molin, S.; Givskov, M.; Tolker-Nielsen, T.; Bjarnsholt, T. The clinical impact of bacterial biofilms. Int. J. Oral Sci. 2011, 3, 55–65. [Google Scholar] [CrossRef] [Green Version]
  15. Khatoon, Z.; McTiernan, C.D.; Suuronen, E.J.; Mah, T.F.; Alarcon, E.I. Bacterial biofilm formation on implantable devices and approaches to its treatment and prevention. Heliyon 2018, 4, e01067. [Google Scholar] [CrossRef] [Green Version]
  16. Chen, X.; Daliri, E.B.; Kim, N.; Kim, J.R.; Yoo, D.; Oh, D.H. Microbial etiology and prevention of dental caries: Exploiting natural products to inhibit cariogenic biofilms. Pathogens 2020, 9, 569. [Google Scholar] [CrossRef] [PubMed]
  17. Hall, C.W.; Mah, T.F. Molecular mechanisms of biofilm-based antibiotic resistance and tolerance in pathogenic bacteria. FEMS Microbiol. Rev. 2017, 41, 276–301. [Google Scholar] [CrossRef]
  18. Mah, T.F.; Pitts, B.; Pellock, B.; Walker, G.C.; Stewart, P.S.; O’Toole, G.A. A genetic basis for Pseudomonas aeruginosa biofilm antibiotic resistance. Nature 2003, 426, 306–310. [Google Scholar] [CrossRef]
  19. Stewart, P.S. Mechanisms of antibiotic resistance in bacterial biofilms. Int. J. Med. Microbiol. 2002, 292, 107–113. [Google Scholar] [CrossRef]
  20. Uruén, C.; Chopo-Escuin, G.; Tommassen, J.; Mainar-Jaime, R.C.; Arenas, J. Biofilms as promoters of bacterial antibiotic resistance and tolerance. Antibiotics 2020, 10, 3. [Google Scholar] [CrossRef]
  21. Shin, H.-J.; Yang, S.; Lim, Y. Antibiotic susceptibility of Staphylococcus aureus with different degrees of biofilm formation. J. Anal. Sci. Techol. 2021, 12, 41. [Google Scholar] [CrossRef]
  22. Rice, L.B. Federal funding for the study of antimicrobial resistance in nosocomial pathogens: No ESKAPE. J. Infect. Dis. 2008, 197, 1079–1081. [Google Scholar] [CrossRef] [PubMed]
  23. Rice, L.B. Progress and challenges in implementing the research on ESKAPE pathogens. Infect. Control Hosp. Epidemiol. 2010, 31 (Suppl. 1), S7–S10. [Google Scholar] [CrossRef] [PubMed]
  24. Vale de Macedo, G.H.R.; Costa, G.D.E.; Oliveira, E.R.; Damasceno, G.V.; Mendonça, J.S.P.; Silva, L.D.S.; Chagas, V.L.; Bazán, J.M.N.; Aliança, A.; Miranda, R.C.M.; et al. Interplay between ESKAPE Pathogens and immunity in skin infections: An overview of the major determinants of virulence and antibiotic resistance. Pathogens 2021, 10, 148. [Google Scholar] [CrossRef]
  25. Santajit, S.; Indrawattana, N. Mechanisms of antimicrobial resistance in ESKAPE pathogens. BioMed. Res. Int. 2016, 2016, 2475067. [Google Scholar] [CrossRef] [Green Version]
  26. Pendleton, J.N.; Gorman, S.P.; Gilmore, B.F. Clinical relevance of the ESKAPE pathogens. Expert Rev. Anti-Infect. Ther. 2013, 11, 297–308. [Google Scholar] [CrossRef]
  27. Mancuso, G.; Midiri, A.; Gerace, E.; Biondo, C. Bacterial antibiotic resistance: The most critical pathogens. Pathogens 2021, 10, 1310. [Google Scholar] [CrossRef]
  28. De Oliveira, D.M.P.; Forde, B.M.; Kidd, T.J.; Harris, P.N.A.; Schembri, M.A.; Beatson, S.A.; Paterson, D.L.; Walker, M.J. Antimicrobial Resistance in ESKAPE Pathogens. Clin. Microbiol. Rev. 2020, 33, e00181-19. [Google Scholar] [CrossRef]
  29. Ma, Y.X.; Wang, C.Y.; Li, Y.Y.; Li, J.; Wan, Q.Q.; Chen, J.H.; Tay, F.R.; Niu, L.N. Considerations and caveats in combating ESKAPE pathogens against nosocomial infections. Adv. Sci. 2020, 7, 1901872. [Google Scholar] [CrossRef] [Green Version]
  30. Blair, J.M.; Webber, M.A.; Baylay, A.J.; Ogbolu, D.O.; Piddock, L.J. Molecular mechanisms of antibiotic resistance. Nat. Rev. Microbiol. 2015, 13, 42–51. [Google Scholar] [CrossRef]
  31. Blanco, P.; Hernando-Amado, S.; Reales-Calderon, J.A.; Corona, F.; Lira, F.; Alcalde-Rico, M.; Bernardini, A.; Sanchez, M.B.; Martinez, J.L. Bacterial multidrug efflux pumps: Much more than antibiotic resistance determinants. Microorganisms 2016, 4, 14. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  32. Choi, U.; Lee, C.R. Distinct roles of outer membrane porins in antibiotic resistance and membrane integrity in Escherichia coli. Front. Microbiol. 2019, 10, 953. [Google Scholar] [CrossRef] [PubMed]
  33. Dar, D.; Sorek, R. Regulation of antibiotic-resistance by non-coding RNAs in bacteria. Curr. Opin. Microbiol. 2017, 36, 111–117. [Google Scholar] [CrossRef] [PubMed]
  34. Ma, P.; He, L.L.; Pironti, A.; Laibinis, H.H.; Ernst, C.M.; Manson, A.L.; Bhattacharyya, R.P.; Earl, A.M.; Livny, J.; Hung, D.T. Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics. Elife 2021, 10, e67310. [Google Scholar] [CrossRef]
  35. McCarthy, R.R.; Larrouy-Maumus, G.J.; Meiqi Tan, M.G.C.; Wareham, D.W. Antibiotic resistance mechanisms and their transmission in Acinetobacter baumannii. Adv. Exp. Med. Biol. 2021, 1313, 135–153. [Google Scholar] [CrossRef]
  36. Mediati, D.G.; Wu, S.; Wu, W.; Tree, J.J. Networks of resistance: Small RNA control of antibiotic resistance. Trends Genet. 2021, 37, 35–45. [Google Scholar] [CrossRef]
  37. Goldberger, O.; Livny, J.; Bhattacharyya, R.; Amster-Choder, O. Wisdom of the crowds: A suggested polygenic plan for small-RNA-mediated regulation in bacteria. iScience 2021, 24, 103096. [Google Scholar] [CrossRef]
  38. Haaber, J.; Penadés, J.R.; Ingmer, H. Transfer of antibiotic resistance in Staphylococcus aureus. Trends Microbiol. 2017, 25, 893–905. [Google Scholar] [CrossRef]
  39. Munita, J.M.; Arias, C.A. Mechanisms of antibiotic resistance. Microbiol. Spectr. 2016, 4, VMBF-0016-2015. [Google Scholar] [CrossRef] [Green Version]
  40. Chetri, S.; Singha, K.; Bhowmik, D.; Chanda, D.D.; Chakravarty, A.; Bhattacharjee, A. Sub-inhibitory concentration of ertapenem induces overexpression of regulator of antibiotic resistance A in Escherichia coli. Indian J. Med. Microbiol. 2018, 36, 569–571. [Google Scholar] [CrossRef]
  41. Harms, A.; Maisonneuve, E.; Gerdes, K. Mechanisms of bacterial persistence during stress and antibiotic exposure. Science 2016, 354, aaf4268. [Google Scholar] [CrossRef] [PubMed]
  42. Partridge, S.R.; Kwong, S.M.; Firth, N.; Jensen, S.O. Mobile genetic elements associated with antimicrobial resistance. Clin. Microbiol. Rev. 2018, 31, e00088-17. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  43. Limansky, A.S.; Mussi, M.A.; Viale, A.M. Loss of a 29-kilodalton outer membrane protein in Acinetobacter baumannii is associated with imipenem resistance. J. Clin. Microbiol. 2002, 40, 4776–4778. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  44. Clark, R.B. Imipenem resistance among Acinetobacter baumannii: Association with reduced expression of a 33–36 kDa outer membrane protein. J. Antimicrob. Chemother. 1996, 38, 245–251. [Google Scholar] [CrossRef] [Green Version]
  45. Luo, L.; Jiang, X.; Wu, Q.; Wei, L.; Li, J.; Ying, C. Efflux pump overexpression in conjunction with alternation of outer membrane protein may induce Acinetobacter baumannii resistant to imipenem. Chemotherapy 2011, 57, 77–84. [Google Scholar] [CrossRef]
  46. Zieliński, M.; Park, J.; Sleno, B.; Berghuis, A.M. Structural and functional insights into esterase-mediated macrolide resistance. Nat. Commun. 2021, 12, 1732. [Google Scholar] [CrossRef]
  47. Golkar, T.; Zieliński, M.; Berghuis, A.M. Look and outlook on enzyme-mediated macrolide resistance. Front. Microbiol. 2018, 9, 1942. [Google Scholar] [CrossRef] [Green Version]
  48. Ramirez, M.S.; Tolmasky, M.E. Aminoglycoside modifying enzymes. Drug Resist. Updat. 2010, 13, 151–171. [Google Scholar] [CrossRef] [Green Version]
  49. Fong, D.H.; Burk, D.L.; Blanchet, J.; Yan, A.Y.; Berghuis, A.M. Structural basis for kinase-mediated macrolide antibiotic resistance. Structure 2017, 25, 750–761.e755. [Google Scholar] [CrossRef] [Green Version]
  50. Sun, J.; Chen, C.; Cui, C.Y.; Zhang, Y.; Liu, X.; Cui, Z.H.; Ma, X.Y.; Feng, Y.; Fang, L.X.; Lian, X.L.; et al. Plasmid-encoded tet(X) genes that confer high-level tigecycline resistance in Escherichia coli. Nat. Microbiol. 2019, 4, 1457–1464. [Google Scholar] [CrossRef]
  51. Cheung, G.Y.; Rigby, K.; Wang, R.; Queck, S.Y.; Braughton, K.R.; Whitney, A.R.; Teintze, M.; DeLeo, F.R.; Otto, M. Staphylococcus epidermidis strategies to avoid killing by human neutrophils. PLoS Pathog. 2010, 6, e1001133. [Google Scholar] [CrossRef] [PubMed]
  52. Hinz, A.; Lee, S.; Jacoby, K.; Manoil, C. Membrane proteases and aminoglycoside antibiotic resistance. J. Bacteriol. 2011, 193, 4790–4797. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  53. Li, Y.X.; Zhong, Z.; Hou, P.; Zhang, W.P.; Qian, P.Y. Resistance to nonribosomal peptide antibiotics mediated by D-stereospecific peptidases. Nat. Chem. Biol. 2018, 14, 381–387. [Google Scholar] [CrossRef]
  54. Meziane-Cherif, D.; Stogios, P.J.; Evdokimova, E.; Savchenko, A.; Courvalin, P. Structural basis for the evolution of vancomycin resistance D,D-peptidases. Proc. Natl. Acad. Sci. USA 2014, 111, 5872–5877. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  55. Ambrose, K.D.; Nisbet, R.; Stephens, D.S. Macrolide efflux in Streptococcus pneumoniae is mediated by a dual efflux pump (mel and mef) and is erythromycin inducible. Antimicrob. Agents Chemother. 2005, 49, 4203–4209. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  56. Anes, J.; McCusker, M.P.; Fanning, S.; Martins, M. The ins and outs of RND efflux pumps in Escherichia coli. Front. Microbiol. 2015, 6, 587. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  57. Costa, S.S.; Viveiros, M.; Amaral, L.; Couto, I. Multidrug efflux pumps in Staphylococcus aureus: An update. Open Microbiol. J 2013, 7, 59–71. [Google Scholar] [CrossRef] [Green Version]
  58. Nikaido, H.; Pagès, J.M. Broad-specificity efflux pumps and their role in multidrug resistance of Gram-negative bacteria. FEMS Microbiol. Rev. 2012, 36, 340–363. [Google Scholar] [CrossRef] [Green Version]
  59. Lv, F.; Cai, J.; He, Q.; Wang, W.; Luo, Y.; Wang, X.; Mi, N.; Zhao, Z.; Li, G.; Luo, W. Overexpression of efflux pumps mediate pan resistance of Klebsiella pneumoniae sequence type 11. Microb. Drug Resist. 2021, 27, 1405–1411. [Google Scholar] [CrossRef]
  60. Ayoub Moubareck, C.; Hammoudi Halat, D. Insights into Acinetobacter baumannii: A Review of microbiological, virulence, and resistance traits in a threatening nosocomial pathogen. Antibiotics 2020, 9, 119. [Google Scholar] [CrossRef] [Green Version]
  61. Chancey, S.T.; Zhou, X.; Zähner, D.; Stephens, D.S. Induction of efflux-mediated macrolide resistance in Streptococcus pneumoniae. Antimicrob. Agents Chemother. 2011, 55, 3413–3422. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  62. Peacock, S.J.; Paterson, G.K. Mechanisms of methicillin resistance in Staphylococcus aureus. Annu. Rev. Biochem. 2015, 84, 577–601. [Google Scholar] [CrossRef] [PubMed]
  63. Srinivasan, V.B.; Singh, B.B.; Priyadarshi, N.; Chauhan, N.K.; Rajamohan, G. Role of novel multidrug efflux pump involved in drug resistance in Klebsiella pneumoniae. PLoS ONE 2014, 9, e96288. [Google Scholar] [CrossRef] [PubMed]
  64. Davin-Regli, A.; Pages, J.M.; Ferrand, A. Clinical status of efflux resistance mechanisms in gram-negative bacteria. Antibiotics 2021, 10, 1117. [Google Scholar] [CrossRef] [PubMed]
  65. Mao, W.; Warren, M.S.; Lee, A.; Mistry, A.; Lomovskaya, O. MexXY-OprM efflux pump is required for antagonism of aminoglycosides by divalent cations in Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 2001, 45, 2001–2007. [Google Scholar] [CrossRef] [Green Version]
  66. Muller, C.; Plésiat, P.; Jeannot, K. A two-component regulatory system interconnects resistance to polymyxins, aminoglycosides, fluoroquinolones, and β-lactams in Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 2011, 55, 1211–1221. [Google Scholar] [CrossRef] [Green Version]
  67. Coyne, S.; Rosenfeld, N.; Lambert, T.; Courvalin, P.; Périchon, B. Overexpression of resistance-nodulation-cell division pump AdeFGH confers multidrug resistance in Acinetobacter baumannii. Antimicrob. Agents Chemother. 2010, 54, 4389–4393. [Google Scholar] [CrossRef] [Green Version]
  68. Damier-Piolle, L.; Magnet, S.; Brémont, S.; Lambert, T.; Courvalin, P. AdeIJK, a resistance-nodulation-cell division pump effluxing multiple antibiotics in Acinetobacter baumannii. Antimicrob. Agents Chemother. 2008, 52, 557–562. [Google Scholar] [CrossRef] [Green Version]
  69. Schaffner, S.H.; Lee, A.V.; Pham, M.T.N.; Kassaye, B.B.; Li, H.; Tallada, S.; Lis, C.; Lang, M.; Liu, Y.; Ahmed, N.; et al. Extreme acid modulates fitness trade-offs of multidrug efflux pumps MdtEF-TolC and AcrAB-TolC in Escherichia coli K-12. Appl. Environ. Microbiol. 2021, 87, e0072421. [Google Scholar] [CrossRef]
  70. Yousefian, N.; Ornik-Cha, A.; Poussard, S.; Decossas, M.; Berbon, M.; Daury, L.; Taveau, J.C.; Dupuy, J.W.; Đorđević-Marquardt, S.; Lambert, O.; et al. Structural characterization of the EmrAB-TolC efflux complex from E. coli. Biochim. Biophys. Acta Biomembr. 2021, 1863, 183488. [Google Scholar] [CrossRef]
  71. Yoshikai, H.; Kizaki, H.; Saito, Y.; Omae, Y.; Sekimizu, K.; Kaito, C. Multidrug-resistance transporter AbcA secretes Staphylococcus aureus cytolytic toxins. J. Infect. Dis. 2016, 213, 295–304. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  72. Chatterjee, S.S.; Joo, H.S.; Duong, A.C.; Dieringer, T.D.; Tan, V.Y.; Song, Y.; Fischer, E.R.; Cheung, G.Y.; Li, M.; Otto, M. Essential Staphylococcus aureus toxin export system. Nat. Med. 2013, 19, 364–367. [Google Scholar] [CrossRef]
  73. Short, F.L.; Liu, Q.; Shah, B.; Clift, H.E.; Naidu, V.; Li, L.; Prity, F.T.; Mabbutt, B.C.; Hassan, K.A.; Paulsen, I.T. The Acinetobacter baumannii disinfectant resistance protein, AmvA, is a spermidine and spermine efflux pump. Commun. Biol. 2021, 4, 1114. [Google Scholar] [CrossRef] [PubMed]
  74. Zheng, J.X.; Lin, Z.W.; Sun, X.; Lin, W.H.; Chen, Z.; Wu, Y.; Qi, G.B.; Deng, Q.W.; Qu, D.; Yu, Z.J. Overexpression of OqxAB and MacAB efflux pumps contributes to eravacycline resistance and heteroresistance in clinical isolates of Klebsiella pneumoniae. Emerg. Microbes Infect. 2018, 7, 139. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  75. Coyne, S.; Courvalin, P.; Périchon, B. Efflux-mediated antibiotic resistance in Acinetobacter spp. Antimicrob. Agents Chemother. 2011, 55, 947–953. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  76. Eswarappa, S.M.; Panguluri, K.K.; Hensel, M.; Chakravortty, D. The yejABEF operon of Salmonella confers resistance to antimicrobial peptides and contributes to its virulence. Microbiology 2008, 154, 666–678. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  77. Du, D.; Wang-Kan, X.; Neuberger, A.; van Veen, H.W.; Pos, K.M.; Piddock, L.J.V.; Luisi, B.F. Multidrug efflux pumps: Structure, function and regulation. Nat. Rev. Microbiol. 2018, 16, 523–539. [Google Scholar] [CrossRef]
  78. Liu, J.; Chen, D.; Peters, B.M.; Li, L.; Li, B.; Xu, Z.; Shirliff, M.E. Staphylococcal chromosomal cassettes mec (SCCmec): A mobile genetic element in methicillin-resistant Staphylococcus aureus. Microb. Pathog. 2016, 101, 56–67. [Google Scholar] [CrossRef]
  79. Roberts, M.C. Update on macrolide-lincosamide-streptogramin, ketolide, and oxazolidinone resistance genes. FEMS Microbiol. Lett. 2008, 282, 147–159. [Google Scholar] [CrossRef] [Green Version]
  80. Canu, A.; Malbruny, B.; Coquemont, M.; Davies, T.A.; Appelbaum, P.C.; Leclercq, R. Diversity of ribosomal mutations conferring resistance to macrolides, clindamycin, streptogramin, and telithromycin in Streptococcus pneumoniae. Antimicrob. Agents Chemother. 2002, 46, 125–131. [Google Scholar] [CrossRef] [Green Version]
  81. Varughese, L.R.; Rajpoot, M.; Goyal, S.; Mehra, R.; Chhokar, V.; Beniwal, V. Analytical profiling of mutations in quinolone resistance determining region of gyrA gene among UPEC. PLoS ONE 2018, 13, e0190729. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  82. Moon, D.C.; Seol, S.Y.; Gurung, M.; Jin, J.S.; Choi, C.H.; Kim, J.; Lee, Y.C.; Cho, D.T.; Lee, J.C. Emergence of a new mutation and its accumulation in the topoisomerase IV gene confers high levels of resistance to fluoroquinolones in Escherichia coli isolates. Int. J. Antimicrob. Agents 2010, 35, 76–79. [Google Scholar] [CrossRef] [PubMed]
  83. Villa, L.; Feudi, C.; Fortini, D.; García-Fernández, A.; Carattoli, A. Genomics of KPC-producing Klebsiella pneumoniae sequence type 512 clone highlights the role of RamR and ribosomal S10 protein mutations in conferring tigecycline resistance. Antimicrob. Agents Chemother. 2014, 58, 1707–1712. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  84. Shigemura, K.; Tanaka, K.; Yamamichi, F.; Shirakawa, T.; Miyake, H.; Fujisawa, M. Does mutation in gyrA and/or parC or efflux pump expression play the main role in fluoroquinolone resistance in Escherichia coli urinary tract infections?: A statistical analysis study. Int. J. Antimicrob. Agents 2012, 40, 516–520. [Google Scholar] [CrossRef] [PubMed]
  85. Lee, J.K.; Lee, Y.S.; Park, Y.K.; Kim, B.S. Mutations in the gyrA and parC genes in ciprofloxacin-resistant clinical isolates of Acinetobacter baumannii in Korea. Microbiol. Immunol. 2005, 49, 647–653. [Google Scholar] [CrossRef]
  86. Dalmolin, T.V.; de Lima-Morales, D.; Barth, A.L. Plasmid-mediated Colistin resistance: What do we know? J. Infect. 2018, 1, 16–22. [Google Scholar] [CrossRef]
  87. Bugg, T.D.; Wright, G.D.; Dutka-Malen, S.; Arthur, M.; Courvalin, P.; Walsh, C.T. Molecular basis for vancomycin resistance in Enterococcus faecium BM4147: Biosynthesis of a depsipeptide peptidoglycan precursor by vancomycin resistance proteins VanH and VanA. Biochemistry 1991, 30, 10408–10415. [Google Scholar] [CrossRef]
  88. Hong, H.J.; Hutchings, M.I.; Buttner, M.J. Vancomycin resistance VanS/VanR two-component systems. Adv. Exp. Med. Biol. 2008, 631, 200–213. [Google Scholar] [CrossRef]
  89. Gupta, P.; Sothiselvam, S.; Vázquez-Laslop, N.; Mankin, A.S. Deregulation of translation due to post-transcriptional modification of rRNA explains why erm genes are inducible. Nat. Commun. 2013, 4, 1984. [Google Scholar] [CrossRef]
  90. Fernández, L.; Alvarez-Ortega, C.; Wiegand, I.; Olivares, J.; Kocíncová, D.; Lam, J.S.; Martínez, J.L.; Hancock, R.E. Characterization of the polymyxin B resistome of Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 2013, 57, 110–119. [Google Scholar] [CrossRef] [Green Version]
  91. Thaipisuttikul, I.; Hittle, L.E.; Chandra, R.; Zangari, D.; Dixon, C.L.; Garrett, T.A.; Rasko, D.A.; Dasgupta, N.; Moskowitz, S.M.; Malmström, L.; et al. A divergent Pseudomonas aeruginosa palmitoyltransferase essential for cystic fibrosis-specific lipid A. Mol. Microbiol. 2014, 91, 158–174. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  92. Vester, B. The cfr and cfr-like multiple resistance genes. Res. Microbiol. 2018, 169, 61–66. [Google Scholar] [CrossRef] [PubMed]
  93. Stojković, V.; Noda-Garcia, L.; Tawfik, D.S.; Fujimori, D.G. Antibiotic resistance evolved via inactivation of a ribosomal RNA methylating enzyme. Nucleic Acids Res. 2016, 44, 8897–8907. [Google Scholar] [CrossRef] [Green Version]
  94. Tran, J.H.; Jacoby, G.A.; Hooper, D.C. Interaction of the plasmid-encoded quinolone resistance protein QnrA with Escherichia coli topoisomerase IV. Antimicrob. Agents Chemother. 2005, 49, 3050–3052. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  95. Tran, J.H.; Jacoby, G.A.; Hooper, D.C. Interaction of the plasmid-encoded quinolone resistance protein Qnr with Escherichia coli DNA gyrase. Antimicrob. Agents Chemother. 2005, 49, 118–125. [Google Scholar] [CrossRef] [Green Version]
  96. Kim, E.S.; Chen, C.; Braun, M.; Kim, H.Y.; Okumura, R.; Wang, Y.; Jacoby, G.A.; Hooper, D.C. Interactions between QnrB, QnrB mutants, and DNA gyrase. Antimicrob. Agents Chemother. 2015, 59, 5413–5419. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  97. Pachanon, R.; Koide, K.; Kongsoi, S.; Nakajima, C.; Kapalamula, T.F.; Suthienkul, O.; Suzuki, Y. Interaction of the plasmid-encoded quinolone resistance protein QnrB19 with Salmonella Typhimurium DNA gyrase. J. Infect. Chemother. 2020, 26, 1139–1145. [Google Scholar] [CrossRef]
  98. Su, W.; Kumar, V.; Ding, Y.; Ero, R.; Serra, A.; Lee, B.S.T.; Wong, A.S.W.; Shi, J.; Sze, S.K.; Yang, L.; et al. Ribosome protection by antibiotic resistance ATP-binding cassette protein. Proc. Natl. Acad. Sci. USA 2018, 115, 5157–5162. [Google Scholar] [CrossRef] [Green Version]
  99. Wilson, D.N. Ribosome-targeting antibiotics and mechanisms of bacterial resistance. Nat. Rev. Microbiol. 2014, 12, 35–48. [Google Scholar] [CrossRef]
  100. Sharkey, L.K.; Edwards, T.A.; O’Neill, A.J. ABC-F proteins mediate antibiotic resistance through ribosomal protection. mBio 2016, 7, e01975. [Google Scholar] [CrossRef] [Green Version]
  101. Ero, R.; Kumar, V.; Su, W.; Gao, Y.G. Ribosome protection by ABC-F proteins-Molecular mechanism and potential drug design. Protein Sci. 2019, 28, 684–693. [Google Scholar] [CrossRef] [PubMed]
  102. Crowe-McAuliffe, C.; Murina, V.; Turnbull, K.J.; Kasari, M.; Mohamad, M.; Polte, C.; Takada, H.; Vaitkevicius, K.; Johansson, J.; Ignatova, Z.; et al. Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens. Nat. Commun. 2021, 12, 3577. [Google Scholar] [CrossRef] [PubMed]
  103. Connell, S.R.; Tracz, D.M.; Nierhaus, K.H.; Taylor, D.E. Ribosomal protection proteins and their mechanism of tetracycline resistance. Antimicrob. Agents Chemother. 2003, 47, 3675–3681. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  104. Singh, S.; Singh, S.K.; Chowdhury, I.; Singh, R. Understanding the mechanism of bacterial biofilms resistance to antimicrobial agents. Open Microbiol. J. 2017, 11, 53–62. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  105. Conibear, T.C.; Collins, S.L.; Webb, J.S. Role of mutation in Pseudomonas aeruginosa biofilm development. PLoS ONE 2009, 4, e6289. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  106. Singh, R.; Ray, P.; Das, A.; Sharma, M. Penetration of antibiotics through Staphylococcus aureus and Staphylococcus epidermidis biofilms. J. Antimicrob. Chemother. 2010, 65, 1955–1958. [Google Scholar] [CrossRef] [Green Version]
  107. Toussaint, A.; Chandler, M. Prokaryote genome fluidity: Toward a system approach of the mobilome. Methods Mol. Biol. 2012, 804, 57–80. [Google Scholar] [CrossRef]
  108. Islam, M.A.; Islam, M.; Hasan, R.; Hossain, M.I.; Nabi, A.; Rahman, M.; Goessens, W.H.F.; Endtz, H.P.; Boehm, A.B.; Faruque, S.M. Environmental spread of New Delhi Metallo-β-Lactamase-1-producing multidrug-resistant bacteria in Dhaka, Bangladesh. Appl. Environ. Microbiol. 2017, 83, e00793-17. [Google Scholar] [CrossRef] [Green Version]
  109. Ribera, A.; Roca, I.; Ruiz, J.; Gibert, I.; Vila, J. Partial characterization of a transposon containing the tet(A) determinant in a clinical isolate of Acinetobacter baumannii. J. Antimicrob. Chemother. 2003, 52, 477–480. [Google Scholar] [CrossRef] [Green Version]
  110. Zhu, Y.; Yi, Y.; Liu, F.; Lv, N.; Yang, X.; Li, J.; Hu, Y.; Zhu, B. Distribution and molecular profiling of class 1 integrons in MDR Acinetobacter baumannii isolates and whole genome-based analysis of antibiotic resistance mechanisms in a representative strain. Microbiol. Res. 2014, 169, 811–816. [Google Scholar] [CrossRef]
  111. Liu, Y.Y.; Wang, Y.; Walsh, T.R.; Yi, L.X.; Zhang, R.; Spencer, J.; Doi, Y.; Tian, G.; Dong, B.; Huang, X.; et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: A microbiological and molecular biological study. Lancet Infect. Dis. 2016, 16, 161–168. [Google Scholar] [CrossRef]
  112. Yin, W.; Li, H.; Shen, Y.; Liu, Z.; Wang, S.; Shen, Z.; Zhang, R.; Walsh, T.R.; Shen, J.; Wang, Y. Novel plasmid-mediated colistin resistance gene mcr-3 in Escherichia coli. mBio 2017, 8, e00543-17. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  113. Shore, A.C.; Coleman, D.C. Staphylococcal cassette chromosome mec: Recent advances and new insights. Int. J. Med. Microbiol. 2013, 303, 350–359. [Google Scholar] [CrossRef] [PubMed]
  114. Zgurskaya, H.I.; Rybenkov, V.V. Permeability barriers of Gram-negative pathogens. Ann. N. Y. Acad. Sci. 2020, 1459, 5–18. [Google Scholar] [CrossRef]
  115. Iyer, R.; Moussa, S.H.; Durand-Réville, T.F.; Tommasi, R.; Miller, A. Acinetobacter baumannii OmpA is a selective antibiotic permeant porin. ACS Infect. Dis. 2018, 4, 373–381. [Google Scholar] [CrossRef]
  116. Smani, Y.; Fàbrega, A.; Roca, I.; Sánchez-Encinales, V.; Vila, J.; Pachón, J. Role of OmpA in the multidrug resistance phenotype of Acinetobacter baumannii. Antimicrob. Agents Chemother. 2014, 58, 1806–1808. [Google Scholar] [CrossRef] [Green Version]
  117. Kwon, H.I.; Kim, S.; Oh, M.H.; Na, S.H.; Kim, Y.J.; Jeon, Y.H.; Lee, J.C. Outer membrane protein A contributes to antimicrobial resistance of Acinetobacter baumannii through the OmpA-like domain. J. Antimicrob. Chemother. 2017, 72, 3012–3015. [Google Scholar] [CrossRef]
  118. Sugawara, E.; Nikaido, H. OmpA is the principal nonspecific slow porin of Acinetobacter baumannii. J. Bacteriol. 2012, 194, 4089–4096. [Google Scholar] [CrossRef] [Green Version]
  119. Bhamidimarri, S.P.; Zahn, M.; Prajapati, J.D.; Schleberger, C.; Söderholm, S.; Hoover, J.; West, J.; Kleinekathöfer, U.; Bumann, D.; Winterhalter, M.; et al. A multidisciplinary approach toward identification of antibiotic scaffolds for Acinetobacter baumannii. Structure 2019, 27, 268–280.e266. [Google Scholar] [CrossRef] [Green Version]
  120. Gaddy, J.A.; Tomaras, A.P.; Actis, L.A. The Acinetobacter baumannii 19606 OmpA protein plays a role in biofilm formation on abiotic surfaces and in the interaction of this pathogen with eukaryotic cells. Infect. Immun. 2009, 77, 3150–3160. [Google Scholar] [CrossRef] [Green Version]
  121. Nie, D.; Hu, Y.; Chen, Z.; Li, M.; Hou, Z.; Luo, X.; Mao, X.; Xue, X. Outer membrane protein A (OmpA) as a potential therapeutic target for Acinetobacter baumannii infection. J. Biomed. Sci. 2020, 27, 26. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  122. Na, S.H.; Jeon, H.; Oh, M.H.; Kim, Y.J.; Chu, M.; Lee, I.Y.; Lee, J.C. Therapeutic effects of inhibitor of ompA expression against carbapenem-resistant Acinetobacter baumannii strains. Int. J. Mol. Sci. 2021, 22, 12257. [Google Scholar] [CrossRef] [PubMed]
  123. Pagès, J.M.; James, C.E.; Winterhalter, M. The porin and the permeating antibiotic: A selective diffusion barrier in Gram-negative bacteria. Nat. Rev. Microbiol. 2008, 6, 893–903. [Google Scholar] [CrossRef] [Green Version]
  124. Ziervogel, B.K.; Roux, B. The bind.ding of antibiotics in OmpF porin. Structure 2013, 21, 76–87. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  125. Sugawara, E.; Kojima, S.; Nikaido, H. Klebsiella pneumoniae major porins OmpK35 and OmpK36 allow more efficient diffusion of β-Lactams than their Escherichia coli homologs OmpF and OmpC. J. Bacteriol. 2016, 198, 3200–3208. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  126. Moya-Torres, A.; Mulvey, M.R.; Kumar, A.; Oresnik, I.J.; Brassinga, A.K.C. The lack of OmpF, but not OmpC, contributes to increased antibiotic resistance in Serratia marcescens. Microbiology 2014, 160, 1882–1892. [Google Scholar] [CrossRef]
  127. Li, H.; Luo, Y.F.; Williams, B.J.; Blackwell, T.S.; Xie, C.M. Structure and function of OprD protein in Pseudomonas aeruginosa: From antibiotic resistance to novel therapies. Int. J. Med. Microbiol. 2012, 302, 63–68. [Google Scholar] [CrossRef] [Green Version]
  128. Thiolas, A.; Bornet, C.; Davin-Régli, A.; Pagès, J.M.; Bollet, C. Resistance to imipenem, cefepime, and cefpirome associated with mutation in Omp36 osmoporin of Enterobacter aerogenes. Biochem. Biophys. Res. Commun. 2004, 317, 851–856. [Google Scholar] [CrossRef]
  129. Lee, C.H.; Chu, C.; Liu, J.W.; Chen, Y.S.; Chiu, C.J.; Su, L.H. Collateral damage of flomoxef therapy: In vivo development of porin deficiency and acquisition of blaDHA-1 leading to ertapenem resistance in a clinical isolate of Klebsiella pneumoniae producing CTX-M-3 and SHV-5 beta-lactamases. J. Antimicrob. Chemother. 2007, 60, 410–413. [Google Scholar] [CrossRef] [Green Version]
  130. Pulzova, L.; Navratilova, L.; Comor, L. Alterations in outer membrane permeability favor drug-resistant phenotype of Klebsiella pneumoniae. Microb. Drug Resist. 2017, 23, 413–420. [Google Scholar] [CrossRef]
  131. Bowers, J.R.; Kitchel, B.; Driebe, E.M.; MacCannell, D.R.; Roe, C.; Lemmer, D.; de Man, T.; Rasheed, J.K.; Engelthaler, D.M.; Keim, P.; et al. Genomic analysis of the emergence and rapid global dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic. PLoS ONE 2015, 10, e0133727. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  132. Fukuoka, T.; Ohya, S.; Narita, T.; Katsuta, M.; Iijima, M.; Masuda, N.; Yasuda, H.; Trias, J.; Nikaido, H. Activity of the carbapenem panipenem and role of the OprD (D2) protein in its diffusion through the Pseudomonas aeruginosa outer membrane. Antimicrob. Agents Chemother. 1993, 37, 322–327. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  133. Chevalier, S.; Bouffartigues, E.; Bodilis, J.; Maillot, O.; Lesouhaitier, O.; Feuilloley, M.G.J.; Orange, N.; Dufour, A.; Cornelis, P. Structure, function and regulation of Pseudomonas aeruginosa porins. FEMS Microbiol. Rev. 2017, 41, 698–722. [Google Scholar] [CrossRef] [PubMed]
  134. Nestorovich, E.M.; Sugawara, E.; Nikaido, H.; Bezrukov, S.M. Pseudomonas aeruginosa porin OprF: Properties of the channel. J. Biol. Chem. 2006, 281, 16230–16237. [Google Scholar] [CrossRef] [Green Version]
  135. Bouffartigues, E.; Moscoso, J.A.; Duchesne, R.; Rosay, T.; Fito-Boncompte, L.; Gicquel, G.; Maillot, O.; Bénard, M.; Bazire, A.; Brenner-Weiss, G.; et al. The absence of the Pseudomonas aeruginosa OprF protein leads to increased biofilm formation through variation in c-di-GMP level. Front. Microbiol. 2015, 6, 630. [Google Scholar] [CrossRef] [Green Version]
  136. Gupta, N.; Limbago, B.M.; Patel, J.B.; Kallen, A.J. Carbapenem-resistant Enterobacteriaceae: Epidemiology and prevention. Clin. Infect. Dis. 2011, 53, 60–67. [Google Scholar] [CrossRef] [Green Version]
  137. Tehrani, K.; Martin, N.I. β-lactam/β-lactamase inhibitor combinations: An update. Medchemcomm 2018, 9, 1439–1456. [Google Scholar] [CrossRef]
  138. Yang, W.; Moore, I.F.; Koteva, K.P.; Bareich, D.C.; Hughes, D.W.; Wright, G.D. TetX is a flavin-dependent monooxygenase conferring resistance to tetracycline antibiotics. J. Biol. Chem. 2004, 279, 52346–52352. [Google Scholar] [CrossRef] [Green Version]
  139. Moore, I.F.; Hughes, D.W.; Wright, G.D. Tigecycline is modified by the flavin-dependent monooxygenase TetX. Biochemistry 2005, 44, 11829–11835. [Google Scholar] [CrossRef]
  140. He, T.; Wang, R.; Liu, D.; Walsh, T.R.; Zhang, R.; Lv, Y.; Ke, Y.; Ji, Q.; Wei, R.; Liu, Z.; et al. Emergence of plasmid-mediated high-level tigecycline resistance genes in animals and humans. Nat. Microbiol. 2019, 4, 1450–1456. [Google Scholar] [CrossRef]
  141. Park, J.; Gasparrini, A.J.; Reck, M.R.; Symister, C.T.; Elliott, J.L.; Vogel, J.P.; Wencewicz, T.A.; Dantas, G.; Tolia, N.H. Plasticity, dynamics, and inhibition of emerging tetracycline resistance enzymes. Nat. Chem. Biol. 2017, 13, 730–736. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  142. Markley, J.L.; Wencewicz, T.A. Tetracycline-inactivating enzymes. Front. Microbiol. 2018, 9, 1058. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  143. Monecke, S.; Jatzwauk, L.; Müller, E.; Nitschke, H.; Pfohl, K.; Slickers, P.; Reissig, A.; Ruppelt-Lorz, A.; Ehricht, R. Diversity of SCCmec elements in Staphylococcus aureus as observed in South-Eastern Germany. PLoS ONE 2016, 11, e0162654. [Google Scholar] [CrossRef] [PubMed]
  144. Guffey, A.A.; Loll, P.J. Regulation of Resistance in Vancomycin-Resistant Enterococci: The VanRS two-component system. Microorganisms 2021, 9, 2026. [Google Scholar] [CrossRef] [PubMed]
  145. Reynolds, P.E.; Arias, C.A.; Courvalin, P. Gene vanXYC encodes D,D -dipeptidase (VanX) and D,D-carboxypeptidase (VanY) activities in vancomycin-resistant Enterococcus gallinarum BM4174. Mol. Microbiol. 1999, 34, 341–349. [Google Scholar] [CrossRef] [PubMed]
  146. Arthur, M.; Depardieu, F.; Cabanié, L.; Reynolds, P.; Courvalin, P. Requirement of the VanY and VanX D,D-peptidases for glycopeptide resistance in enterococci. Mol. Microbiol. 1998, 30, 819–830. [Google Scholar] [CrossRef]
  147. Poole, K.; Srikumar, R. Multidrug efflux in Pseudomonas aeruginosa: Components, mechanisms and clinical significance. Curr. Top. Med. Chem. 2001, 1, 59–71. [Google Scholar] [CrossRef]
  148. Alvarez-Ortega, C.; Olivares, J.; Martínez, J.L. RND multidrug efflux pumps: What are they good for? Front. Microbiol. 2013, 4, 7. [Google Scholar] [CrossRef] [Green Version]
  149. Rosner, J.L.; Martin, R.G. Reduction of cellular stress by TolC-dependent efflux pumps in Escherichia coli indicated by BaeSR and CpxARP activation of spy in efflux mutants. J. Bacteriol. 2013, 195, 1042–1050. [Google Scholar] [CrossRef] [Green Version]
  150. Tatsumi, R.; Wachi, M. TolC-dependent exclusion of porphyrins in Escherichia coli. J. Bacteriol. 2008, 190, 6228–6233. [Google Scholar] [CrossRef] [Green Version]
  151. Piddock, L.J. Multidrug-resistance efflux pumps—Not just for resistance. Nat. Rev. Microbiol. 2006, 4, 629–636. [Google Scholar] [CrossRef] [PubMed]
  152. Alav, I.; Sutton, J.M.; Rahman, K.M. Role of bacterial efflux pumps in biofilm formation. J. Antimicrob. Chemother. 2018, 73, 2003–2020. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  153. Kvist, M.; Hancock, V.; Klemm, P. Inactivation of efflux pumps abolishes bacterial biofilm formation. Appl. Environ. Microbiol. 2008, 74, 7376–7382. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  154. Zimmermann, S.; Klinger-Strobel, M.; Bohnert, J.A.; Wendler, S.; Rödel, J.; Pletz, M.W.; Löffler, B.; Tuchscherr, L. Clinically approved drugs inhibit the Staphylococcus aureus multidrug NorA efflux pump and reduce biofilm formation. Front. Microbiol. 2019, 10, 2762. [Google Scholar] [CrossRef] [Green Version]
  155. Baugh, S.; Ekanayaka, A.S.; Piddock, L.J.; Webber, M.A. Loss of or inhibition of all multidrug resistance efflux pumps of Salmonella enterica serovar Typhimurium results in impaired ability to form a biofilm. J. Antimicrob. Chemother. 2012, 67, 2409–2417. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  156. Lopes, L.A.A.; Dos Santos Rodrigues, J.B.; Magnani, M.; de Souza, E.L.; de Siqueira-Júnior, J.P. Inhibitory effects of flavonoids on biofilm formation by Staphylococcus aureus that overexpresses efflux protein genes. Microb. Pathog. 2017, 107, 193–197. [Google Scholar] [CrossRef] [PubMed]
  157. Wang-Kan, X.; Blair, J.M.A.; Chirullo, B.; Betts, J.; La Ragione, R.M.; Ivens, A.; Ricci, V.; Opperman, T.J.; Piddock, L.J.V. Lack of AcrB efflux function confers loss of virulence on Salmonella enterica Serovar Typhimurium. mBio 2017, 8, e00968-17. [Google Scholar] [CrossRef] [Green Version]
  158. Matsumura, K.; Furukawa, S.; Ogihara, H.; Morinaga, Y. Roles of multidrug efflux pumps on the biofilm formation of Escherichia coli K-12. Biocontrol Sci. 2011, 16, 69–72. [Google Scholar] [CrossRef] [Green Version]
  159. Hassan, K.A.; Liu, Q.; Elbourne, L.D.H.; Ahmad, I.; Sharples, D.; Naidu, V.; Chan, C.L.; Li, L.; Harborne, S.P.D.; Pokhrel, A.; et al. Pacing across the membrane: The novel PACE family of efflux pumps is widespread in Gram-negative pathogens. Res. Microbiol. 2018, 169, 450–454. [Google Scholar] [CrossRef]
  160. Housseini, B.I.K.; Phan, G.; Broutin, I. Functional mechanism of the efflux pumps transcription regulators from Pseudomonas aeruginosa based on 3D structures. Front. Mol. BioSci. 2018, 5, 57. [Google Scholar] [CrossRef] [Green Version]
  161. Mousa, J.J.; Bruner, S.D. Structural and mechanistic diversity of multidrug transporters. Nat. Prod. Rep. 2016, 33, 1255–1267. [Google Scholar] [CrossRef] [PubMed]
  162. Thakur, V.; Uniyal, A.; Tiwari, V. A comprehensive review on pharmacology of efflux pumps and their inhibitors in antibiotic resistance. Eur. J. Pharmacol. 2021, 903, 174151. [Google Scholar] [CrossRef] [PubMed]
  163. Li, X.Z.; Nikaido, H. Efflux-mediated drug resistance in bacteria. Drugs 2004, 64, 159–204. [Google Scholar] [CrossRef] [PubMed]
  164. Sun, J.; Deng, Z.; Yan, A. Bacterial multidrug efflux pumps: Mechanisms, Physiology and pharmacological exploitations. Biochem. Biophys. Res. Commun. 2014, 453, 254–267. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  165. Piddock, L.J. Clinically relevant chromosomally encoded multidrug resistance efflux pumps in bacteria. Clin. Microbiol. Rev. 2006, 19, 382–402. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  166. Schumacher, M.A.; Brennan, R.G. Structural mechanisms of multidrug recognition and regulation by bacterial multidrug transcription factors. Mol. Microbiol. 2002, 45, 885–893. [Google Scholar] [CrossRef]
  167. Takeuchi, K.; Imai, M.; Shimada, I. Conformational equilibrium defines the variable induction of the multidrug-binding transcriptional repressor QacR. Proc. Natl. Acad. Sci. USA 2019, 116, 19963–19972. [Google Scholar] [CrossRef] [Green Version]
  168. Wade, H. MD recognition by MDR gene regulators. Curr. Opin. Struct. Biol. 2010, 20, 489–496. [Google Scholar] [CrossRef]
  169. Bachas, S.; Eginton, C.; Gunio, D.; Wade, H. Structural contributions to multidrug recognition in the multidrug resistance (MDR) gene regulator, BmrR. Proc. Natl. Acad. Sci. USA 2011, 108, 11046–11051. [Google Scholar] [CrossRef] [Green Version]
  170. Ahmed, M.; Borsch, C.M.; Taylor, S.S.; Vázquez-Laslop, N.; Neyfakh, A.A. A protein that activates expression of a multidrug efflux transporter upon binding the transporter substrates. J. Biol. Chem. 1994, 269, 28506–28513. [Google Scholar] [CrossRef]
  171. Alguel, Y.; Meng, C.; Terán, W.; Krell, T.; Ramos, J.L.; Gallegos, M.T.; Zhang, X. Crystal structures of multidrug binding protein TtgR in complex with antibiotics and plant antimicrobials. J. Mol. Biol. 2007, 369, 829–840. [Google Scholar] [CrossRef] [PubMed]
  172. Hinrichs, W.; Kisker, C.; Düvel, M.; Müller, A.; Tovar, K.; Hillen, W.; Saenger, W. Structure of the Tet repressor-tetracycline complex and regulation of antibiotic resistance. Science 1994, 264, 418–420. [Google Scholar] [CrossRef] [PubMed]
  173. Schumacher, M.A.; Miller, M.C.; Grkovic, S.; Brown, M.H.; Skurray, R.A.; Brennan, R.G. Structural mechanisms of QacR induction and multidrug recognition. Science 2001, 294, 2158–2163. [Google Scholar] [CrossRef] [PubMed]
  174. Terán, W.; Krell, T.; Ramos, J.L.; Gallegos, M.T. Effector-repressor interactions, binding of a single effector molecule to the operator-bound TtgR homodimer mediates derepression. J. Biol. Chem. 2006, 281, 7102–7109. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  175. Hillen, W.; Berens, C. Mechanisms underlying expression of Tn10 encoded tetracycline resistance. Annu. Rev. Microbiol. 1994, 48, 345–369. [Google Scholar] [CrossRef] [PubMed]
  176. Grkovic, S.; Brown, M.H.; Roberts, N.J.; Paulsen, I.T.; Skurray, R.A. QacR is a repressor protein that regulates expression of the Staphylococcus aureus multidrug efflux pump QacA. J. Biol. Chem. 1998, 273, 18665–18673. [Google Scholar] [CrossRef] [Green Version]
  177. Lomovskaya, O.; Lewis, K.; Matin, A. EmrR is a negative regulator of the Escherichia coli multidrug resistance pump EmrAB. J. Bacteriol. 1995, 177, 2328–2334. [Google Scholar] [CrossRef] [Green Version]
  178. Xiong, A.; Gottman, A.; Park, C.; Baetens, M.; Pandza, S.; Matin, A. The EmrR protein represses the Escherichia coli emrRAB multidrug resistance operon by directly binding to its promoter region. Antimicrob. Agents Chemother. 2000, 44, 2905–2907. [Google Scholar] [CrossRef] [Green Version]
  179. Turner, A.K.; Eckert, S.E.; Turner, D.J.; Yasir, M.; Webber, M.A.; Charles, I.G.; Parkhill, J.; Wain, J. A whole-genome screen identifies Salmonella enterica serovar Typhi genes involved in fluoroquinolone susceptibility. J. Antimicrob. Chemother. 2020, 75, 2516–2525. [Google Scholar] [CrossRef]
  180. Chen, S.; Cui, S.; McDermott, P.F.; Zhao, S.; White, D.G.; Paulsen, I.; Meng, J. Contribution of target gene mutations and efflux to decreased susceptibility of Salmonella enterica serovar typhimurium to fluoroquinolones and other antimicrobials. Antimicrob. Agents Chemother. 2007, 51, 535–542. [Google Scholar] [CrossRef] [Green Version]
  181. Kaatz, G.W.; Seo, S.M. Inducible NorA-mediated multidrug resistance in Staphylococcus aureus. Antimicrob. Agents Chemother. 1995, 39, 2650–2655. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  182. Fournier, B.; Aras, R.; Hooper, D.C. Expression of the multidrug resistance transporter NorA from Staphylococcus aureus is modified by a two-component regulatory system. J. Bacteriol. 2000, 182, 664–671. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  183. Truong-Bolduc, Q.C.; Zhang, X.; Hooper, D.C. Characterization of NorR protein, a multifunctional regulator of norA expression in Staphylococcus aureus. J. Bacteriol. 2003, 185, 3127–3138. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  184. Truong-Bolduc, Q.C.; Dunman, P.M.; Eidem, T.; Hooper, D.C. Transcriptional profiling analysis of the global regulator NorG, a GntR-like protein of Staphylococcus aureus. J. Bacteriol. 2011, 193, 6207–6214. [Google Scholar] [CrossRef] [Green Version]
  185. Kaatz, G.W.; Thyagarajan, R.V.; Seo, S.M. Effect of promoter region mutations and mgrA overexpression on transcription of norA, which encodes a Staphylococcus aureus multidrug efflux transporter. Antimicrob. Agents Chemother. 2005, 49, 161–169. [Google Scholar] [CrossRef] [Green Version]
  186. Truong-Bolduc, Q.C.; Wang, Y.; Reedy, J.L.; Vyas, J.M.; Hooper, D.C. Staphylococcus aureus efflux pumps and tolerance to ciprofloxacin and chlorhexidine following induction by mupirocin. Antimicrob. Agents Chemother. 2021, 66, e0184521. [Google Scholar] [CrossRef]
  187. Zähner, D.; Zhou, X.; Chancey, S.T.; Pohl, J.; Shafer, W.M.; Stephens, D.S. Human antimicrobial peptide LL-37 induces MefE/Mel-mediated macrolide resistance in Streptococcus pneumoniae. Antimicrob. Agents Chemother. 2010, 54, 3516–3519. [Google Scholar] [CrossRef] [Green Version]
  188. Skiada, A.; Markogiannakis, A.; Plachouras, D.; Daikos, G.L. Adaptive resistance to cationic compounds in Pseudomonas aeruginosa. Int. J. Antimicrob. Agents 2011, 37, 187–193. [Google Scholar] [CrossRef]
  189. Puja, H.; Bolard, A.; Noguès, A.; Plésiat, P.; Jeannot, K. The efflux pump MexXY/OprM contributes to the tolerance and acquired resistance of Pseudomonas aeruginosa to colistin. Antimicrob. Agents Chemother. 2020, 64, e02033-02019. [Google Scholar] [CrossRef]
  190. Jeannot, K.; Sobel, M.L.; El Garch, F.; Poole, K.; Plésiat, P. Induction of the MexXY efflux pump in Pseudomonas aeruginosa is dependent on drug-ribosome interaction. J. Bacteriol. 2005, 187, 5341–5346. [Google Scholar] [CrossRef] [Green Version]
  191. Caughlan, R.E.; Sriram, S.; Daigle, D.M.; Woods, A.L.; Buco, J.; Peterson, R.L.; Dzink-Fox, J.; Walker, S.; Dean, C.R. Fmt bypass in Pseudomonas aeruginosa causes induction of MexXY efflux pump expression. Antimicrob. Agents Chemother. 2009, 53, 5015–5021. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  192. El’Garch, F.; Jeannot, K.; Hocquet, D.; Llanes-Barakat, C.; Plésiat, P. Cumulative effects of several nonenzymatic mechanisms on the resistance of Pseudomonas aeruginosa to aminoglycosides. Antimicrob. Agents Chemother. 2007, 51, 1016–1021. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  193. Westbrock-Wadman, S.; Sherman, D.R.; Hickey, M.J.; Coulter, S.N.; Zhu, Y.Q.; Warrener, P.; Nguyen, L.Y.; Shawar, R.M.; Folger, K.R.; Stover, C.K. Characterization of a Pseudomonas aeruginosa efflux pump contributing to aminoglycoside impermeability. Antimicrob. Agents Chemother. 1999, 43, 2975–2983. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  194. Shi, J.; Jin, Y.; Bian, T.; Li, K.; Sun, Z.; Cheng, Z.; Jin, S.; Wu, W. SuhB is a novel ribosome associated protein that regulates expression of MexXY by modulating ribosome stalling in Pseudomonas aeruginosa. Mol. Microbiol. 2015, 98, 370–383. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  195. Yamamoto, M.; Ueda, A.; Kudo, M.; Matsuo, Y.; Fukushima, J.; Nakae, T.; Kaneko, T.; Ishigatsubo, Y. Role of MexZ and PA5471 in transcriptional regulation of mexXY in Pseudomonas aeruginosa. Microbiology 2009, 155, 3312–3321. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  196. Poole, K.; Tetro, K.; Zhao, Q.; Neshat, S.; Heinrichs, D.E.; Bianco, N. Expression of the multidrug resistance operon mexA-mexB-oprM in Pseudomonas aeruginosa: mexR encodes a regulator of operon expression. Antimicrob. Agents Chemother. 1996, 40, 2021–2028. [Google Scholar] [CrossRef] [Green Version]
  197. Lau, C.H.; Krahn, T.; Gilmour, C.; Mullen, E.; Poole, K. AmgRS-mediated envelope stress-inducible expression of the mexXY multidrug efflux operon of Pseudomonas aeruginosa. Microbiologyopen 2015, 4, 121–135. [Google Scholar] [CrossRef]
  198. Alguel, Y.; Lu, D.; Quade, N.; Sauter, S.; Zhang, X. Crystal structure of MexZ, a key repressor responsible for antibiotic resistance in Pseudomonas aeruginosa. J. Struct. Biol. 2010, 172, 305–310. [Google Scholar] [CrossRef]
  199. Jahandideh, S. Diversity in structural consequences of MexZ mutations in Pseudomonas aeruginosa. Chem. Biol. Drug Des. 2013, 81, 600–606. [Google Scholar] [CrossRef]
  200. Guénard, S.; Muller, C.; Monlezun, L.; Benas, P.; Broutin, I.; Jeannot, K.; Plésiat, P. Multiple mutations lead to MexXY-OprM-dependent aminoglycoside resistance in clinical strains of Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 2014, 58, 221–228. [Google Scholar] [CrossRef] [Green Version]
  201. Gipson, K.S.; Nickerson, K.P.; Drenkard, E.; Llanos-Chea, A.; Dogiparthi, S.K.; Lanter, B.B.; Hibbler, R.M.; Yonker, L.M.; Hurley, B.P.; Faherty, C.S. The great ESKAPE: Exploring the crossroads of bile and antibiotic resistance in bacterial pathogens. Infect. Immun. 2020, 88, e00865-19. [Google Scholar] [CrossRef] [PubMed]
  202. Sistrunk, J.R.; Nickerson, K.P.; Chanin, R.B.; Rasko, D.A.; Faherty, C.S. Survival of the fittest: How bacterial pathogens utilize bile to enhance infection. Clin. Microbiol. Rev. 2016, 29, 819–836. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  203. Chand, D.; Panigrahi, P.; Varshney, N.; Ramasamy, S.; Suresh, C.G. Structure and function of a highly active Bile Salt Hydrolase (BSH) from Enterococcus faecalis and post-translational processing of BSH enzymes. Biochim. Biophys. Acta Proteins Proteom. 2018, 1866, 507–518. [Google Scholar] [CrossRef]
  204. Kristich, C.J.; Wells, C.L.; Dunny, G.M. A eukaryotic-type Ser/Thr kinase in Enterococcus faecalis mediates antimicrobial resistance and intestinal persistence. Proc. Natl. Acad. Sci. USA 2007, 104, 3508–3513. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  205. Kristich, C.J.; Little, J.L.; Hall, C.L.; Hoff, J.S. Reciprocal regulation of cephalosporin resistance in Enterococcus faecalis. mBio 2011, 2, e00199-11. [Google Scholar] [CrossRef] [Green Version]
  206. Solheim, M.; Aakra, A.; Vebø, H.; Snipen, L.; Nes, I.F. Transcriptional responses of Enterococcus faecalis V583 to bovine bile and sodium dodecyl sulfate. Appl. Environ. Microbiol. 2007, 73, 5767–5774. [Google Scholar] [CrossRef] [Green Version]
  207. Reen, F.J.; Flynn, S.; Woods, D.F.; Dunphy, N.; Chróinín, M.N.; Mullane, D.; Stick, S.; Adams, C.; O’Gara, F. Bile signalling promotes chronic respiratory infections and antibiotic tolerance. Sci. Rep. 2016, 6, 29768. [Google Scholar] [CrossRef] [Green Version]
  208. Koskenniemi, K.; Laakso, K.; Koponen, J.; Kankainen, M.; Greco, D.; Auvinen, P.; Savijoki, K.; Nyman, T.A.; Surakka, A.; Salusjärvi, T.; et al. Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG. Mol. Cell Proteom. 2011, 10, S1–S18. [Google Scholar] [CrossRef] [Green Version]
  209. Kus, J.V.; Gebremedhin, A.; Dang, V.; Tran, S.L.; Serbanescu, A.; Barnett Foster, D. Bile salts induce resistance to polymyxin in enterohemorrhagic Escherichia coli O157:H7. J. Bacteriol. 2011, 193, 4509–4515. [Google Scholar] [CrossRef] [Green Version]
  210. Zhou, L.; Wang, L.; Tian, P.; Bao, T.; Li, L.; Zhao, X. The LiaFSR and BsrXRS systems contribute to bile salt resistance in Enterococcus faecium isolates. Front. Microbiol. 2019, 10, 1048. [Google Scholar] [CrossRef]
  211. Srinivasan, V.B.; Vaidyanathan, V.; Mondal, A.; Rajamohan, G. Role of the two component signal transduction system CpxAR in conferring cefepime and chloramphenicol resistance in Klebsiella pneumoniae NTUH-K2044. PLoS ONE 2012, 7, e33777. [Google Scholar] [CrossRef] [Green Version]
  212. Hirakawa, H.; Inazumi, Y.; Masaki, T.; Hirata, T.; Yamaguchi, A. Indole induces the expression of multidrug exporter genes in Escherichia coli. Mol. Microbiol. 2005, 55, 1113–1126. [Google Scholar] [CrossRef] [PubMed]
  213. Nikaido, E.; Giraud, E.; Baucheron, S.; Yamasaki, S.; Wiedemann, A.; Okamoto, K.; Takagi, T.; Yamaguchi, A.; Cloeckaert, A.; Nishino, K. Effects of indole on drug resistance and virulence of Salmonella enterica serovar Typhimurium revealed by genome-wide analyses. Gut Pathog. 2012, 4, 5. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  214. Nikaido, E.; Shirosaka, I.; Yamaguchi, A.; Nishino, K. Regulation of the AcrAB multidrug efflux pump in Salmonella enterica serovar Typhimurium in response to indole and paraquat. Microbiology 2011, 157, 648–655. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  215. Kawamura-Sato, K.; Shibayama, K.; Horii, T.; Iimuma, Y.; Arakawa, Y.; Ohta, M. Role of multiple efflux pumps in Escherichia coli in indole expulsion. FEMS Microbiol. Lett. 1999, 179, 345–352. [Google Scholar] [CrossRef]
  216. Poole, K. Bacterial multidrug efflux pumps serve other functions. Microbe (Am. Soc. Microbiol.) 2008, 3, 179–185. [Google Scholar] [CrossRef]
  217. Li, R.; Han, Y.; Zhou, Y.; Du, Z.; Wu, H.; Wang, J.; Chen, Y. Tigecycline susceptibility and molecular resistance mechanisms among clinical Klebsiella pneumoniae strains isolated during non-tigecycline treatment. Microb. Drug Resist. 2017, 23, 139–146. [Google Scholar] [CrossRef]
  218. Fang, L.; Chen, Q.; Shi, K.; Li, X.; Shi, Q.; He, F.; Zhou, J.; Yu, Y.; Hua, X. Step-wise increase in Tigecycline resistance in Klebsiella pneumoniae associated with mutations in ramR, lon and rpsJ. PLoS ONE 2016, 11, e0165019. [Google Scholar] [CrossRef]
  219. Hentschke, M.; Wolters, M.; Sobottka, I.; Rohde, H.; Aepfelbacher, M. ramR mutations in clinical isolates of Klebsiella pneumoniae with reduced susceptibility to tigecycline. Antimicrob. Agents Chemother. 2010, 54, 2720–2723. [Google Scholar] [CrossRef] [Green Version]
  220. Campos, C.B.; Aepfelbacher, M.; Hentschke, M. Molecular analysis of the ramRA locus in clinical Klebsiella pneumoniae isolates with reduced susceptibility to tigecycline. New Microbiol. 2017, 40, 135–138. [Google Scholar]
  221. Abouzeed, Y.M.; Baucheron, S.; Cloeckaert, A. ramR mutations involved in efflux-mediated multidrug resistance in Salmonella enterica serovar Typhimurium. Antimicrob. Agents Chemother. 2008, 52, 2428–2434. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  222. De Majumdar, S.; Veleba, M.; Finn, S.; Fanning, S.; Schneiders, T. Elucidating the regulon of multidrug resistance regulator RarA in Klebsiella pneumoniae. Antimicrob. Agents Chemother. 2013, 57, 1603–1609. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  223. Bratu, S.; Landman, D.; George, A.; Salvani, J.; Quale, J. Correlation of the expression of acrB and the regulatory genes marA, soxS and ramA with antimicrobial resistance in clinical isolates of Klebsiella pneumoniae endemic to New York City. J. Antimicrob. Chemother. 2009, 64, 278–283. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  224. Pérez, A.; Poza, M.; Aranda, J.; Latasa, C.; Medrano, F.J.; Tomás, M.; Romero, A.; Lasa, I.; Bou, G. Effect of transcriptional activators SoxS, RobA, and RamA on expression of multidrug efflux pump AcrAB-TolC in Enterobacter cloacae. Antimicrob. Agents Chemother. 2012, 56, 6256–6266. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  225. Linkevicius, M.; Sandegren, L.; Andersson, D.I. Mechanisms and fitness costs of tigecycline resistance in Escherichia coli. J. Antimicrob. Chemother. 2013, 68, 2809–2819. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  226. Ruzin, A.; Keeney, D.; Bradford, P.A. AdeABC multidrug efflux pump is associated with decreased susceptibility to tigecycline in Acinetobacter calcoaceticus-Acinetobacter baumannii complex. J. Antimicrob. Chemother. 2007, 59, 1001–1004. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  227. Nielsen, L.E.; Snesrud, E.C.; Onmus-Leone, F.; Kwak, Y.I.; Avilés, R.; Steele, E.D.; Sutter, D.E.; Waterman, P.E.; Lesho, E.P. IS5 element integration, a novel mechanism for rapid in vivo emergence of tigecycline nonsusceptibility in Klebsiella pneumoniae. Antimicrob. Agents Chemother. 2014, 58, 6151–6156. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  228. Olliver, A.; Vallé, M.; Chaslus-Dancla, E.; Cloeckaert, A. Overexpression of the multidrug efflux operon acrEF by insertional activation with IS1 or IS10 elements in Salmonella enterica serovar typhimurium DT204 acrB mutants selected with fluoroquinolones. Antimicrob. Agents Chemother. 2005, 49, 289–301. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  229. Morita, Y.; Cao, L.; Gould, V.C.; Avison, M.B.; Poole, K. nalD encodes a second repressor of the mexAB-oprM multidrug efflux operon of Pseudomonas aeruginosa. J. Bacteriol. 2006, 188, 8649–8654. [Google Scholar] [CrossRef] [Green Version]
  230. Liao, J.; Schurr, M.J.; Sauer, K. The MerR-like regulator BrlR confers biofilm tolerance by activating multidrug efflux pumps in Pseudomonas aeruginosa biofilms. J. Bacteriol. 2013, 195, 3352–3363. [Google Scholar] [CrossRef] [Green Version]
  231. Tian, Z.X.; Yi, X.X.; Cho, A.; O’Gara, F.; Wang, Y.P. CpxR activates MexAB-OprM efflux pump expression and enhances antibiotic resistance in both laboratory and clinical nalB-type isolates of Pseudomonas aeruginosa. PLoS Pathog. 2016, 12, e1005932. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  232. Okazaki, T.; Hirai, K. Cloning and nucleotide sequence of the Pseudomonas aeruginosa nfxB gene, conferring resistance to new quinolones. FEMS Microbiol. Lett. 1992, 76, 197–202. [Google Scholar] [CrossRef] [PubMed]
  233. Köhler, T.; Epp, S.F.; Curty, L.K.; Pechère, J.C. Characterization of MexT, the regulator of the MexE-MexF-OprN multidrug efflux system of Pseudomonas aeruginosa. J. Bacteriol. 1999, 181, 6300–6305. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  234. Ma, Z.; Xu, C.; Zhang, X.; Wang, D.; Pan, X.; Liu, H.; Zhu, G.; Bai, F.; Cheng, Z.; Wu, W.; et al. A MexR mutation which confers aztreonam resistance to Pseudomonas aeruginosa. Front. Microbiol. 2021, 12, 659808. [Google Scholar] [CrossRef] [PubMed]
  235. Braz, V.S.; Furlan, J.P.; Fernandes, A.F.; Stehling, E.G. Mutations in NalC induce MexAB-OprM overexpression resulting in high level of aztreonam resistance in environmental isolates of Pseudomonas aeruginosa. FEMS Microbiol. Lett. 2016, 363, fnw166. [Google Scholar] [CrossRef] [Green Version]
  236. Suresh, M.; Nithya, N.; Jayasree, P.R.; Vimal, K.P.; Manish Kumar, P.R. Mutational analyses of regulatory genes, mexR, nalC, nalD and mexZ of mexAB-oprM and mexXY operons, in efflux pump hyperexpressing multidrug-resistant clinical isolates of Pseudomonas aeruginosa. World J. Microbiol. Biotechnol. 2018, 34, 83. [Google Scholar] [CrossRef]
  237. Aendekerk, S.; Diggle, S.P.; Song, Z.; Høiby, N.; Cornelis, P.; Williams, P.; Cámara, M. The MexGHI-OpmD multidrug efflux pump controls growth, antibiotic susceptibility and virulence in Pseudomonas aeruginosa via 4-quinolone-dependent cell-to-cell communication. Microbiology 2005, 151, 1113–1125. [Google Scholar] [CrossRef] [Green Version]
  238. Sakhtah, H.; Koyama, L.; Zhang, Y.; Morales, D.K.; Fields, B.L.; Price-Whelan, A.; Hogan, D.A.; Shepard, K.; Dietrich, L.E. The Pseudomonas aeruginosa efflux pump MexGHI-OpmD transports a natural phenazine that controls gene expression and biofilm development. Proc. Natl. Acad. Sci. USA 2016, 113, E3538–E3547. [Google Scholar] [CrossRef] [Green Version]
  239. Dietrich, L.E.; Price-Whelan, A.; Petersen, A.; Whiteley, M.; Newman, D.K. The phenazine pyocyanin is a terminal signalling factor in the quorum sensing network of Pseudomonas aeruginosa. Mol. Microbiol. 2006, 61, 1308–1321. [Google Scholar] [CrossRef]
  240. Duval, V.; Lister, I.M. MarA, SoxS and Rob of Escherichia coli—Global regulators of multidrug resistance, virulence and stress response. Int. J. Biotechnol. Wellness Ind. 2013, 2, 101–124. [Google Scholar] [CrossRef] [Green Version]
  241. Jiménez-Castellanos, J.C.; Wan Ahmad Kamil, W.N.; Cheung, C.H.; Tobin, M.S.; Brown, J.; Isaac, S.G.; Heesom, K.J.; Schneiders, T.; Avison, M.B. Comparative effects of overproducing the AraC-type transcriptional regulators MarA, SoxS, RarA and RamA on antimicrobial drug susceptibility in Klebsiella pneumoniae. J. Antimicrob. Chemother. 2016, 71, 1820–1825. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  242. Rahmati, S.; Yang, S.; Davidson, A.L.; Zechiedrich, E.L. Control of the AcrAB multidrug efflux pump by quorum-sensing regulator SdiA. Mol. Microbiol. 2002, 43, 677–685. [Google Scholar] [CrossRef] [PubMed]
  243. Li, M.; Gu, R.; Su, C.C.; Routh, M.D.; Harris, K.C.; Jewell, E.S.; McDermott, G.; Yu, E.W. Crystal structure of the transcriptional regulator AcrR from Escherichia coli. J. Mol. Biol. 2007, 374, 591–603. [Google Scholar] [CrossRef] [PubMed]
  244. Rosenberg, E.Y.; Bertenthal, D.; Nilles, M.L.; Bertrand, K.P.; Nikaido, H. Bile salts and fatty acids induce the expression of Escherichia coli AcrAB multidrug efflux pump through their interaction with Rob regulatory protein. Mol. Microbiol. 2003, 48, 1609–1619. [Google Scholar] [CrossRef]
  245. Prajapat, M.K.; Jain, K.; Saini, S. Control of MarRAB operon in Escherichia coli via autoactivation and autorepression. Biophys. J. 2015, 109, 1497–1508. [Google Scholar] [CrossRef] [Green Version]
  246. Vinué, L.; McMurry, L.M.; Levy, S.B. The 216-bp marB gene of the marRAB operon in Escherichia coli encodes a periplasmic protein which reduces the transcription rate of marA. FEMS Microbiol. Lett. 2013, 345, 49–55. [Google Scholar] [CrossRef] [Green Version]
  247. Sulavik, M.C.; Gambino, L.F.; Miller, P.F. The MarR repressor of the multiple antibiotic resistance (mar) operon in Escherichia coli: Prototypic member of a family of bacterial regulatory proteins involved in sensing phenolic compounds. Mol. Med. 1995, 1, 436–446. [Google Scholar] [CrossRef] [Green Version]
  248. Randall, L.P.; Woodward, M.J. The multiple antibiotic resistance (mar) locus and its significance. Res. Vet. Sci. 2002, 72, 87–93. [Google Scholar] [CrossRef]
  249. Li, W.; Xue, M.; Yu, L.; Qi, K.; Ni, J.; Chen, X.; Deng, R.; Shang, F.; Xue, T. QseBC is involved in the biofilm formation and antibiotic resistance in Escherichia coli isolated from bovine mastitis. PeerJ 2020, 8, e8833. [Google Scholar] [CrossRef] [Green Version]
  250. Chubiz, L.M.; Rao, C.V. Role of the mar-sox-rob regulon in regulating outer membrane porin expression. J. Bacteriol. 2011, 193, 2252–2260. [Google Scholar] [CrossRef] [Green Version]
  251. Veleba, M.; Higgins, P.G.; Gonzalez, G.; Seifert, H.; Schneiders, T. Characterization of RarA, a novel AraC family multidrug resistance regulator in Klebsiella pneumoniae. Antimicrob. Agents Chemother. 2012, 56, 4450–4458. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  252. Touati, D. Sensing and protecting against superoxide stress in Escherichia coli-how many ways are there to trigger soxRS response? Redox Rep. 2000, 5, 287–293. [Google Scholar] [CrossRef] [PubMed]
  253. Nunoshiba, T.; Hidalgo, E.; Amábile Cuevas, C.F.; Demple, B. Two-stage control of an oxidative stress regulon: The Escherichia coli SoxR protein triggers redox-inducible expression of the soxS regulatory gene. J. Bacteriol. 1992, 174, 6054–6060. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  254. Zheng, M.; Aslund, F.; Storz, G. Activation of the OxyR transcription factor by reversible disulfide bond formation. Science 1998, 279, 1718–1721. [Google Scholar] [CrossRef]
  255. Anes, J.; Dever, K.; Eshwar, A.; Nguyen, S.; Cao, Y.; Sivasankaran, S.K.; Sakalauskaitė, S.; Lehner, A.; Devineau, S.; Daugelavičius, R.; et al. Analysis of the oxidative stress regulon identifies soxS as a genetic target for resistance reversal in multidrug-resistant Klebsiella pneumoniae. mBio 2021, 12, e0086721. [Google Scholar] [CrossRef] [PubMed]
  256. Bhaskar, B.V.; Babu, T.M.; Reddy, N.V.; Rajendra, W. Homology modeling, molecular dynamics, and virtual screening of NorA efflux pump inhibitors of Staphylococcus aureus. Drug Des. Devel. Ther. 2016, 10, 3237–3252. [Google Scholar] [CrossRef] [Green Version]
  257. Costa, S.S.; Sobkowiak, B.; Parreira, R.; Edgeworth, J.D.; Viveiros, M.; Clark, T.G.; Couto, I. Genetic diversity of norA, coding for a main efflux pump of Staphylococcus aureus. Front. Genet. 2018, 9, 710. [Google Scholar] [CrossRef]
  258. Villet, R.A.; Truong-Bolduc, Q.C.; Wang, Y.; Estabrooks, Z.; Medeiros, H.; Hooper, D.C. Regulation of expression of abcA and its response to environmental conditions. J. Bacteriol. 2014, 196, 1532–1539. [Google Scholar] [CrossRef] [Green Version]
  259. Truong-Bolduc, Q.C.; Hooper, D.C. The transcriptional regulators NorG and MgrA modulate resistance to both quinolones and beta-lactams in Staphylococcus aureus. J. Bacteriol. 2007, 189, 2996–3005. [Google Scholar] [CrossRef] [Green Version]
  260. Schrader-Fischer, G.; Berger-Bächi, B. The AbcA transporter of Staphylococcus aureus affects cell autolysis. Antimicrob. Agents Chemother. 2001, 45, 407–412. [Google Scholar] [CrossRef] [Green Version]
  261. Cheung, G.Y.; Duong, A.C.; Otto, M. Direct and synergistic hemolysis caused by Staphylococcus phenol-soluble modulins: Implications for diagnosis and pathogenesis. Microbes Infect. 2012, 14, 380–386. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  262. Li, S.; Huang, H.; Rao, X.; Chen, W.; Wang, Z.; Hu, X. Phenol-soluble modulins: Novel virulence-associated peptides of Staphylococci. Future Microbiol. 2014, 9, 203–216. [Google Scholar] [CrossRef] [PubMed]
  263. Liu, J.; Yang, L.; Hou, Y.; Soteyome, T.; Zeng, B.; Su, J.; Li, L.; Li, B.; Chen, D.; Li, Y.; et al. Transcriptomics study on Staphylococcus aureus Biofilm under low concentration of ampicillin. Front. Microbiol. 2018, 9, 2413. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  264. Lin, J.; Zhou, D.; Steitz, T.A.; Polikanov, Y.S.; Gagnon, M.G. Ribosome-targeting antibiotics: Modes of action, mechanisms of resistance, and implications for drug design. Annu. Rev. Biochem. 2018, 87, 451–478. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  265. Carvalho, A.; Mazel, D.; Baharoglu, Z. Deficiency in cytosine DNA methylation leads to high chaperonin expression and tolerance to aminoglycosides in Vibrio cholerae. PLoS Genet. 2021, 17, e1009748. [Google Scholar] [CrossRef]
  266. Murina, V.; Kasari, M.; Takada, H.; Hinnu, M.; Saha, C.K.; Grimshaw, J.W.; Seki, T.; Reith, M.; Putrinš, M.; Tenson, T.; et al. ABCF ATPases involved in protein synthesis, ribosome assembly and antibiotic resistance: Structural and functional diversification across the tree of life. J. Mol. Biol. 2019, 431, 3568–3590. [Google Scholar] [CrossRef]
  267. Fostier, C.R.; Monlezun, L.; Ousalem, F.; Singh, S.; Hunt, J.F.; Boël, G. ABC-F translation factors: From antibiotic resistance to immune response. FEBS Lett. 2021, 595, 675–706. [Google Scholar] [CrossRef]
  268. Murina, V.; Kasari, M.; Hauryliuk, V.; Atkinson, G.C. Antibiotic resistance ABCF proteins reset the peptidyl transferase centre of the ribosome to counter translational arrest. Nucleic Acids Res. 2018, 46, 3753–3763. [Google Scholar] [CrossRef]
  269. Sharkey, L.K.R.; O’Neill, A.J. Antibiotic resistance ABC-F proteins: Bringing target protection into the limelight. ACS Infect. Dis. 2018, 4, 239–246. [Google Scholar] [CrossRef]
  270. Eyraud, A.; Tattevin, P.; Chabelskaya, S.; Felden, B. A small RNA controls a protein regulator involved in antibiotic resistance in Staphylococcus aureus. Nucleic Acids Res. 2014, 42, 4892–4905. [Google Scholar] [CrossRef]
  271. Zhao, X.; Liu, R.; Tang, H.; Osei-Adjei, G.; Xu, S.; Zhang, Y.; Huang, X. A 3′ UTR-derived non-coding RNA RibS increases expression of cfa and promotes biofilm formation of Salmonella enterica serovar Typhi. Res. Microbiol. 2018, 169, 279–288. [Google Scholar] [CrossRef] [PubMed]
  272. Yin, L.; Zhu, W.; Chen, D.; Zhou, Y.; Lin, H. Small noncoding RNA sRNA0426 is involved in regulating biofilm formation in Streptococcus mutans. Microbiologyopen 2020, 9, e1096. [Google Scholar] [CrossRef] [PubMed]
  273. Liu, Z.; Gao, X.; Wang, H.; Fang, H.; Yan, Y.; Liu, L.; Chen, R.; Zhou, D.; Yang, R.; Han, Y. Plasmid pPCP1-derived sRNA HmsA promotes biofilm formation of Yersinia pestis. BMC Microbiol. 2016, 16, 176. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  274. Papenfort, K.; Förstner, K.U.; Cong, J.P.; Sharma, C.M.; Bassler, B.L. Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation. Proc. Natl. Acad. Sci. USA 2015, 112, E766–E775. [Google Scholar] [CrossRef] [Green Version]
  275. Bordeau, V.; Felden, B. Curli synthesis and biofilm formation in enteric bacteria are controlled by a dynamic small RNA module made up of a pseudoknot assisted by an RNA chaperone. Nucleic Acids Res. 2014, 42, 4682–4696. [Google Scholar] [CrossRef] [Green Version]
  276. Jørgensen, M.G.; Thomason, M.K.; Havelund, J.; Valentin-Hansen, P.; Storz, G. Dual function of the McaS small RNA in controlling biofilm formation. Genes Dev. 2013, 27, 1132–1145. [Google Scholar] [CrossRef] [Green Version]
  277. Mann, B.; van Opijnen, T.; Wang, J.; Obert, C.; Wang, Y.D.; Carter, R.; McGoldrick, D.J.; Ridout, G.; Camilli, A.; Tuomanen, E.I.; et al. Control of virulence by small RNAs in Streptococcus pneumoniae. PLoS Pathog. 2012, 8, e1002788. [Google Scholar] [CrossRef]
  278. Danger, J.L.; Cao, T.N.; Cao, T.H.; Sarkar, P.; Treviño, J.; Pflughoeft, K.J.; Sumby, P. The small regulatory RNA FasX enhances group A Streptococcus virulence and inhibits pilus expression via serotype-specific targets. Mol. Microbiol. 2015, 96, 249–262. [Google Scholar] [CrossRef] [Green Version]
  279. Reinhart, A.A.; Powell, D.A.; Nguyen, A.T.; O’Neill, M.; Djapgne, L.; Wilks, A.; Ernst, R.K.; Oglesby-Sherrouse, A.G. The prrF-encoded small regulatory RNAs are required for iron homeostasis and virulence of Pseudomonas aeruginosa. Infect. Immun. 2015, 83, 863–875. [Google Scholar] [CrossRef] [Green Version]
  280. Michaux, C.; Hartke, A.; Martini, C.; Reiss, S.; Albrecht, D.; Budin-Verneuil, A.; Sanguinetti, M.; Engelmann, S.; Hain, T.; Verneuil, N.; et al. Involvement of Enterococcus faecalis small RNAs in stress response and virulence. Infect. Immun. 2014, 82, 3599–3611. [Google Scholar] [CrossRef] [Green Version]
  281. Koo, J.T.; Alleyne, T.M.; Schiano, C.A.; Jafari, N.; Lathem, W.W. Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia-specific small, noncoding RNAs required for virulence. Proc. Natl. Acad. Sci. USA 2011, 108, E709–E717. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  282. Chao, Y.; Vogel, J. A 3′ UTR-derived small RNA provides the regulatory noncoding arm of the inner membrane stress response. Mol. Cell 2016, 61, 352–363. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  283. Vogt, S.L.; Evans, A.D.; Guest, R.L.; Raivio, T.L. The Cpx envelope stress response regulates and is regulated by small noncoding RNAs. J. Bacteriol. 2014, 196, 4229–4238. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  284. Guo, M.S.; Updegrove, T.B.; Gogol, E.B.; Shabalina, S.A.; Gross, C.A.; Storz, G. MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein. Genes Dev. 2014, 28, 1620–1634. [Google Scholar] [CrossRef] [Green Version]
  285. Zhang, H.; Song, T.; Qin, C.; Xu, H.; Qiao, M. A novel non-coding RNA CsiR regulates the ciprofloxacin resistance in Proteus vulgaris by interacting with emrB mRNA. Int. J. Mol. Sci. 2021, 22, 10627. [Google Scholar] [CrossRef]
  286. Arenz, S.; Meydan, S.; Starosta, A.L.; Berninghausen, O.; Beckmann, R.; Vázquez-Laslop, N.; Wilson, D.N. Drug sensing by the ribosome induces translational arrest via active site perturbation. Mol. Cell 2014, 56, 446–452. [Google Scholar] [CrossRef] [Green Version]
  287. Schulthess, B.; Meier, S.; Homerova, D.; Goerke, C.; Wolz, C.; Kormanec, J.; Berger-Bächi, B.; Bischoff, M. Functional characterization of the sigmaB-dependent yabJ-spoVG operon in Staphylococcus aureus: Role in methicillin and glycopeptide resistance. Antimicrob. Agents Chemother. 2009, 53, 1832–1839. [Google Scholar] [CrossRef] [Green Version]
  288. Liu, X.; Zhang, S.; Sun, B. SpoVG regulates cell wall metabolism and oxacillin resistance in methicillin-resistant Staphylococcus aureus strain N315. Antimicrob. Agents Chemother. 2016, 60, 3455–3461. [Google Scholar] [CrossRef] [Green Version]
  289. Groicher, K.H.; Firek, B.A.; Fujimoto, D.F.; Bayles, K.W. The Staphylococcus aureus lrgAB operon modulates murein hydrolase activity and penicillin tolerance. J. Bacteriol. 2000, 182, 1794–1801. [Google Scholar] [CrossRef] [Green Version]
  290. Mukherjee, S.; Bassler, B.L. Bacterial quorum sensing in complex and dynamically changing environments. Nat. Rev. Microbiol. 2019, 17, 371–382. [Google Scholar] [CrossRef]
  291. Shih, P.C.; Huang, C.T. Effects of quorum-sensing deficiency on Pseudomonas aeruginosa biofilm formation and antibiotic resistance. J. Antimicrob. Chemother. 2002, 49, 309–314. [Google Scholar] [CrossRef] [PubMed]
  292. Saipriya, K.; Swathi, C.H.; Ratnakar, K.S.; Sritharan, V. Quorum-sensing system in Acinetobacter baumannii: A potential target for new drug development. J. Appl. Microbiol. 2020, 128, 15–27. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  293. Ahmed, U.K.B.; Ballard, J.D. Autoinducing peptide-based quorum signaling systems in Clostridioides difficile. Curr. Opin. Microbiol. 2021, 65, 81–86. [Google Scholar] [CrossRef] [PubMed]
  294. Ishii, E.; Eguchi, Y. Diversity in sensing and signaling of bacterial sensor histidine kinases. Biomolecules 2021, 11, 1524. [Google Scholar] [CrossRef] [PubMed]
  295. Chadha, J.; Harjai, K.; Chhibber, S. Revisiting the virulence hallmarks of Pseudomonas aeruginosa: A chronicle through the perspective of quorum sensing. Environ. Microbiol. 2021, in press. [Google Scholar] [CrossRef]
  296. Lee, J.; Zhang, L. The hierarchy quorum sensing network in Pseudomonas aeruginosa. Protein Cell 2015, 6, 26–41. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  297. Hassett, D.J.; Ma, J.F.; Elkins, J.G.; McDermott, T.R.; Ochsner, U.A.; West, S.E.; Huang, C.T.; Fredericks, J.; Burnett, S.; Stewart, P.S.; et al. Quorum sensing in Pseudomonas aeruginosa controls expression of catalase and superoxide dismutase genes and mediates biofilm susceptibility to hydrogen peroxide. Mol. Microbiol. 1999, 34, 1082–1093. [Google Scholar] [CrossRef] [PubMed]
  298. Wu, S.; Xu, C.; Liu, J.; Liu, C.; Qiao, J. Vertical and horizontal quorum-sensing-based multicellular communications. Trends Microbiol. 2021, 29, 1130–1142. [Google Scholar] [CrossRef] [PubMed]
  299. Svenningsen, S.L. Small RNA-based regulation of bacterial quorum sensing and biofilm formation. Microbiol. Spectr. 2018, 6, RWR-0017-2018. [Google Scholar] [CrossRef] [PubMed]
  300. Rajput, A.; Seif, Y.; Choudhary, K.S.; Dalldorf, C.; Poudel, S.; Monk, J.M.; Palsson, B.O. Pangenome analytics reveal two-component systems as conserved targets in ESKAPEE pathogens. mSystems 2021, 6, e00981-20. [Google Scholar] [CrossRef] [PubMed]
  301. Mikkelsen, H.; Sivaneson, M.; Filloux, A. Key two-component regulatory systems that control biofilm formation in Pseudomonas aeruginosa. Environ. Microbiol. 2011, 13, 1666–1681. [Google Scholar] [CrossRef] [PubMed]
  302. Tierney, A.R.; Rather, P.N. Roles of two-component regulatory systems in antibiotic resistance. Future Microbiol. 2019, 14, 533–552. [Google Scholar] [CrossRef]
  303. Gooderham, W.J.; Hancock, R.E. Regulation of virulence and antibiotic resistance by two-component regulatory systems in Pseudomonas aeruginosa. FEMS Microbiol. Rev. 2009, 33, 279–294. [Google Scholar] [CrossRef] [Green Version]
  304. Balasubramanian, D.; Schneper, L.; Kumari, H.; Mathee, K. A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence. Nucleic Acids Res. 2013, 41, 1–20. [Google Scholar] [CrossRef]
  305. Rodrigue, A.; Quentin, Y.; Lazdunski, A.; Méjean, V.; Foglino, M. Two-component systems in Pseudomonas aeruginosa: Why so many? Trends Microbiol. 2000, 8, 498–504. [Google Scholar] [CrossRef]
  306. Mizuno, T. Compilation of all genes encoding two-component phosphotransfer signal transducers in the genome of Escherichia coli. DNA Res. 1997, 4, 161–168. [Google Scholar] [CrossRef] [Green Version]
  307. Fabret, C.; Feher, V.A.; Hoch, J.A. Two-component signal transduction in Bacillus subtilis: How one organism sees its world. J. Bacteriol. 1999, 181, 1975–1983. [Google Scholar] [CrossRef] [Green Version]
  308. Haag, A.F.; Bagnoli, F. The role of two-component signal transduction systems in Staphylococcus aureus virulence regulation. Curr. Top. Microbiol. Immunol. 2017, 409, 145–198. [Google Scholar] [CrossRef]
  309. Kuroda, M.; Ohta, T.; Uchiyama, I.; Baba, T.; Yuzawa, H.; Kobayashi, I.; Cui, L.; Oguchi, A.; Aoki, K.; Nagai, Y.; et al. Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet 2001, 357, 1225–1240. [Google Scholar] [CrossRef]
  310. Bleul, L.; Francois, P.; Wolz, C. Two-component systems of S. aureus: Signaling and sensing mechanisms. Genes 2021, 13, 34. [Google Scholar] [CrossRef]
  311. Wu, S.; Lin, K.; Liu, Y.; Zhang, H.; Lei, L. Two-component signaling pathways modulate drug resistance of Staphylococcus aureus (Review). Biomed. Rep. 2020, 13, 5. [Google Scholar] [CrossRef]
  312. Ortet, P.; Whitworth, D.E.; Santaella, C.; Achouak, W.; Barakat, M. P2CS: Updates of the prokaryotic two-component systems database. Nucleic Acids Res. 2015, 43, D536–D541. [Google Scholar] [CrossRef] [Green Version]
  313. De Silva, P.M.; Kumar, A. Signal transduction proteins in Acinetobacter baumannii: Role in antibiotic resistance, virulence, and potential as drug targets. Front. Microbiol. 2019, 10, 49. [Google Scholar] [CrossRef] [Green Version]
  314. Waters, C.M.; Bassler, B.L. Quorum sensing: Cell-to-cell communication in bacteria. Annu. Rev. Cell Dev. Biol. 2005, 21, 319–346. [Google Scholar] [CrossRef] [Green Version]
  315. Li, Z.; Nair, S.K. Quorum sensing: How bacteria can coordinate activity and synchronize their response to external signals? Protein Sci. 2012, 21, 1403–1417. [Google Scholar] [CrossRef]
  316. Mull, R.W.; Harrington, A.; Sanchez, L.A.; Tal-Gan, Y. Cyclic peptides that govern signal transduction pathways: From prokaryotes to multi-cellular organisms. Curr. Top. Med. Chem. 2018, 18, 625–644. [Google Scholar] [CrossRef]
  317. Hense, B.A.; Schuster, M. Core principles of bacterial autoinducer systems. Microbiol. Mol. Biol. Rev. 2015, 79, 153–169. [Google Scholar] [CrossRef] [Green Version]
  318. Eickhoff, M.J.; Bassler, B.L. SnapShot: Bacterial quorum sensing. Cell 2018, 174, 1328–1328.e1. [Google Scholar] [CrossRef]
  319. Kaplan, H.B.; Greenberg, E.P. Diffusion of autoinducer is involved in regulation of the Vibrio fischeri luminescence system. J. Bacteriol. 1985, 163, 1210–1214. [Google Scholar] [CrossRef] [Green Version]
  320. Pearson, J.P.; Van Delden, C.; Iglewski, B.H. Active efflux and diffusion are involved in transport of Pseudomonas aeruginosa cell-to-cell signals. J. Bacteriol. 1999, 181, 1203–1210. [Google Scholar] [CrossRef] [Green Version]
  321. Mashburn, L.M.; Whiteley, M. Membrane vesicles traffic signals and facilitate group activities in a prokaryote. Nature 2005, 437, 422–425. [Google Scholar] [CrossRef]
  322. Evans, K.; Passador, L.; Srikumar, R.; Tsang, E.; Nezezon, J.; Poole, K. Influence of the MexAB-OprM multidrug efflux system on quorum sensing in Pseudomonas aeruginosa. J. Bacteriol. 1998, 180, 5443–5447. [Google Scholar] [CrossRef] [Green Version]
  323. Minagawa, S.; Inami, H.; Kato, T.; Sawada, S.; Yasuki, T.; Miyairi, S.; Horikawa, M.; Okuda, J.; Gotoh, N. RND type efflux pump system MexAB-OprM of Pseudomonas aeruginosa selects bacterial languages, 3-oxo-acyl-homoserine lactones, for cell-to-cell communication. BMC Microbiol. 2012, 12, 70. [Google Scholar] [CrossRef] [Green Version]
  324. Köhler, T.; van Delden, C.; Curty, L.K.; Hamzehpour, M.M.; Pechere, J.C. Overexpression of the MexEF-OprN multidrug efflux system affects cell-to-cell signaling in Pseudomonas aeruginosa. J. Bacteriol. 2001, 183, 5213–5222. [Google Scholar] [CrossRef] [Green Version]
  325. Lamarche, M.G.; Déziel, E. MexEF-OprN efflux pump exports the Pseudomonas quinolone signal (PQS) precursor HHQ (4-hydroxy-2-heptylquinoline). PLoS ONE 2011, 6, e24310. [Google Scholar] [CrossRef]
  326. Hammer, B.K.; Bassler, B.L. Quorum sensing controls biofilm formation in Vibrio cholerae. Mol. Microbiol. 2003, 50, 101–104. [Google Scholar] [CrossRef]
  327. Higgins, D.A.; Pomianek, M.E.; Kraml, C.M.; Taylor, R.K.; Semmelhack, M.F.; Bassler, B.L. The major Vibrio cholerae autoinducer and its role in virulence factor production. Nature 2007, 450, 883–886. [Google Scholar] [CrossRef]
  328. Papenfort, K.; Silpe, J.E.; Schramma, K.R.; Cong, J.P.; Seyedsayamdost, M.R.; Bassler, B.L. A Vibrio cholerae autoinducer-receptor pair that controls biofilm formation. Nat. Chem. Biol. 2017, 13, 551–557. [Google Scholar] [CrossRef] [Green Version]
  329. Chen, X.; Schauder, S.; Potier, N.; Van Dorsselaer, A.; Pelczer, I.; Bassler, B.L.; Hughson, F.M. Structural identification of a bacterial quorum-sensing signal containing boron. Nature 2002, 415, 545–549. [Google Scholar] [CrossRef]
  330. Surette, M.G.; Miller, M.B.; Bassler, B.L. Quorum sensing in Escherichia coli, Salmonella typhimurium, and Vibrio harveyi: A new family of genes responsible for autoinducer production. Proc. Natl. Acad. Sci. USA 1999, 96, 1639–1644. [Google Scholar] [CrossRef] [Green Version]
  331. Rutherford, S.T.; Bassler, B.L. Bacterial quorum sensing: Its role in virulence and possibilities for its control. Cold Spring Harb. Perspect. Med. 2012, 2, a012427. [Google Scholar] [CrossRef]
  332. Lenz, D.H.; Mok, K.C.; Lilley, B.N.; Kulkarni, R.V.; Wingreen, N.S.; Bassler, B.L. The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell 2004, 118, 69–82. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  333. Rutherford, S.T.; van Kessel, J.C.; Shao, Y.; Bassler, B.L. AphA and LuxR/HapR reciprocally control quorum sensing in Vibrios. Genes Dev. 2011, 25, 397–408. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  334. Yang, M.; Frey, E.M.; Liu, Z.; Bishar, R.; Zhu, J. The virulence transcriptional activator AphA enhances biofilm formation by Vibrio cholerae by activating expression of the biofilm regulator VpsT. Infect. Immun. 2010, 78, 697–703. [Google Scholar] [CrossRef] [Green Version]
  335. Waters, C.M.; Lu, W.; Rabinowitz, J.D.; Bassler, B.L. Quorum sensing controls biofilm formation in Vibrio cholerae through modulation of cyclic di-GMP levels and repression of vpsT. J. Bacteriol. 2008, 190, 2527–2536. [Google Scholar] [CrossRef] [Green Version]
  336. Zhu, J.; Mekalanos, J.J. Quorum sensing-dependent biofilms enhance colonization in Vibrio cholerae. Dev. Cell 2003, 5, 647–656. [Google Scholar] [CrossRef] [Green Version]
  337. Pompeani, A.J.; Irgon, J.J.; Berger, M.F.; Bulyk, M.L.; Wingreen, N.S.; Bassler, B.L. The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters. Mol. Microbiol. 2008, 70, 76–88. [Google Scholar] [CrossRef] [Green Version]
  338. Waters, C.M.; Bassler, B.L. The Vibrio harveyi quorum-sensing system uses shared regulatory components to discriminate between multiple autoinducers. Genes Dev. 2006, 20, 2754–2767. [Google Scholar] [CrossRef] [Green Version]
  339. Ng, W.L.; Bassler, B.L. Bacterial quorum-sensing network architectures. Annu. Rev. Genet. 2009, 43, 197–222. [Google Scholar] [CrossRef] [Green Version]
  340. Ball, A.S.; Chaparian, R.R.; van Kessel, J.C. Quorum sensing gene regulation by LuxR/HapR master regulators in Vibrios. J. Bacteriol. 2017, 199, e00105-17. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  341. Pereira, C.S.; Thompson, J.A.; Xavier, K.B. AI-2-mediated signalling in bacteria. FEMS Microbiol. Rev. 2013, 37, 156–181. [Google Scholar] [CrossRef] [Green Version]
  342. Moslehi-Jenabian, S.; Gori, K.; Jespersen, L. AI-2 signalling is induced by acidic shock in probiotic strains of Lactobacillus spp. Int. J. Food Microbiol. 2009, 135, 295–302. [Google Scholar] [CrossRef]
  343. Schauder, S.; Shokat, K.; Surette, M.G.; Bassler, B.L. The LuxS family of bacterial autoinducers: Biosynthesis of a novel quorum-sensing signal molecule. Mol. Microbiol. 2001, 41, 463–476. [Google Scholar] [CrossRef]
  344. Niazy, A.A. LuxS quorum sensing system and biofilm formation of oral microflora: A short review article. Saudi Dent. J. 2021, 33, 116–123. [Google Scholar] [CrossRef]
  345. Wang, Y.; Liu, B.; Grenier, D.; Yi, L. Regulatory mechanisms of the LuxS/AI-2 system and bacterial resistance. Antimicrob. Agents Chemother. 2019, 63, e01186-19. [Google Scholar] [CrossRef] [Green Version]
  346. Yao, Y.; Martinez-Yamout, M.A.; Dickerson, T.J.; Brogan, A.P.; Wright, P.E.; Dyson, H.J. Structure of the Escherichia coli quorum sensing protein SdiA: Activation of the folding switch by acyl homoserine lactones. J Mol. Biol. 2006, 355, 262–273. [Google Scholar] [CrossRef]
  347. Styles, M.J.; Blackwell, H.E. Non-native autoinducer analogs capable of modulating the SdiA quorum sensing receptor in Salmonella enterica serovar Typhi.imurium. Beilstein J. Org. Chem. 2018, 14, 2651–2664. [Google Scholar] [CrossRef] [Green Version]
  348. Zhang, L.; Li, S.; Liu, X.; Wang, Z.; Jiang, M.; Wang, R.; Xie, L.; Liu, Q.; Xie, X.; Shang, D.; et al. Sensing of autoinducer-2 by functionally distinct receptors in prokaryotes. Nat. Commun. 2020, 11, 5371. [Google Scholar] [CrossRef]
  349. Li, J.; Attila, C.; Wang, L.; Wood, T.K.; Valdes, J.J.; Bentley, W.E. Quorum sensing in Escherichia coli is signaled by AI-2/LsrR: Effects on small RNA and biofilm architecture. J. Bacteriol. 2007, 189, 6011–6020. [Google Scholar] [CrossRef] [Green Version]
  350. Xavier, K.B.; Bassler, B.L. Regulation of uptake and processing of the quorum-sensing autoinducer AI-2 in Escherichia coli. J. Bacteriol. 2005, 187, 238–248. [Google Scholar] [CrossRef] [Green Version]
  351. Ilangovan, A.; Fletcher, M.; Rampioni, G.; Pustelny, C.; Rumbaugh, K.; Heeb, S.; Cámara, M.; Truman, A.; Chhabra, S.R.; Emsley, J.; et al. Structural basis for native agonist and synthetic inhibitor recognition by the Pseudomonas aeruginosa quorum sensing regulator PqsR (MvfR). PLoS Pathog. 2013, 9, e1003508. [Google Scholar] [CrossRef] [Green Version]
  352. Lee, J.; Wu, J.; Deng, Y.; Wang, J.; Wang, C.; Wang, J.; Chang, C.; Dong, Y.; Williams, P.; Zhang, L.H. A cell-cell communication signal integrates quorum sensing and stress response. Nat. Chem. Biol. 2013, 9, 339–343. [Google Scholar] [CrossRef]
  353. Passos da Silva, D.; Schofield, M.C.; Parsek, M.R.; Tseng, B.S. An update on the sociomicrobiology of quorum sensing in gram-negative biofilm development. Pathogens 2017, 6, 51. [Google Scholar] [CrossRef]
  354. Williams, P.; Cámara, M. Quorum sensing and environmental adaptation in Pseudomonas aeruginosa: A tale of regulatory networks and multifunctional signal molecules. Curr. Opin. Microbiol. 2009, 12, 182–191. [Google Scholar] [CrossRef]
  355. Schuster, M.; Greenberg, E.P. A network of networks: Quorum-sensing gene regulation in Pseudomonas aeruginosa. Int. J. Med. Microbiol. 2006, 296, 73–81. [Google Scholar] [CrossRef]
  356. Huang, H.; Shao, X.; Xie, Y.; Wang, T.; Zhang, Y.; Wang, X.; Deng, X. An integrated genomic regulatory network of virulence-related transcriptional factors in Pseudomonas aeruginosa. Nat. Commun. 2019, 10, 2931. [Google Scholar] [CrossRef] [Green Version]
  357. Brint, J.M.; Ohman, D.E. Synthesis of multiple exoproducts in Pseudomonas aeruginosa is under the control of RhlR-RhlI, another set of regulators in strain PAO1 with homology to the autoinducer-responsive LuxR-LuxI family. J. Bacteriol. 1995, 177, 7155–7163. [Google Scholar] [CrossRef] [Green Version]
  358. McGrath, S.; Wade, D.S.; Pesci, E.C. Dueling quorum sensing systems in Pseudomonas aeruginosa control the production of the Pseudomonas quinolone signal (PQS). FEMS Microbiol. Lett. 2004, 230, 27–34. [Google Scholar] [CrossRef]
  359. Sultan, M.; Arya, R.; Kim, K.K. Roles of two-component systems in Pseudomonas aeruginosa virulence. Int. J. Mol. Sci. 2021, 22, 12152. [Google Scholar] [CrossRef]
  360. Rampioni, G.; Falcone, M.; Heeb, S.; Frangipani, E.; Fletcher, M.P.; Dubern, J.F.; Visca, P.; Leoni, L.; Cámara, M.; Williams, P. Unravelling the genome-wide contributions of specific 2-Alkyl-4-Quinolones and PqsE to quorum sensing in Pseudomonas aeruginosa. PLoS Pathog. 2016, 12, e1006029. [Google Scholar] [CrossRef]
  361. García-Reyes, S.; Soberón-Chávez, G.; Cocotl-Yanez, M. The third quorum-sensing system of Pseudomonas aeruginosa: Pseudomonas quinolone signal and the enigmatic PqsE protein. J. Med. Microbiol. 2020, 69, 25–34. [Google Scholar] [CrossRef]
  362. Li, S.; Chen, S.; Fan, J.; Cao, Z.; Ouyang, W.; Tong, N.; Hu, X.; Hu, J.; Li, P.; Feng, Z.; et al. Anti-biofilm effect of novel thiazole acid analogs against Pseudomonas aeruginosa through IQS pathways. Eur. J. Med. Chem. 2018, 145, 64–73. [Google Scholar] [CrossRef]
  363. Balasubramanian, D.; Kong, K.F.; Jayawardena, S.R.; Leal, S.M.; Sautter, R.T.; Mathee, K. Co-regulation of b-lactam resistance, alginate production and quorum sensing in Pseudomonas aeruginosa. J. Med. Microbiol. 2011, 60, 147–156. [Google Scholar] [CrossRef] [Green Version]
  364. Kong, K.F.; Jayawardena, S.R.; Indulkar, S.D.; Del Puerto, A.; Koh, C.L.; Høiby, N.; Mathee, K. Pseudomonas aeruginosa AmpR is a global transcriptional factor that regulates expression of AmpC and PoxB beta-lactamases, proteases, quorum sensing, and other virulence factors. Antimicrob. Agents Chemother. 2005, 49, 4567–4575. [Google Scholar] [CrossRef] [Green Version]
  365. Balasubramanian, D.; Schneper, L.; Merighi, M.; Smith, R.; Narasimhan, G.; Lory, S.; Mathee, K. The regulatory repertoire of Pseudomonas aeruginosa AmpC b-lactamase regulator AmpR includes virulence genes. PLoS ONE 2012, 7, e34067. [Google Scholar] [CrossRef] [Green Version]
  366. George, E.A.; Novick, R.P.; Muir, T.W. Cyclic peptide inhibitors of staphylococcal virulence prepared by Fmoc-based thiolactone peptide synthesis. J. Am. Chem. Soc. 2008, 130, 4914–4924. [Google Scholar] [CrossRef]
  367. Liu, Q.; Yeo, W.S.; Bae, T. The SaeRS two-component system of Staphylococcus aureus. Genes 2016, 7, 81. [Google Scholar] [CrossRef] [Green Version]
  368. Liang, X.; Zheng, L.; Landwehr, C.; Lunsford, D.; Holmes, D.; Ji, Y. Global regulation of gene expression by ArlRS, a two-component signal transduction regulatory system of Staphylococcus aureus. J. Bacteriol. 2005, 187, 5486–5492. [Google Scholar] [CrossRef] [Green Version]
  369. Ramirez, A.M.; Beenken, K.E.; Byrum, S.D.; Tackett, A.J.; Shaw, L.N.; Gimza, B.D.; Smeltzer, M.S. SarA plays a predominant role in controlling the production of extracellular proteases in the diverse clinical isolates of Staphylococcus aureus LAC and UAMS-1. Virulence 2020, 11, 1738–1762. [Google Scholar] [CrossRef]
  370. Wang, B.; Muir, T.W. Regulation of virulence in Staphylococcus aureus: Molecular mechanisms and remaining puzzles. Cell Chem. Biol. 2016, 23, 214–224. [Google Scholar] [CrossRef] [Green Version]
  371. Dufour, P.; Jarraud, S.; Vandenesch, F.; Greenland, T.; Novick, R.P.; Bes, M.; Etienne, J.; Lina, G. High genetic variability of the agr locus in Staphylococcus species. J. Bacteriol. 2002, 184, 1180–1186. [Google Scholar] [CrossRef] [Green Version]
  372. Fechter, P.; Caldelari, I.; Lioliou, E.; Romby, P. Novel aspects of RNA regulation in Staphylococcus aureus. FEBS Lett. 2014, 588, 2523–2529. [Google Scholar] [CrossRef] [Green Version]
  373. Morfeldt, E.; Taylor, D.; von Gabain, A.; Arvidson, S. Activation of alpha-toxin translation in Staphylococcus aureus by the trans-encoded antisense RNA, RNAIII. EMBO J. 1995, 14, 4569–4577. [Google Scholar] [CrossRef]
  374. Gupta, R.K.; Luong, T.T.; Lee, C.Y. RNAIII of the Staphylococcus aureus agr system activates global regulator MgrA by stabilizing mRNA. Proc. Natl. Acad. Sci. USA 2015, 112, 14036–14041. [Google Scholar] [CrossRef] [Green Version]
  375. Benito, Y.; Kolb, F.A.; Romby, P.; Lina, G.; Etienne, J.; Vandenesch, F. Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory RNA, and identification of the RNA domain involved in repression of protein A expression. Rna 2000, 6, 668–679. [Google Scholar] [CrossRef] [Green Version]
  376. Saïd-Salim, B.; Dunman, P.M.; McAleese, F.M.; Macapagal, D.; Murphy, E.; McNamara, P.J.; Arvidson, S.; Foster, T.J.; Projan, S.J.; Kreiswirth, B.N. Global regulation of Staphylococcus aureus genes by Rot. J. Bacteriol. 2003, 185, 610–619. [Google Scholar] [CrossRef] [Green Version]
  377. Reyes, D.; Andrey, D.O.; Monod, A.; Kelley, W.L.; Zhang, G.; Cheung, A.L. Coordinated regulation by AgrA, SarA, and SarR to control agr expression in Staphylococcus aureus. J. Bacteriol. 2011, 193, 6020–6031. [Google Scholar] [CrossRef] [Green Version]
  378. Liu, Y.; Gao, W.; Yang, J.; Guo, H.; Zhang, J.; Ji, Y. Contribution of coagulase and its regulator SaeRS to lethality of CA-MRSA 923 bacteremia. Pathogens 2021, 10, 1396. [Google Scholar] [CrossRef]
  379. Nygaard, T.K.; Pallister, K.B.; Ruzevich, P.; Griffith, S.; Vuong, C.; Voyich, J.M. SaeR binds a consensus sequence within virulence gene promoters to advance USA300 pathogenesis. J. Infect. Dis. 2010, 201, 241–254. [Google Scholar] [CrossRef] [Green Version]
  380. Kawada-Matsuo, M.; Le, M.N.; Komatsuzawa, H. Antibacterial peptides resistance in Staphylococcus aureus: Various mechanisms and the association with pathogenicity. Genes 2021, 12, 1527. [Google Scholar] [CrossRef]
  381. Li, M.; Cha, D.J.; Lai, Y.; Villaruz, A.E.; Sturdevant, D.E.; Otto, M. The antimicrobial peptide-sensing system aps of Staphylococcus aureus. Mol. Microbiol. 2007, 66, 1136–1147. [Google Scholar] [CrossRef]
  382. Peschel, A.; Otto, M.; Jack, R.W.; Kalbacher, H.; Jung, G.; Götz, F. Inactivation of the dlt operon in Staphylococcus aureus confers sensitivity to defensins, protegrins, and other antimicrobial peptides. J. Biol. Chem. 1999, 274, 8405–8410. [Google Scholar] [CrossRef] [Green Version]
  383. Peschel, A.; Jack, R.W.; Otto, M.; Collins, L.V.; Staubitz, P.; Nicholson, G.; Kalbacher, H.; Nieuwenhuizen, W.F.; Jung, G.; Tarkowski, A.; et al. Staphylococcus aureus resistance to human defensins and evasion of neutrophil killing via the novel virulence factor MprF is based on modification of membrane lipids with l-lysine. J. Exp. Med. 2001, 193, 1067–1076. [Google Scholar] [CrossRef] [Green Version]
  384. Matsuo, M.; Oogai, Y.; Kato, F.; Sugai, M.; Komatsuzawa, H. Growth-phase dependence of susceptibility to antimicrobial peptides in Staphylococcus aureus. Microbiology 2011, 157, 1786–1797. [Google Scholar] [CrossRef] [Green Version]
  385. Pena, R.T.; Blasco, L.; Ambroa, A.; González-Pedrajo, B.; Fernández-García, L.; López, M.; Bleriot, I.; Bou, G.; García-Contreras, R.; Wood, T.K.; et al. Relationship between quorum sensing and secretion systems. Front. Microbiol. 2019, 10, 1100. [Google Scholar] [CrossRef] [Green Version]
  386. Bhagirath, A.Y.; Li, Y.; Patidar, R.; Yerex, K.; Ma, X.; Kumar, A.; Duan, K. Two component regulatory systems and antibiotic resistance in Gram-negative pathogens. Int. J. Mol. Sci. 2019, 20, 1781. [Google Scholar] [CrossRef] [Green Version]
  387. Dou, Y.; Song, F.; Guo, F.; Zhou, Z.; Zhu, C.; Xiang, J.; Huan, J. Acinetobacter baumannii quorum-sensing signalling molecule induces the expression of drug-resistance genes. Mol. Med. Rep. 2017, 15, 4061–4068. [Google Scholar] [CrossRef] [Green Version]
  388. Chan, Y.Y.; Chua, K.L. The Burkholderia pseudomallei BpeAB-OprB efflux pump: Expression and impact on quorum sensing and virulence. J. Bacteriol. 2005, 187, 4707–4719. [Google Scholar] [CrossRef] [Green Version]
  389. Marchand, I.; Damier-Piolle, L.; Courvalin, P.; Lambert, T. Expression of the RND-type efflux pump AdeABC in Acinetobacter baumannii is regulated by the AdeRS two-component system. Antimicrob. Agents Chemother. 2004, 48, 3298–3304. [Google Scholar] [CrossRef] [Green Version]
  390. Ouyang, Z.; Zheng, F.; Zhu, L.; Felix, J.; Wu, D.; Wu, K.; Gutsche, I.; Wu, Y.; Hwang, P.M.; She, J.; et al. Proteolysis and multimerization regulate signaling along the two-component regulatory system AdeRS. iScience 2021, 24, 102476. [Google Scholar] [CrossRef]
  391. Richmond, G.E.; Evans, L.P.; Anderson, M.J.; Wand, M.E.; Bonney, L.C.; Ivens, A.; Chua, K.L.; Webber, M.A.; Sutton, J.M.; Peterson, M.L.; et al. The Acinetobacter baumannii two-component system AdeRS regulates genes required for multidrug efflux, biofilm formation, and virulence in a strain-specific manner. mBio 2016, 7, e00430-16. [Google Scholar] [CrossRef] [Green Version]
  392. Adams, F.G.; Stroeher, U.H.; Hassan, K.A.; Marri, S.; Brown, M.H. Resistance to pentamidine is mediated by AdeAB, regulated by AdeRS, and influenced by growth conditions in Acinetobacter baumannii ATCC 17978. PLoS ONE 2018, 13, e0197412. [Google Scholar] [CrossRef] [Green Version]
  393. Sun, H.; Yang, Y.; Xue, T.; Sun, B. Modulation of cell wall synthesis and susceptibility to vancomycin by the two-component system AirSR in Staphylococcus aureus NCTC8325. BMC Microbiol. 2013, 13, 286. [Google Scholar] [CrossRef] [Green Version]
  394. Sun, F.; Ji, Q.; Jones, M.B.; Deng, X.; Liang, H.; Frank, B.; Telser, J.; Peterson, S.N.; Bae, T.; He, C. AirSR, a [2Fe-2S] cluster-containing two-component system, mediates global oxygen sensing and redox signaling in Staphylococcus aureus. J. Am. Chem. Soc. 2012, 134, 305–314. [Google Scholar] [CrossRef] [Green Version]
  395. Lau, C.H.; Fraud, S.; Jones, M.; Peterson, S.N.; Poole, K. Mutational activation of the AmgRS two-component system in aminoglycoside-resistant Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 2013, 57, 2243–2251. [Google Scholar] [CrossRef] [Green Version]
  396. Poole, K.; Hay, T.; Gilmour, C.; Fruci, M. The aminoglycoside resistance-promoting AmgRS envelope stress-responsive two-component system in Pseudomonas aeruginosa is zinc-activated and protects cells from zinc-promoted membrane damage. Microbiology 2019, 165, 563–571. [Google Scholar] [CrossRef]
  397. Fruci, M.; Poole, K. Aminoglycoside-inducible expression of the mexAB-oprM multidrug efflux operon in Pseudomonas aeruginosa: Involvement of the envelope stress-responsive AmgRS two-component system. PLoS ONE 2018, 13, e0205036. [Google Scholar] [CrossRef]
  398. Crosby, H.A.; Tiwari, N.; Kwiecinski, J.M.; Xu, Z.; Dykstra, A.; Jenul, C.; Fuentes, E.J.; Horswill, A.R. The Staphylococcus aureus ArlRS two-component system regulates virulence factor expression through MgrA. Mol. Microbiol. 2020, 113, 103–122. [Google Scholar] [CrossRef]
  399. Bai, J.; Zhu, X.; Zhao, K.; Yan, Y.; Xu, T.; Wang, J.; Zheng, J.; Huang, W.; Shi, L.; Shang, Y.; et al. The role of ArlRS in regulating oxacillin susceptibility in methicillin-resistant Staphylococcus aureus indicates it is a potential target for antimicrobial resistance breakers. Emerg. Microbes Infect. 2019, 8, 503–515. [Google Scholar] [CrossRef] [Green Version]
  400. Jousselin, A.; Kelley, W.L.; Barras, C.; Lew, D.P.; Renzoni, A. The Staphylococcus aureus thiol/oxidative stress global regulator Spx controls trfA, a gene implicated in cell wall antibiotic resistance. Antimicrob. Agents Chemother. 2013, 57, 3283–3292. [Google Scholar] [CrossRef] [Green Version]
  401. Baranova, N.; Nikaido, H. The BaeSR two-component regulatory system activates transcription of the yegMNOB (mdtABCD) transporter gene cluster in Escherichia coli and increases its resistance to novobiocin and deoxycholate. J. Bacteriol. 2002, 184, 4168–4176. [Google Scholar] [CrossRef] [Green Version]
  402. Nagakubo, S.; Nishino, K.; Hirata, T.; Yamaguchi, A. The putative response regulator BaeR stimulates multidrug resistance of Escherichia coli via a novel multidrug exporter system, MdtABC. J. Bacteriol. 2002, 184, 4161–4167. [Google Scholar] [CrossRef] [Green Version]
  403. Hirakawa, H.; Nishino, K.; Yamada, J.; Hirata, T.; Yamaguchi, A. Beta-lactam resistance modulated by the overexpression of response regulators of two-component signal transduction systems in Escherichia coli. J. Antimicrob. Chemother. 2003, 52, 576–582. [Google Scholar] [CrossRef]
  404. Guerrero, P.; Collao, B.; Morales, E.H.; Calderón, I.L.; Ipinza, F.; Parra, S.; Saavedra, C.P.; Gil, F. Characterization of the BaeSR two-component system from Salmonella Typhimurium and its role in ciprofloxacin-induced mdtA expression. Arch. Microbiol. 2012, 194, 453–460. [Google Scholar] [CrossRef]
  405. Lin, M.F.; Lin, Y.Y.; Lan, C.Y. The role of the two-component system BaeSR in disposing chemicals through regulating transporter systems in Acinetobacter baumannii. PLoS ONE 2015, 10, e0132843. [Google Scholar] [CrossRef]
  406. Lin, M.F.; Lin, Y.Y.; Yeh, H.W.; Lan, C.Y. Role of the BaeSR two-component system in the regulation of Acinetobacter baumannii adeAB genes and its correlation with tigecycline susceptibility. BMC Microbiol. 2014, 14, 119. [Google Scholar] [CrossRef] [Green Version]
  407. Yu, L.; Li, W.; Xue, M.; Li, J.; Chen, X.; Ni, J.; Shang, F.; Xue, T. Regulatory role of the two-component system BasSR in the expression of the EmrD multidrug efflux in Escherichia coli. Microb. Drug Resist. 2020, 26, 1163–1173. [Google Scholar] [CrossRef]
  408. Kreamer, N.N.; Costa, F.; Newman, D.K. The ferrous iron-responsive BqsRS two-component system activates genes that promote cationic stress tolerance. mBio 2015, 6, e02549. [Google Scholar] [CrossRef] [Green Version]
  409. Hiron, A.; Falord, M.; Valle, J.; Débarbouillé, M.; Msadek, T. Bacitracin and nisin resistance in Staphylococcus aureus: A novel pathway involving the BraS/BraR two-component system (SA2417/SA2418) and both the BraD/BraE and VraD/VraE ABC transporters. Mol. Microbiol. 2011, 81, 602–622. [Google Scholar] [CrossRef]
  410. Kawada-Matsuo, M.; Yoshida, Y.; Zendo, T.; Nagao, J.; Oogai, Y.; Nakamura, Y.; Sonomoto, K.; Nakamura, N.; Komatsuzawa, H. Three distinct two-component systems are involved in resistance to the class I bacteriocins, Nukacin ISK-1 and nisin A, in Staphylococcus aureus. PLoS ONE 2013, 8, e69455. [Google Scholar] [CrossRef] [Green Version]
  411. Guzmán Prieto, A.M.; Wijngaarden, J.; Braat, J.C.; Rogers, M.R.C.; Majoor, E.; Brouwer, E.C.; Zhang, X.; Bayjanov, J.R.; Bonten, M.J.M.; Willems, R.J.L.; et al. The two-component system ChtRS contributes to chlorhexidine tolerance in Enterococcus faecium. Antimicrob. Agents Chemother. 2017, 61, e02122-16. [Google Scholar] [CrossRef] [Green Version]
  412. Mascher, T.; Heintz, M.; Zähner, D.; Merai, M.; Hakenbeck, R. The CiaRH system of Streptococcus pneumoniae prevents lysis during stress induced by treatment with cell wall inhibitors and by mutations in pbp2x involved in beta-lactam resistance. J. Bacteriol. 2006, 188, 1959–1968. [Google Scholar] [CrossRef] [Green Version]
  413. Quach, D.; van Sorge, N.M.; Kristian, S.A.; Bryan, J.D.; Shelver, D.W.; Doran, K.S. The CiaR response regulator in group B Streptococcus promotes intracellular survival and resistance to innate immune defenses. J. Bacteriol. 2009, 191, 2023–2032. [Google Scholar] [CrossRef] [Green Version]
  414. He, L.Y.; Le, Y.J.; Guo, Z.; Li, S.; Yang, X.Y. The role and regulatory network of the CiaRH two-component system in Streptococcal species. Front. Microbiol. 2021, 12, 693858. [Google Scholar] [CrossRef]
  415. Nowicki, E.M.; O’Brien, J.P.; Brodbelt, J.S.; Trent, M.S. Extracellular zinc induces phosphoethanolamine addition to Pseudomonas aeruginosa lipid A via the ColRS two-component system. Mol. Microbiol. 2015, 97, 166–178. [Google Scholar] [CrossRef] [Green Version]
  416. Ducret, V.; Gonzalez, M.R.; Scrignari, T.; Perron, K. OprD repression upon metal treatment requires the RNA Chaperone Hfq in Pseudomonas aeruginosa. Genes 2016, 7, 82. [Google Scholar] [CrossRef]
  417. Caille, O.; Rossier, C.; Perron, K. A copper-activated two-component system interacts with zinc and imipenem resistance in Pseudomonas aeruginosa. J. Bacteriol. 2007, 189, 4561–4568. [Google Scholar] [CrossRef] [Green Version]
  418. Fernández, L.; Jenssen, H.; Bains, M.; Wiegand, I.; Gooderham, W.J.; Hancock, R.E. The two-component system CprRS senses cationic peptides and triggers adaptive resistance in Pseudomonas aeruginosa independently of ParRS. Antimicrob. Agents Chemother. 2012, 56, 6212–6222. [Google Scholar] [CrossRef] [Green Version]
  419. Lee, J.Y.; Chung, E.S.; Na, I.Y.; Kim, H.; Shin, D.; Ko, K.S. Development of colistin resistance in pmrA-, phoP-, parR- and cprR-inactivated mutants of Pseudomonas aeruginosa. J. Antimicrob. Chemother. 2014, 69, 2966–2971. [Google Scholar] [CrossRef] [Green Version]
  420. Audrain, B.; Ferrières, L.; Zairi, A.; Soubigou, G.; Dobson, C.; Coppée, J.Y.; Beloin, C.; Ghigo, J.M. Induction of the Cpx envelope stress pathway contributes to Escherichia coli tolerance to antimicrobial peptides. Appl. Environ. Microbiol. 2013, 79, 7770–7779. [Google Scholar] [CrossRef] [Green Version]
  421. Srinivasan, V.B.; Rajamohan, G. KpnEF, a new member of the Klebsiella pneumoniae cell envelope stress response regulon, is an SMR-type efflux pump involved in broad-spectrum antimicrobial resistance. Antimicrob. Agents Chemother. 2013, 57, 4449–4462. [Google Scholar] [CrossRef] [Green Version]
  422. Raivio, T.L.; Leblanc, S.K.; Price, N.L. The Escherichia coli Cpx envelope stress response regulates genes of diverse function that impact antibiotic resistance and membrane integrity. J. Bacteriol. 2013, 195, 2755–2767. [Google Scholar] [CrossRef] [Green Version]
  423. Weatherspoon-Griffin, N.; Yang, D.; Kong, W.; Hua, Z.; Shi, Y. The CpxR/CpxA two-component regulatory system up-regulates the multidrug resistance cascade to facilitate Escherichia coli resistance to a model antimicrobial peptide. J. Biol. Chem. 2014, 289, 32571–32582. [Google Scholar] [CrossRef] [Green Version]
  424. Weatherspoon-Griffin, N.; Zhao, G.; Kong, W.; Kong, Y.; Andrews-Polymenis, H.; McClelland, M.; Shi, Y. The CpxR/CpxA two-component system up-regulates two Tat-dependent peptidoglycan amidases to confer bacterial resistance to antimicrobial peptide. J. Biol. Chem. 2011, 286, 5529–5539. [Google Scholar] [CrossRef] [Green Version]
  425. Batchelor, E.; Walthers, D.; Kenney, L.J.; Goulian, M. The Escherichia coli CpxA-CpxR envelope stress response system regulates expression of the porins ompF and ompC. J. Bacteriol. 2005, 187, 5723–5731. [Google Scholar] [CrossRef] [Green Version]
  426. Zamorano, L.; Moyà, B.; Juan, C.; Mulet, X.; Blázquez, J.; Oliver, A. The Pseudomonas aeruginosa CreBC two-component system plays a major role in the response to β-lactams, fitness, biofilm growth, and global regulation. Antimicrob. Agents Chemother. 2014, 58, 5084–5095. [Google Scholar] [CrossRef] [Green Version]
  427. Kellogg, S.L.; Kristich, C.J. Convergence of PASTA kinase and two-component signaling in response to cell wall stress in Enterococcus faecalis. J. Bacteriol. 2018, 200, e00086-18. [Google Scholar] [CrossRef] [Green Version]
  428. Kellogg, S.L.; Kristich, C.J. Functional dissection of the CroRS two-component system required for resistance to cell wall stressors in Enterococcus faecalis. J. Bacteriol. 2016, 198, 1326–1336. [Google Scholar] [CrossRef] [Green Version]
  429. Kellogg, S.L.; Little, J.L.; Hoff, J.S.; Kristich, C.J. Requirement of the CroRS two-component system for resistance to cell wall-targeting antimicrobials in Entero.ococcus faecium. Antimicrob. Agents Chemother. 2017, 61, e02461-16. [Google Scholar] [CrossRef] [Green Version]
  430. Comenge, Y.; Quintiliani, R., Jr.; Li, L.; Dubost, L.; Brouard, J.P.; Hugonnet, J.E.; Arthur, M. The CroRS two-component regulatory system is required for intrinsic beta-lactam resistance in Enterococcus faecalis. J. Bacteriol. 2003, 185, 7184–7192. [Google Scholar] [CrossRef] [Green Version]
  431. Dieppois, G.; Ducret, V.; Caille, O.; Perron, K. The transcriptional regulator CzcR modulates antibiotic resistance and quorum sensing in Pseudomonas aeruginosa. PLoS ONE 2012, 7, e38148. [Google Scholar] [CrossRef] [Green Version]
  432. Perron, K.; Caille, O.; Rossier, C.; Van Delden, C.; Dumas, J.L.; Köhler, T. CzcR-CzcS, a two-component system involved in heavy metal and carbapenem resistance in Pseudomonas aeruginosa. J. Biol. Chem. 2004, 279, 8761–8768. [Google Scholar] [CrossRef] [Green Version]
  433. Wang, D.; Chen, W.; Huang, S.; He, Y.; Liu, X.; Hu, Q.; Wei, T.; Sang, H.; Gan, J.; Chen, H. Structural basis of Zn(II) induced metal detoxification and antibiotic resistance by histidine kinase CzcS in Pseudomonas aeruginosa. PLoS Pathog. 2017, 13, e1006533. [Google Scholar] [CrossRef] [Green Version]
  434. Nishino, K.; Yamaguchi, A. Overexpression of the response regulator evgA of the two-component signal transduction system modulates multidrug resistance conferred by multidrug resistance transporters. J. Bacteriol. 2001, 183, 1455–1458. [Google Scholar] [CrossRef] [Green Version]
  435. Nishino, K.; Yamaguchi, A. EvgA of the two-component signal transduction system modulates production of the yhiUV multidrug transporter in Escherichia coli. J. Bacteriol. 2002, 184, 2319–2323. [Google Scholar] [CrossRef] [Green Version]
  436. Kato, A.; Ohnishi, H.; Yamamoto, K.; Furuta, E.; Tanabe, H.; Utsumi, R. Transcription of emrKY is regulated by the EvgA-EvgS two-component system in Escherichia coli K-12. Biosci. Biotechnol. Biochem. 2000, 64, 1203–1209. [Google Scholar] [CrossRef]
  437. Eguchi, Y.; Oshima, T.; Mori, H.; Aono, R.; Yamamoto, K.; Ishihama, A.; Utsumi, R. Transcriptional regulation of drug efflux genes by EvgAS, a two-component system in Escherichia coli. Microbiology 2003, 149, 2819–2828. [Google Scholar] [CrossRef]
  438. Hirakawa, H.; Nishino, K.; Hirata, T.; Yamaguchi, A. Comprehensive studies of drug resistance mediated by overexpression of response regulators of two-component signal transduction systems in Escherichia coli. J. Bacteriol. 2003, 185, 1851–1856. [Google Scholar] [CrossRef] [Green Version]
  439. Yang, S.J.; Bayer, A.S.; Mishra, N.N.; Meehl, M.; Ledala, N.; Yeaman, M.R.; Xiong, Y.Q.; Cheung, A.L. The Staphylococcus aureus two-component regulatory system, GraRS, senses and confers resistance to selected cationic antimicrobial peptides. Infect. Immun. 2012, 80, 74–81. [Google Scholar] [CrossRef] [Green Version]
  440. Cheung, A.L.; Bayer, A.S.; Yeaman, M.R.; Xiong, Y.Q.; Waring, A.J.; Memmi, G.; Donegan, N.; Chaili, S.; Yang, S.J. Site-specific mutation of the sensor kinase GraS in Staphylococcus aureus alters the adaptive response to distinct cationic antimicrobial peptides. Infect. Immun. 2014, 82, 5336–5345. [Google Scholar] [CrossRef] [Green Version]
  441. Chen, L.; Wang, Z.; Xu, T.; Ge, H.; Zhou, F.; Zhu, X.; Li, X.; Qu, D.; Zheng, C.; Wu, Y.; et al. The role of graRS in regulating virulence and antimicrobial resistance in methicillin-resistant Staphylococcus aureus. Front. Microbiol. 2021, 12, 727104. [Google Scholar] [CrossRef]
  442. Meehl, M.; Herbert, S.; Götz, F.; Cheung, A. Interaction of the GraRS two-component system with the VraFG ABC transporter to support vancomycin-intermediate resistance in Staphylococcus aureus. Antimicrob. Agents Chemother. 2007, 51, 2679–2689. [Google Scholar] [CrossRef] [Green Version]
  443. Kraus, D.; Herbert, S.; Kristian, S.A.; Khosravi, A.; Nizet, V.; Götz, F.; Peschel, A. The GraRS regulatory system controls Staphylococcus aureus susceptibility to antimicrobial host defenses. BMC Microbiol. 2008, 8, 85. [Google Scholar] [CrossRef] [Green Version]
  444. Reyes, J.; Panesso, D.; Tran, T.T.; Mishra, N.N.; Cruz, M.R.; Munita, J.M.; Singh, K.V.; Yeaman, M.R.; Murray, B.E.; Shamoo, Y.; et al. A liaR deletion restores susceptibility to daptomycin and antimicrobial peptides in multidrug-resistant Enterococcus faecalis. J. Infect. Dis. 2015, 211, 1317–1325. [Google Scholar] [CrossRef]
  445. Yang, S.J.; Xiong, Y.Q.; Yeaman, M.R.; Bayles, K.W.; Abdelhady, W.; Bayer, A.S. Role of the LytSR two-component regulatory system in adaptation to cationic antimicrobial peptides in Staphylococcus aureus. Antimicrob. Agents Chemother. 2013, 57, 3875–3882. [Google Scholar] [CrossRef] [Green Version]
  446. Brunskill, E.W.; Bayles, K.W. Identification of LytSR-regulated genes from Staphylococcus aureus. J. Bacteriol. 1996, 178, 5810–5812. [Google Scholar] [CrossRef] [Green Version]
  447. Randall, C.P.; Gupta, A.; Utley-Drew, B.; Lee, S.Y.; Morrison-Williams, G.; O’Neill, A.J. Acquired nisin resistance in Staphylococcus aureus involves constitutive activation of an intrinsic peptide antibiotic detoxification module. mSphere 2018, 3, e00633-18. [Google Scholar] [CrossRef] [Green Version]
  448. Kolar, S.L.; Nagarajan, V.; Oszmiana, A.; Rivera, F.E.; Miller, H.K.; Davenport, J.E.; Riordan, J.T.; Potempa, J.; Barber, D.S.; Koziel, J.; et al. NsaRS is a cell-envelope-stress-sensing two-component system of Staphylococcus aureus. Microbiology 2011, 157, 2206–2219. [Google Scholar] [CrossRef] [Green Version]
  449. Fernández, L.; Gooderham, W.J.; Bains, M.; McPhee, J.B.; Wiegand, I.; Hancock, R.E. Adaptive resistance to the "last hope" antibiotics polymyxin B and colistin in Pseudomonas aeruginosa is mediated by the novel two-component regulatory system ParR-ParS. Antimicrob. Agents Chemother. 2010, 54, 3372–3382. [Google Scholar] [CrossRef] [Green Version]
  450. Wang, D.; Seeve, C.; Pierson, L.S., 3rd; Pierson, E.A. Transcriptome profiling reveals links between ParS/ParR, MexEF-OprN, and quorum sensing in the regulation of adaptation and virulence in Pseudomonas aeruginosa. BMC Genom. 2013, 14, 618. [Google Scholar] [CrossRef] [Green Version]
  451. Srinivasan, V.B.; Venkataramaiah, M.; Mondal, A.; Vaidyanathan, V.; Govil, T.; Rajamohan, G. Functional characterization of a novel outer membrane porin KpnO, regulated by PhoBR two-component system in Klebsiella pneumoniae NTUH-K2044. PLoS ONE 2012, 7, e41505. [Google Scholar] [CrossRef] [Green Version]
  452. Macfarlane, E.L.; Kwasnicka, A.; Ochs, M.M.; Hancock, R.E. PhoP-PhoQ homologues in Pseudomonas aeruginosa regulate expression of the outer-membrane protein OprH and polymyxin B resistance. Mol. Microbiol. 1999, 34, 305–316. [Google Scholar] [CrossRef] [Green Version]
  453. McPhee, J.B.; Bains, M.; Winsor, G.; Lewenza, S.; Kwasnicka, A.; Brazas, M.D.; Brinkman, F.S.; Hancock, R.E. Contribution of the PhoP-PhoQ and PmrA-PmrB two-component regulatory systems to Mg2+-induced gene regulation in Pseudomonas aeruginosa. J. Bacteriol. 2006, 188, 3995–4006. [Google Scholar] [CrossRef] [Green Version]
  454. Wilton, M.; Charron-Mazenod, L.; Moore, R.; Lewenza, S. Extracellular DNA acidifies biofilms and induces aminoglycoside resistance in Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 2016, 60, 544–553. [Google Scholar] [CrossRef] [Green Version]
  455. Macfarlane, E.L.A.; Kwasnicka, A.; Hancock, R.E.W. Role of Pseudomonas aeruginosa PhoP-PhoQ in resistance to antimicrobial cationic peptides and aminoglycosides. Microbiology 2000, 146 Pt 10, 2543–2554. [Google Scholar] [CrossRef] [Green Version]
  456. Yang, B.; Liu, C.; Pan, X.; Fu, W.; Fan, Z.; Jin, Y.; Bai, F.; Cheng, Z.; Wu, W. Identification of novel PhoP-PhoQ regulated genes that contribute to polymyxin b tolerance in Pseudomonas aeruginosa. Microorganisms 2021, 9, 344. [Google Scholar] [CrossRef]
  457. Shi, Y.; Cromie, M.J.; Hsu, F.F.; Turk, J.; Groisman, E.A. PhoP-regulated Salmonella resistance to the antimicrobial peptides magainin 2 and polymyxin B. Mol. Microbiol. 2004, 53, 229–241. [Google Scholar] [CrossRef]
  458. Cheng, H.Y.; Chen, Y.F.; Peng, H.L. Molecular characterization of the PhoPQ-PmrD-PmrAB mediated pathway regulating polymyxin B resistance in Klebsiella pneumoniae CG43. J. Biomed. Sci. 2010, 17, 60. [Google Scholar] [CrossRef] [Green Version]
  459. Beceiro, A.; Llobet, E.; Aranda, J.; Bengoechea, J.A.; Doumith, M.; Hornsey, M.; Dhanji, H.; Chart, H.; Bou, G.; Livermore, D.M.; et al. Phosphoethanolamine modification of lipid A in colistin-resistant variants of Acinetobacter baumannii mediated by the pmrAB two-component regulatory system. Antimicrob. Agents Chemother. 2011, 55, 3370–3379. [Google Scholar] [CrossRef] [Green Version]
  460. Adams, M.D.; Nickel, G.C.; Bajaksouzian, S.; Lavender, H.; Murthy, A.R.; Jacobs, M.R.; Bonomo, R.A. Resistance to colistin in Acinetobacter baumannii associated with mutations in the PmrAB two-component system. Antimicrob. Agents Chemother. 2009, 53, 3628–3634. [Google Scholar] [CrossRef] [Green Version]
  461. Xiao, Y.; Nie, L.; Chen, H.; He, M.; Liang, Q.; Nie, H.; Chen, W.; Huang, Q. The two-component system TarR-TarS is regulated by c-di-GMP/FleQ and FliA and modulates antibiotic susceptibility in Pseudomonas putida. Environ. Microbiol. 2021, 23, 5239–5257. [Google Scholar] [CrossRef]
  462. Hughes, C.S.; Longo, E.; Phillips-Jones, M.K.; Hussain, R. Characterisation of the selective binding of antibiotics vancomycin and teicoplanin by the VanS receptor regulating type A vancomycin resistance in the enterococci. Biochim. Biophys. Acta Gen. Subj. 2017, 1861, 1951–1959. [Google Scholar] [CrossRef] [PubMed]
  463. Lee, H.; Boyle-Vavra, S.; Ren, J.; Jarusiewicz, J.A.; Sharma, L.K.; Hoagland, D.T.; Yin, S.; Zhu, T.; Hevener, K.E.; Ojeda, I.; et al. Identification of small molecules exhibiting oxacillin synergy through a novel assay for inhibition of vraTSR expression in methicillin-resistant Staphylococcus aureus. Antimicrob. Agents Chemother. 2019, 63, e02593-18. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  464. Boyle-Vavra, S.; Yin, S.; Jo, D.S.; Montgomery, C.P.; Daum, R.S. VraT/YvqF is required for methicillin resistance and activation of the VraSR regulon in Staphylococcus aureus. Antimicrob. Agents Chemother. 2013, 57, 83–95. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  465. Gardete, S.; Wu, S.W.; Gill, S.; Tomasz, A. Role of VraSR in antibiotic resistance and antibiotic-induced stress response in Staphylococcus aureus. Antimicrob. Agents Chemother. 2006, 50, 3424–3434. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  466. Kuroda, M.; Kuroda, H.; Oshima, T.; Takeuchi, F.; Mori, H.; Hiramatsu, K. Two-component system VraSR positively modulates the regulation of cell-wall biosynthesis pathway in Staphylococcus aureus. Mol. Microbiol. 2003, 49, 807–821. [Google Scholar] [CrossRef]
  467. Wu, Y.; Meng, Y.; Qian, L.; Ding, B.; Han, H.; Chen, H.; Bai, L.; Qu, D.; Wu, Y. The vancomycin resistance-associated regulatory system VraSR modulates biofilm formation of Staphylococcus epidermidis in an ica-dependent manner. mSphere 2021, 6, e0064121. [Google Scholar] [CrossRef]
  468. Howden, B.P.; McEvoy, C.R.; Allen, D.L.; Chua, K.; Gao, W.; Harrison, P.F.; Bell, J.; Coombs, G.; Bennett-Wood, V.; Porter, J.L.; et al. Evolution of multidrug resistance during Staphylococcus aureus infection involves mutation of the essential two component regulator WalKR. PLoS Pathog. 2011, 7, e1002359. [Google Scholar] [CrossRef]
  469. Poupel, O.; Proux, C.; Jagla, B.; Msadek, T.; Dubrac, S. SpdC, a novel virulence factor, controls histidine kinase activity in Staphylococcus aureus. PLoS Pathog. 2018, 14, e1006917. [Google Scholar] [CrossRef] [Green Version]
  470. Hu, Q.; Peng, H.; Rao, X. Molecular events for promotion of vancomycin resistance in vancomycin intermediate Staphylococcus aureus. Front. Microbiol. 2016, 7, 1601. [Google Scholar] [CrossRef] [Green Version]
  471. Lewenza, S. Extracellular DNA-induced antimicrobial peptide resistance mechanisms in Pseudomonas aeruginosa. Front. Microbiol. 2013, 4, 21. [Google Scholar] [CrossRef] [Green Version]
  472. Mulcahy, H.; Charron-Mazenod, L.; Lewenza, S. Extracellular DNA chelates cations and induces antibiotic resistance in Pseudomonas aeruginosa biofilms. PLoS Pathog. 2008, 4, e1000213. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  473. Huang, J.; Li, C.; Song, J.; Velkov, T.; Wang, L.; Zhu, Y.; Li, J. Regulating polymyxin resistance in Gram-negative bacteria: Roles of two-component systems PhoPQ and PmrAB. Future Microbiol. 2020, 15, 445–459. [Google Scholar] [CrossRef] [PubMed]
  474. Wright, M.S.; Jacobs, M.R.; Bonomo, R.A.; Adams, M.D. Transcriptome remodeling of Acinetobacter baumannii during infection and treatment. mBio 2017, 8, e02193-16. [Google Scholar] [CrossRef] [Green Version]
  475. Richards, S.M.; Strandberg, K.L.; Gunn, J.S. Salmonella-regulated lipopolysaccharide modifications. Subcell Biochem. 2010, 53, 101–122. [Google Scholar] [CrossRef] [PubMed]
  476. Shprung, T.; Wani, N.A.; Wilmes, M.; Mangoni, M.L.; Bitler, A.; Shimoni, E.; Sahl, H.G.; Shai, Y. Opposing effects of PhoPQ and PmrAB on the properties of Salmonella enterica serovar Typhimurium: Implications on resistance to antimicrobial peptides. Biochemistry 2021, 60, 2943–2955. [Google Scholar] [CrossRef]
  477. Mahoney, T.F.; Silhavy, T.J. The Cpx stress response confers resistance to some, but not all, bactericidal antibiotics. J. Bacteriol. 2013, 195, 1869–1874. [Google Scholar] [CrossRef] [Green Version]
  478. Liu, X.; Omar, M.; Nagaraja, K.V.; Goyal, S.M.; Vidovic, S. Novel insight into the effects of CpxR on Salmonella enteritidis cells during the chlorhexidine treatment and non-stressful growing conditions. Int. J. Mol. Sci. 2021, 22, 8938. [Google Scholar] [CrossRef]
  479. Yi, Z.; Wang, D.; Xin, S.; Zhou, D.; Li, T.; Tian, M.; Qi, J.; Ding, C.; Wang, S.; Yu, S. The CpxR regulates type VI secretion system 2 expression and facilitates the interbacterial competition activity and virulence of avian pathogenic Escherichia coli. Vet. Res. 2019, 50, 40. [Google Scholar] [CrossRef] [Green Version]
  480. Ma, Q.; Wood, T.K. OmpA influences Escherichia coli biofilm formation by repressing cellulose production through the CpxRA two-component system. Environ. Microbiol. 2009, 11, 2735–2746. [Google Scholar] [CrossRef]
  481. Dorel, C.; Lejeune, P.; Rodrigue, A. The Cpx system of Escherichia coli, a strategic signaling pathway for confronting adverse conditions and for settling biofilm communities? Res. Microbiol. 2006, 157, 306–314. [Google Scholar] [CrossRef]
  482. Raivio, T.L. Everything old is new again: An update on current research on the Cpx envelope stress response. Biochim. Biophys. Acta 2014, 1843, 1529–1541. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  483. Otto, K.; Silhavy, T.J. Surface sensing and adhesion of Escherichia coli controlled by the Cpx-signaling pathway. Proc. Natl. Acad. Sci. USA 2002, 99, 2287–2292. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  484. Laubacher, M.E.; Ades, S.E. The Rcs phosphorelay is a cell envelope stress response activated by peptidoglycan stress and contributes to intrinsic antibiotic resistance. J. Bacteriol. 2008, 190, 2065–2074. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  485. Poole, K. At the nexus of antibiotics and metals: The impact of Cu and Zn on antibiotic activity and resistance. Trends Microbiol. 2017, 25, 820–832. [Google Scholar] [CrossRef] [PubMed]
  486. Bernal-Cabas, M.; Ayala, J.A.; Raivio, T.L. The Cpx envelope stress response modifies peptidoglycan cross-linking via the L,D-transpeptidase LdtD and the novel protein YgaU. J. Bacteriol. 2015, 197, 603–614. [Google Scholar] [CrossRef] [Green Version]
  487. Hugonnet, J.E.; Mengin-Lecreulx, D.; Monton, A.; den Blaauwen, T.; Carbonnelle, E.; Veckerlé, C.; Brun, Y.V.; van Nieuwenhze, M.; Bouchier, C.; Tu, K.; et al. Factors essential for L,D-transpeptidase-mediated peptidoglycan cross-linking and β-lactam resistance in Escherichia coli. Elife 2016, 5, e19469. [Google Scholar] [CrossRef]
  488. Weidenmaier, C.; Peschel, A.; Kempf, V.A.; Lucindo, N.; Yeaman, M.R.; Bayer, A.S. DltABCD- and MprF-mediated cell envelope modifications of Staphylococcus aureus confer resistance to platelet microbicidal proteins and contribute to virulence in a rabbit endocarditis model. Infect. Immun. 2005, 73, 8033–8038. [Google Scholar] [CrossRef] [Green Version]
  489. Pinto, R.M.; Soares, F.A.; Reis, S.; Nunes, C.; Van Dijck, P. Innovative strategies toward the disassembly of the EPS matrix in bacterial biofilms. Front. Microbiol. 2020, 11, 952. [Google Scholar] [CrossRef]
  490. Campoccia, D.; Montanaro, L.; Arciola, C.R. Tracing the origins of extracellular DNA in bacterial biofilms: Story of death and predation to community benefit. Biofouling 2021, 37, 1022–1039. [Google Scholar] [CrossRef]
  491. Das, T.; Krom, B.P.; van der Mei, H.C.; Busscher, H.J.; Sharma, P.K. DNA-mediated bacterial aggregation is dictated by acid–base interactions. Soft Matter 2011, 7, 2927–2935. [Google Scholar] [CrossRef]
  492. Qin, Z.; Ou, Y.; Yang, L.; Zhu, Y.; Tolker-Nielsen, T.; Molin, S.; Qu, D. Role of autolysin-mediated DNA release in biofilm formation of Staphylococcus epidermidis. Microbiology 2007, 153, 2083–2092. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  493. Heilmann, C.; Hussain, M.; Peters, G.; Götz, F. Evidence for autolysin-mediated primary attachment of Staphylococcus epidermidis to a polystyrene surface. Mol. Microbiol. 1997, 24, 1013–1024. [Google Scholar] [CrossRef] [PubMed]
  494. Christner, M.; Heinze, C.; Busch, M.; Franke, G.; Hentschke, M.; Bayard Dühring, S.; Büttner, H.; Kotasinska, M.; Wischnewski, V.; Kroll, G.; et al. sarA negatively regulates Staphylococcus epidermidis biofilm formation by modulating expression of 1 MDa extracellular matrix binding protein and autolysis-dependent release of eDNA. Mol. Microbiol. 2012, 86, 394–410. [Google Scholar] [CrossRef] [PubMed]
  495. Rice, K.C.; Mann, E.E.; Endres, J.L.; Weiss, E.C.; Cassat, J.E.; Smeltzer, M.S.; Bayles, K.W. The cidA murein hydrolase regulator contributes to DNA release and biofilm development in Staphylococcus aureus. Proc. Natl. Acad. Sci. USA 2007, 104, 8113–8118. [Google Scholar] [CrossRef] [Green Version]
  496. Rabin, N.; Zheng, Y.; Opoku-Temeng, C.; Du, Y.; Bonsu, E.; Sintim, H.O. Biofilm formation mechanisms and targets for developing antibiofilm agents. Future Med. Chem. 2015, 7, 493–512. [Google Scholar] [CrossRef]
  497. López, D.; Vlamakis, H.; Kolter, R. Biofilms. Cold Spring Harb Perspect Biol. 2010, 2, a000398. [Google Scholar] [CrossRef]
  498. Luo, A.; Wang, F.; Sun, D.; Liu, X.; Xin, B. Formation, development, and cross-species interactions in biofilms. Front. Microbiol. 2021, 12, 757327. [Google Scholar] [CrossRef]
  499. Zheng, S.; Bawazir, M.; Dhall, A.; Kim, H.E.; He, L.; Heo, J.; Hwang, G. Implication of surface properties, bacterial motility, and hydrodynamic conditions on bacterial surface sensing and their initial adhesion. Front. Bioeng. Biotechnol. 2021, 9, 643722. [Google Scholar] [CrossRef]
  500. Buzzo, J.R.; Devaraj, A.; Gloag, E.S.; Jurcisek, J.A.; Robledo-Avila, F.; Kesler, T.; Wilbanks, K.; Mashburn-Warren, L.; Balu, S.; Wickham, J.; et al. Z-form extracellular DNA is a structural component of the bacterial biofilm matrix. Cell 2021, 184, 5740–5758. [Google Scholar] [CrossRef]
  501. Ribet, D.; Cossart, P. How bacterial pathogens colonize their hosts and invade deeper tissues. Microbes Infect. 2015, 17, 173–183. [Google Scholar] [CrossRef]
  502. Petrova, O.E.; Sauer, K. Escaping the biofilm in more than one way: Desorption, detachment or dispersion. Curr. Opin. Microbiol. 2016, 30, 67–78. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  503. Abraham, W.R. Going beyond the control of quorum-sensing to combat biofilm infections. Antibiotics 2016, 5, 3. [Google Scholar] [CrossRef] [PubMed]
  504. Karatan, E.; Watnick, P. Signals, regulatory networks, and materials that build and break bacterial biofilms. Microbiol. Mol. Biol. Rev. 2009, 73, 310–347. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  505. Davies, D.G.; Parsek, M.R.; Pearson, J.P.; Iglewski, B.H.; Costerton, J.W.; Greenberg, E.P. The involvement of cell-to-cell signals in the development of a bacterial biofilm. Science 1998, 280, 295–298. [Google Scholar] [CrossRef] [Green Version]
  506. Eze, E.C.; Chenia, H.Y.; El Zowalaty, M.E. Acinetobacter baumannii biofilms: Effects of physicochemical factors, virulence, antibiotic resistance determinants, gene regulation, and future antimicrobial treatments. Infect. Drug Resist. 2018, 11, 2277–2299. [Google Scholar] [CrossRef] [Green Version]
  507. Liu, C.; Sun, D.; Zhu, J.; Liu, W. Two-component signal transduction systems: A major strategy for connecting input stimuli to biofilm formation. Front. Microbiol. 2018, 9, 3279. [Google Scholar] [CrossRef]
  508. Poulin, M.B.; Kuperman, L.L. Regulation of biofilm exopolysaccharide production by cyclic di-guanosine monophosphate. Front. Microbiol. 2021, 12, 730980. [Google Scholar] [CrossRef]
  509. Vetrivel, A.; Ramasamy, M.; Vetrivel, P.; Natchimuthu, S.; Arunachalam, S.; Kim, G.-S.; Murugesan, R. Pseudomonas aeruginosa biofilm formation and its control. Biologics 2021, 1, 19. [Google Scholar] [CrossRef]
  510. Yu, W.; Hallinen, K.M.; Wood, K.B. Interplay between antibiotic efficacy and drug-induced lysis underlies enhanced biofilm formation at subinhibitory drug concentrations. Antimicrob. Agents Chemother. 2018, 62, e01603-17. [Google Scholar] [CrossRef] [Green Version]
  511. Kaplan, J.B. Antibiotic-induced biofilm formation. Int. J. Artif. Organs 2011, 34, 737–751. [Google Scholar] [CrossRef]
  512. Rachid, S.; Ohlsen, K.; Witte, W.; Hacker, J.; Ziebuhr, W. Effect of subinhibitory antibiotic concentrations on polysaccharide intercellular adhesin expression in biofilm-forming Staphylococcus epidermidis. Antimicrob. Agents Chemother. 2000, 44, 3357–3363. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  513. Rychlik, I.; Barrow, P.A. Salmonella stress management and its relevance to behaviour during intestinal colonisation and infection. FEMS Microbiol. Rev. 2005, 29, 1021–1040. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  514. Moradali, M.F.; Ghods, S.; Rehm, B.H. Pseudomonas aeruginosa lifestyle: A paradigm for adaptation, survival, and persistence. Front. Cell Infect. Microbiol. 2017, 7, 39. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  515. Kaplan, J.B.; Izano, E.A.; Gopal, P.; Karwacki, M.T.; Kim, S.; Bose, J.L.; Bayles, K.W.; Horswill, A.R. Low levels of β-lactam antibiotics induce extracellular DNA release and biofilm formation in Staphylococcus aureus. mBio 2012, 3, e00198-12. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  516. Hoffman, L.R.; D’Argenio, D.A.; MacCoss, M.J.; Zhang, Z.; Jones, R.A.; Miller, S.I. Aminoglycoside antibiotics induce bacterial biofilm formation. Nature 2005, 436, 1171–1175. [Google Scholar] [CrossRef]
  517. Valentini, M.; Filloux, A. Biofilms and Cyclic di-GMP (c-di-GMP) signaling: Lessons from Pseudomonas aeruginosa and other bacteria. J. Biol. Chem. 2016, 291, 12547–12555. [Google Scholar] [CrossRef] [Green Version]
  518. Geisinger, E.; Isberg, R.R. Antibiotic modulation of capsular exopolysaccharide and virulence in Acinetobacter baumannii. PLoS Pathog. 2015, 11, e1004691. [Google Scholar] [CrossRef] [Green Version]
  519. Ranieri, M.R.; Whitchurch, C.B.; Burrows, L.L. Mechanisms of biofilm stimulation by subinhibitory concentrations of antimicrobials. Curr. Opin. Microbiol. 2018, 45, 164–169. [Google Scholar] [CrossRef]
  520. Jin, Y.; Guo, Y.; Zhan, Q.; Shang, Y.; Qu, D.; Yu, F. Subinhibitory concentrations of mupirocin stimulate Staphylococcus aureus biofilm formation by upregulating cidA. Antimicrob. Agents Chemother. 2020, 64, e01912-19. [Google Scholar] [CrossRef]
  521. Pérez-Martínez, I.; Haas, D. Azithromycin inhibits expression of the GacA-dependent small RNAs RsmY and RsmZ in Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 2011, 55, 3399–3405. [Google Scholar] [CrossRef] [Green Version]
  522. Imperi, F.; Leoni, L.; Visca, P. Antivirulence activity of azithromycin in Pseudomonas aeruginosa. Front. Microbiol. 2014, 5, 178. [Google Scholar] [CrossRef] [PubMed]
  523. Elsheredy, A.; El-Soudany, I.; Elsherbini, E.; Metwally, D.; Ghazal, A. Effect of azithromycin and phenylalanine-arginine beta-naphthylamide on quorum sensing and virulence factors in clinical isolates of Pseudomonas aeruginosa. Iran. J. Microbiol. 2021, 13, 37–49. [Google Scholar] [CrossRef] [PubMed]
  524. Ryan Kaler, K.M.; Nix, J.C.; Schubot, F.D. RetS inhibits Pseudomonas aeruginosa biofilm formation by disrupting the canonical histidine kinase dimerization interface of GacS. J. Biol. Chem. 2021, 297, 101193. [Google Scholar] [CrossRef] [PubMed]
  525. Balestrino, D.; Haagensen, J.A.; Rich, C.; Forestier, C. Characterization of type 2 quorum sensing in Klebsiella pneumoniae and relationship with biofilm formation. J. Bacteriol. 2005, 187, 2870–2880. [Google Scholar] [CrossRef] [Green Version]
  526. Irie, Y.; Parsek, M.R. Quorum sensing and microbial biofilms. Curr. Top. Microbiol. Immunol. 2008, 322, 67–84. [Google Scholar] [CrossRef]
  527. Li, Y.H.; Tian, X. Quorum sensing and bacterial social interactions in biofilms. Sensors 2012, 12, 2519–2538. [Google Scholar] [CrossRef]
  528. Yarwood, J.M.; Bartels, D.J.; Volper, E.M.; Greenberg, E.P. Quorum sensing in Staphylococcus aureus biofilms. J. Bacteriol. 2004, 186, 1838–1850. [Google Scholar] [CrossRef] [Green Version]
  529. Wolska, K.I.; Grudniak, A.M.; Rudnicka, Z.; Markowska, K. Genetic control of bacterial biofilms. J. Appl. Genet. 2016, 57, 225–238. [Google Scholar] [CrossRef] [Green Version]
  530. Hardie, K.R.; Heurlier, K. Establishing bacterial communities by ‘word of mouth’: LuxS and autoinducer 2 in biofilm development. Nat. Rev. Microbiol. 2008, 6, 635–643. [Google Scholar] [CrossRef]
  531. Brackman, G.; Cos, P.; Maes, L.; Nelis, H.J.; Coenye, T. Quorum sensing inhibitors increase the susceptibility of bacterial biofilms to antibiotics in vitro and in vivo. Antimicrob. Agents Chemother. 2011, 55, 2655–2661. [Google Scholar] [CrossRef] [Green Version]
  532. De Kievit, T.R.; Gillis, R.; Marx, S.; Brown, C.; Iglewski, B.H. Quorum-sensing genes in Pseudomonas aeruginosa biofilms: Their role and expression patterns. Appl. Environ. Microbiol. 2001, 67, 1865–1873. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  533. Kong, K.F.; Vuong, C.; Otto, M. Staphylococcus quorum sensing in biofilm formation and infection. Int. J. Med. Microbiol. 2006, 296, 133–139. [Google Scholar] [CrossRef] [PubMed]
  534. Trappetti, C.; van der Maten, E.; Amin, Z.; Potter, A.J.; Chen, A.Y.; van Mourik, P.M.; Lawrence, A.J.; Paton, A.W.; Paton, J.C. Site of isolation determines biofilm formation and virulence phenotypes of Streptococcus pneumoniae serotype 3 clinical isolates. Infect. Immun. 2013, 81, 505–513. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  535. Tikhomirova, A.; Brazel, E.B.; McLean, K.T.; Agnew, H.N.; Paton, J.C.; Trappetti, C. The role of luxS in the middle ear Streptococcus pneumoniae isolate 947. Pathogens 2022, 11, 216. [Google Scholar] [CrossRef]
  536. Jesudhasan, P.R.; Cepeda, M.L.; Widmer, K.; Dowd, S.E.; Soni, K.A.; Hume, M.E.; Zhu, J.; Pillai, S.D. Transcriptome analysis of genes controlled by luxS/autoinducer-2 in Salmonella enterica serovar Typhimurium. Foodborne Pathog. Dis. 2010, 7, 399–410. [Google Scholar] [CrossRef] [Green Version]
  537. Song, S.; Wood, T.K. The primary physiological roles of Autoinducer 2 in Escherichia coli are chemotaxis and biofilm formation. Microorganisms 2021, 9, 386. [Google Scholar] [CrossRef]
  538. Yu, D.; Zhao, L.; Xue, T.; Sun, B. Staphylococcus aureus autoinducer-2 quorum sensing decreases biofilm formation in an icaR-dependent manner. BMC Microbiol. 2012, 12, 288. [Google Scholar] [CrossRef] [Green Version]
  539. Taga, M.E.; Miller, S.T.; Bassler, B.L. Lsr-mediated transport and processing of AI-2 in Salmonella typhimurium. Mol. Microbiol. 2003, 50, 1411–1427. [Google Scholar] [CrossRef]
  540. Choi, J.; Shin, D.; Ryu, S. Implication of quorum sensing in Salmonella enterica serovar Typhimurium virulence: The luxS gene is necessary for expression of genes in pathogenicity island 1. Infect. Immun. 2007, 75, 4885–4890. [Google Scholar] [CrossRef] [Green Version]
  541. González Barrios, A.F.; Zuo, R.; Hashimoto, Y.; Yang, L.; Bentley, W.E.; Wood, T.K. Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022). J. Bacteriol. 2006, 188, 305–316. [Google Scholar] [CrossRef] [Green Version]
  542. Laganenka, L.; Colin, R.; Sourjik, V. Chemotaxis towards autoinducer 2 mediates autoaggregation in Escherichia coli. Nat. Commun. 2016, 7, 12984. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  543. Limoli, D.H.; Jones, C.J.; Wozniak, D.J. Bacterial extracellular polysaccharides in biofilm formation and function. Microbiol. Spectr. 2015, 3, MB-0011-2014. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  544. Franklin, M.J.; Nivens, D.E.; Weadge, J.T.; Howell, P.L. Biosynthesis of the Pseudomonas aeruginosa extracellular polysaccharides, Alginate, Pel, and Psl. Front. Microbiol. 2011, 2, 167. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  545. Thomas, V.C.; Sadykov, M.R.; Chaudhari, S.S.; Jones, J.; Endres, J.L.; Widhelm, T.J.; Ahn, J.S.; Jawa, R.S.; Zimmerman, M.C.; Bayles, K.W. A central role for carbon-overflow pathways in the modulation of bacterial cell death. PLoS Pathog. 2014, 10, e1004205. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  546. Chaudhari, S.S.; Thomas, V.C.; Sadykov, M.R.; Bose, J.L.; Ahn, D.J.; Zimmerman, M.C.; Bayles, K.W. The LysR-type transcriptional regulator, CidR, regulates stationary phase cell death in Staphylococcus aureus. Mol. Microbiol. 2016, 101, 942–953. [Google Scholar] [CrossRef] [PubMed]
  547. Qu, D.; Hou, Z.; Li, J.; Luo, L.; Su, S.; Ye, Z.; Bai, Y.; Zhang, X.; Chen, G.; Li, Z.; et al. A new coumarin compound DCH combats methicillin-resistant Staphylococcus aureus biofilm by targeting arginine repressor. Sci. Adv. 2020, 6, eaay9597. [Google Scholar] [CrossRef]
  548. Beenken, K.E.; Dunman, P.M.; McAleese, F.; Macapagal, D.; Murphy, E.; Projan, S.J.; Blevins, J.S.; Smeltzer, M.S. Global gene expression in Staphylococcus aureus biofilms. J. Bacteriol. 2004, 186, 4665–4684. [Google Scholar] [CrossRef] [Green Version]
  549. Burgui, S.; Gil, C.; Solano, C.; Lasa, I.; Valle, J. A systematic evaluation of the two-component systems network reveals that ArlRS is a key regulator of catheter colonization by Staphylococcus aureus. Front. Microbiol. 2018, 9, 342. [Google Scholar] [CrossRef] [Green Version]
  550. Jin, Z.; Jiang, Q.; Fang, B.; Sun, B. The ArlR-MgrA regulatory cascade regulates PIA-dependent and protein-mediated biofilm formation in Rbf-dependent and Rbf-independent pathways. Int. J. Med. Microbiol. 2019, 309, 85–96. [Google Scholar] [CrossRef]
  551. Toledo-Arana, A.; Merino, N.; Vergara-Irigaray, M.; Débarbouillé, M.; Penadés, J.R.; Lasa, I. Staphylococcus aureus develops an alternative, ica-independent biofilm in the absence of the arlRS two-component system. J. Bacteriol. 2005, 187, 5318–5329. [Google Scholar] [CrossRef] [Green Version]
  552. Kwiecinski, J.M.; Kratofil, R.M.; Parlet, C.P.; Surewaard, B.G.J.; Kubes, P.; Horswill, A.R. Staphylococcus aureus uses the ArlRS and MgrA cascade to regulate immune evasion during skin infection. Cell Rep. 2021, 36, 109462. [Google Scholar] [CrossRef] [PubMed]
  553. Bose, J.L.; Lehman, M.K.; Fey, P.D.; Bayles, K.W. Contribution of the Staphylococcus aureus Atl AM and GL murein hydrolase activities in cell division, autolysis, and biofilm formation. PLoS ONE 2012, 7, e42244. [Google Scholar] [CrossRef] [PubMed]
  554. Yu, L.; Wang, H.; Han, X.; Li, W.; Xue, M.; Qi, K.; Chen, X.; Ni, J.; Deng, R.; Shang, F.; et al. The two-component system, BasSR, is involved in the regulation of biofilm and virulence in avian pathogenic Escherichia coli. Avian Pathol. 2020, 49, 532–546. [Google Scholar] [CrossRef] [PubMed]
  555. Petrova, O.E.; Sauer, K. SagS contributes to the motile-sessile switch and acts in concert with BfiSR to enable Pseudomonas aeruginosa biofilm formation. J. Bacteriol. 2011, 193, 6614–6628. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  556. Petrova, O.E.; Sauer, K. The novel two-component regulatory system BfiSR regulates biofilm development by controlling the small RNA rsmZ through CafA. J. Bacteriol. 2010, 192, 5275–5288. [Google Scholar] [CrossRef] [Green Version]
  557. Petrova, O.E.; Sauer, K. A novel signaling network essential for regulating Pseudomonas aeruginosa biofilm development. PLoS Pathog. 2009, 5, e1000668. [Google Scholar] [CrossRef] [Green Version]
  558. Russo, T.A.; Manohar, A.; Beanan, J.M.; Olson, R.; MacDonald, U.; Graham, J.; Umland, T.C. The response regulator BfmR is a potential drug target for Acinetobacter baumannii. mSphere 2016, 1, e00082-16. [Google Scholar] [CrossRef] [Green Version]
  559. Tomaras, A.P.; Flagler, M.J.; Dorsey, C.W.; Gaddy, J.A.; Actis, L.A. Characterization of a two-component regulatory system from Acinetobacter baumannii that controls biofilm formation and cellular morphology. Microbiology 2008, 154, 3398–3409. [Google Scholar] [CrossRef] [Green Version]
  560. Liou, M.L.; Soo, P.C.; Ling, S.R.; Kuo, H.Y.; Tang, C.Y.; Chang, K.C. The sensor kinase BfmS mediates virulence in Acinetobacter baumannii. J. Microbiol. Immunol. Infect. 2014, 47, 275–281. [Google Scholar] [CrossRef] [Green Version]
  561. Petrova, O.E.; Schurr, J.R.; Schurr, M.J.; Sauer, K. The novel Pseudomonas aeruginosa two-component regulator BfmR controls bacteriophage-mediated lysis and DNA release during biofilm development through PhdA. Mol. Microbiol. 2011, 81, 767–783. [Google Scholar] [CrossRef] [Green Version]
  562. Liu, C.; Sun, D.; Liu, J.; Chen, Y.; Zhou, X.; Ru, Y.; Zhu, J.; Liu, W. cAMP and c-di-GMP synergistically support biofilm maintenance through the direct interaction of their effectors. Nat. Commun. 2022, 13, 1493. [Google Scholar] [CrossRef] [PubMed]
  563. Ou, Q.; Fan, J.; Duan, D.; Xu, L.; Wang, J.; Zhou, D.; Yang, H.; Li, B. Involvement of cAMP receptor protein in biofilm formation, fimbria production, capsular polysaccharide biosynthesis and lethality in mouse of Klebsiella pneumoniae serotype K1 causing pyogenic liver abscess. J. Med. Microbiol. 2017, 66, 1–7. [Google Scholar] [CrossRef] [PubMed]
  564. Panjaitan, N.S.D.; Horng, Y.T.; Cheng, S.W.; Chung, W.T.; Soo, P.C. EtcABC, a putative EII Complex, regulates Type 3 fimbriae via CRP-cAMP signaling in Klebsiella pneumoniae. Front. Microbiol. 2019, 10, 1558. [Google Scholar] [CrossRef] [PubMed]
  565. Hufnagel, D.A.; Evans, M.L.; Greene, S.E.; Pinkner, J.S.; Hultgren, S.J.; Chapman, M.R. The Catabolite Repressor Protein-Cyclic AMP Complex regulates csgD and biofilm formation in uropathogenic Escherichia coli. J. Bacteriol. 2016, 198, 3329–3334. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  566. Endres, J.L.; Chaudhari, S.S.; Zhang, X.; Prahlad, J.; Wang, S.Q.; Foley, L.A.; Luca, S.; Bose, J.L.; Thomas, V.C.; Bayles, K.W. The Staphylococcus aureus CidA and LrgA Proteins are functional holins involved in the transport of by-products of carbohydrate metabolism. mBio 2022, 13, e0282721. [Google Scholar] [CrossRef]
  567. Lee, V.T.; Matewish, J.M.; Kessler, J.L.; Hyodo, M.; Hayakawa, Y.; Lory, S. A cyclic-di-GMP receptor required for bacterial exopolysaccharide production. Mol. Microbiol. 2007, 65, 1474–1484. [Google Scholar] [CrossRef] [Green Version]
  568. Chambers, J.R.; Liao, J.; Schurr, M.J.; Sauer, K. BrlR from Pseudomonas aeruginosa is a c-di-GMP-responsive transcription factor. Mol. Microbiol. 2014, 92, 471–487. [Google Scholar] [CrossRef] [Green Version]
  569. Gupta, K.; Liao, J.; Petrova, O.E.; Cherny, K.E.; Sauer, K. Elevated levels of the second messenger c-di-GMP contribute to antimicrobial resistance of Pseudomonas aeruginosa. Mol. Microbiol. 2014, 92, 488–506. [Google Scholar] [CrossRef] [Green Version]
  570. Boehm, A.; Steiner, S.; Zaehringer, F.; Casanova, A.; Hamburger, F.; Ritz, D.; Keck, W.; Ackermann, M.; Schirmer, T.; Jenal, U. Second messenger signalling governs Escherichia coli biofilm induction upon ribosomal stress. Mol. Microbiol. 2009, 72, 1500–1516. [Google Scholar] [CrossRef]
  571. Nicastro, G.G.; Kaihami, G.H.; Pereira, T.O.; Meireles, D.A.; Groleau, M.C.; Déziel, E.; Baldini, R.L. Cyclic-di-GMP levels affect Pseudomonas aeruginosa fitness in the presence of imipenem. Environ. Microbiol. 2014, 16, 1321–1333. [Google Scholar] [CrossRef] [Green Version]
  572. Jiale, Z.; Jian, J.; Xinyi, T.; Haoji, X.; Xueqin, H.; Xiao, W. Design of a novel antimicrobial peptide 1018M targeted ppGpp to inhibit MRSA biofilm formation. AMB Express 2021, 11, 49. [Google Scholar] [CrossRef] [PubMed]
  573. Rom, J.S.; Atwood, D.N.; Beenken, K.E.; Meeker, D.G.; Loughran, A.J.; Spencer, H.J.; Lantz, T.L.; Smeltzer, M.S. Impact of Staphylococcus aureus regulatory mutations that modulate biofilm formation in the USA300 strain LAC on virulence in a murine bacteremia model. Virulence 2017, 8, 1776–1790. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  574. Hauryliuk, V.; Atkinson, G.C.; Murakami, K.S.; Tenson, T.; Gerdes, K. Recent functional insights into the role of (p)ppGpp in bacterial physiology. Nat. Rev. Microbiol. 2015, 13, 298–309. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  575. Shetty, D.; Abrahante, J.E.; Chekabab, S.M.; Wu, X.; Korber, D.R.; Vidovic, S. Role of CpxR in biofilm development: Expression of key fimbrial, O-antigen and virulence operons of Salmonella Enteritidis. Int. J. Mol. Sci. 2019, 20, 5146. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  576. Moya, B.; Dötsch, A.; Juan, C.; Blázquez, J.; Zamorano, L.; Haussler, S.; Oliver, A. Beta-lactam resistance response triggered by inactivation of a nonessential penicillin-binding protein. PLoS Pathog. 2009, 5, e1000353. [Google Scholar] [CrossRef] [Green Version]
  577. Ogasawara, H.; Yamamoto, K.; Ishihama, A. Role of the biofilm master regulator CsgD in cross-regulation between biofilm formation and flagellar synthesis. J. Bacteriol. 2011, 193, 2587–2597. [Google Scholar] [CrossRef] [Green Version]
  578. Mika, F.; Hengge, R. Small RNAs in the control of RpoS, CsgD, and biofilm architecture of Escherichia coli. RNA Biol. 2014, 11, 494–507. [Google Scholar] [CrossRef] [Green Version]
  579. Gerstel, U.; Römling, U. The csgD promoter, a control unit for biofilm formation in Salmonella typhimurium. Res. Microbiol. 2003, 154, 659–667. [Google Scholar] [CrossRef]
  580. Zakikhany, K.; Harrington, C.R.; Nimtz, M.; Hinton, J.C.; Römling, U. Unphosphorylated CsgD controls biofilm formation in Salmonella enterica serovar Typhimurium. Mol. Microbiol. 2010, 77, 771–786. [Google Scholar] [CrossRef]
  581. Gross, M.; Cramton, S.E.; Götz, F.; Peschel, A. Key role of teichoic acid net charge in Staphylococcus aureus colonization of artificial surfaces. Infect. Immun. 2001, 69, 3423–3426. [Google Scholar] [CrossRef] [Green Version]
  582. Hancock, L.E.; Perego, M. The Enterococcus faecalis fsr two-component system controls biofilm development through production of gelatinase. J. Bacteriol. 2004, 186, 5629–5639. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  583. Macovei, L.; Ghosh, A.; Thomas, V.C.; Hancock, L.E.; Mahmood, S.; Zurek, L. Enterococcus faecalis with the gelatinase phenotype regulated by the fsr operon and with biofilm-forming capacity are common in the agricultural environment. Environ. Microbiol. 2009, 11, 1540–1547. [Google Scholar] [CrossRef] [PubMed]
  584. Thomas, V.C.; Thurlow, L.R.; Boyle, D.; Hancock, L.E. Regulation of autolysis-dependent extracellular DNA release by Enterococcus faecalis extracellular proteases influences biofilm development. J. Bacteriol. 2008, 190, 5690–5698. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  585. Chambonnier, G.; Roux, L.; Redelberger, D.; Fadel, F.; Filloux, A.; Sivaneson, M.; de Bentzmann, S.; Bordi, C. The hybrid histidine kinase LadS forms a multicomponent signal transduction system with the GacS/GacA two-component system in Pseudomonas aeruginosa. PLoS Genet. 2016, 12, e1006032. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  586. Brencic, A.; McFarland, K.A.; McManus, H.R.; Castang, S.; Mogno, I.; Dove, S.L.; Lory, S. The GacS/GacA signal transduction system of Pseudomonas aeruginosa acts exclusively through its control over the transcription of the RsmY and RsmZ regulatory small RNAs. Mol. Microbiol. 2009, 73, 434–445. [Google Scholar] [CrossRef] [Green Version]
  587. Cerqueira, G.M.; Kostoulias, X.; Khoo, C.; Aibinu, I.; Qu, Y.; Traven, A.; Peleg, A.Y. A global virulence regulator in Acinetobacter baumannii and its control of the phenylacetic acid catabolic pathway. J. Infect. Dis. 2014, 210, 46–55. [Google Scholar] [CrossRef] [Green Version]
  588. Parkins, M.D.; Ceri, H.; Storey, D.G. Pseudomonas aeruginosa GacA, a factor in multihost virulence, is also essential for biofilm formation. Mol. Microbiol. 2001, 40, 1215–1226. [Google Scholar] [CrossRef]
  589. Boles, B.R.; Thoendel, M.; Roth, A.J.; Horswill, A.R. Identification of genes involved in polysaccharide-independent Staphylococcus aureus biofilm formation. PLoS ONE 2010, 5, e10146. [Google Scholar] [CrossRef] [Green Version]
  590. Broder, U.N.; Jaeger, T.; Jenal, U. LadS is a calcium-responsive kinase that induces acute-to-chronic virulence switch in Pseudomonas aeruginosa. Nat. Microbiol. 2016, 2, 16184. [Google Scholar] [CrossRef]
  591. Gilbert, K.B.; Kim, T.H.; Gupta, R.; Greenberg, E.P.; Schuster, M. Global position analysis of the Pseudomonas aeruginosa quorum-sensing transcription factor LasR. Mol. Microbiol. 2009, 73, 1072–1085. [Google Scholar] [CrossRef] [Green Version]
  592. Diggle, S.P.; Stacey, R.E.; Dodd, C.; Cámara, M.; Williams, P.; Winzer, K. The galactophilic lectin, LecA, contributes to biofilm development in Pseudomonas aeruginosa. Environ. Microbiol. 2006, 8, 1095–1104. [Google Scholar] [CrossRef] [PubMed]
  593. Mann, E.E.; Rice, K.C.; Boles, B.R.; Endres, J.L.; Ranjit, D.; Chandramohan, L.; Tsang, L.H.; Smeltzer, M.S.; Horswill, A.R.; Bayles, K.W. Modulation of eDNA release and degradation affects Staphylococcus aureus biofilm maturation. PLoS ONE 2009, 4, e5822. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  594. Ma, R.; Qiu, S.; Jiang, Q.; Sun, H.; Xue, T.; Cai, G.; Sun, B. AI-2 quorum sensing negatively regulates rbf expression and biofilm formation in Staphylococcus aureus. Int. J. Med. Microbiol. 2017, 307, 257–267. [Google Scholar] [CrossRef] [PubMed]
  595. Vidal, J.E.; Ludewick, H.P.; Kunkel, R.M.; Zähner, D.; Klugman, K.P. The LuxS-dependent quorum-sensing system regulates early biofilm formation by Streptococcus pneumoniae strain D39. Infect. Immun. 2011, 79, 4050–4060. [Google Scholar] [CrossRef] [Green Version]
  596. Ju, X.; Li, J.; Zhu, M.; Lu, Z.; Lv, F.; Zhu, X.; Bie, X. Effect of the luxS gene on biofilm formation and antibiotic resistance by Salmonella serovar Dublin. Food Res. Int. 2018, 107, 385–393. [Google Scholar] [CrossRef]
  597. Moscoso, M.; García, E.; López, R. Biofilm formation by Streptococcus pneumoniae: Role of choline, extracellular DNA, and capsular polysaccharide in microbial accretion. J. Bacteriol. 2006, 188, 7785–7795. [Google Scholar] [CrossRef] [Green Version]
  598. Sharma-Kuinkel, B.K.; Mann, E.E.; Ahn, J.S.; Kuechenmeister, L.J.; Dunman, P.M.; Bayles, K.W. The Staphylococcus aureus LytSR two-component regulatory system affects biofilm formation. J. Bacteriol. 2009, 191, 4767–4775. [Google Scholar] [CrossRef] [Green Version]
  599. Patton, T.G.; Yang, S.J.; Bayles, K.W. The role of proton motive force in expression of the Staphylococcus aureus cid and lrg operons. Mol. Microbiol. 2006, 59, 1395–1404. [Google Scholar] [CrossRef]
  600. Crosby, H.A.; Schlievert, P.M.; Merriman, J.A.; King, J.M.; Salgado-Pabón, W.; Horswill, A.R. The Staphylococcus aureus global regulator MgrA modulates clumping and virulence by controlling surface protein expression. PLoS Pathog. 2016, 12, e1005604. [Google Scholar] [CrossRef]
  601. Tatke, G.; Kumari, H.; Silva-Herzog, E.; Ramirez, L.; Mathee, K. Pseudomonas aeruginosa MifS-MifR two-component system is specific for α-ketoglutarate utilization. PLoS ONE 2015, 10, e0129629. [Google Scholar] [CrossRef]
  602. Hadjifrangiskou, M.; Kostakioti, M.; Chen, S.L.; Henderson, J.P.; Greene, S.E.; Hultgren, S.J. A central metabolic circuit controlled by QseC in pathogenic Escherichia coli. Mol. Microbiol. 2011, 80, 1516–1529. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  603. Yamaguchi, Y.; Park, J.H.; Inouye, M. MqsR, a crucial regulator for quorum sensing and biofilm formation, is a GCU-specific mRNA interferase in Escherichia coli. J. Biol. Chem. 2009, 284, 28746–28753. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  604. Ji, Y.; Li, W.; Zhang, Y.; Chen, L.; Zhang, Y.; Zheng, X.; Huang, X.; Ni, B. QseB mediates biofilm formation and invasion in Salmonella enterica serovar Typhi. Microb. Pathog. 2017, 104, 6–11. [Google Scholar] [CrossRef] [PubMed]
  605. Kong, W.; Chen, L.; Zhao, J.; Shen, T.; Surette, M.G.; Shen, L.; Duan, K. Hybrid sensor kinase PA1611 in Pseudomonas aeruginosa regulates transitions between acute and chronic infection through direct interaction with RetS. Mol. Microbiol. 2013, 88, 784–797. [Google Scholar] [CrossRef] [PubMed]
  606. Hobbs, M.; Collie, E.S.; Free, P.D.; Livingston, S.P.; Mattick, J.S. PilS and PilR, a two-component transcriptional regulatory system controlling expression of type 4 fimbriae in Pseudomonas aeruginosa. Mol. Microbiol. 1993, 7, 669–682. [Google Scholar] [CrossRef] [PubMed]
  607. Kilmury, S.L.N.; Burrows, L.L. The Pseudomonas aeruginosa PilSR two-component system regulates both twitching and swimming motilities. mBio 2018, 9, e01310-18. [Google Scholar] [CrossRef] [Green Version]
  608. Izutsu, K.; Wada, A.; Wada, C. Expression of ribosome modulation factor (RMF) in Escherichia coli requires ppGpp. Genes Cells 2001, 6, 665–676. [Google Scholar] [CrossRef]
  609. Kim, K.; Islam, M.; Jung, H.W.; Lim, D.; Kim, K.; Lee, S.G.; Park, C.; Lee, J.C.; Shin, M. ppGpp signaling plays a critical role in virulence of Acinetobacter baumannii. Virulence 2021, 12, 2122–2132. [Google Scholar] [CrossRef]
  610. Wood, T.K.; Song, S. Forming and waking dormant cells: The ppGpp ribosome dimerization persister model. Biofilm 2020, 2, 100018. [Google Scholar] [CrossRef]
  611. Salzer, A.; Keinhörster, D.; Kästle, C.; Kästle, B.; Wolz, C. Small alarmone synthetases RelP and RelQ of Staphylococcus aureus are involved in biofilm formation and maintenance under cell wall stress conditions. Front. Microbiol. 2020, 11, 575882. [Google Scholar] [CrossRef]
  612. Horvatek, P.; Salzer, A.; Hanna, A.M.F.; Gratani, F.L.; Keinhörster, D.; Korn, N.; Borisova, M.; Mayer, C.; Rejman, D.; Mäder, U.; et al. Inducible expression of (pp)pGpp synthetases in Staphylococcus aureus is associated with activation of stress response genes. PLoS Genet. 2020, 16, e1009282. [Google Scholar] [CrossRef] [PubMed]
  613. Geiger, T.; Kästle, B.; Gratani, F.L.; Goerke, C.; Wolz, C. Two small (p)ppGpp synthases in Staphylococcus aureus mediate tolerance against cell envelope stress conditions. J. Bacteriol. 2014, 196, 894–902. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  614. Giraud, C.; Bernard, C.S.; Calderon, V.; Yang, L.; Filloux, A.; Molin, S.; Fichant, G.; Bordi, C.; de Bentzmann, S. The PprA-PprB two-component system activates CupE, the first non-archetypal Pseudomonas aeruginosa chaperone-usher pathway system assembling fimbriae. Environ. Microbiol. 2011, 13, 666–683. [Google Scholar] [CrossRef] [PubMed]
  615. de Bentzmann, S.; Giraud, C.; Bernard, C.S.; Calderon, V.; Ewald, F.; Plésiat, P.; Nguyen, C.; Grunwald, D.; Attree, I.; Jeannot, K.; et al. Unique biofilm signature, drug susceptibility and decreased virulence in Drosophila through the Pseudomonas aeruginosa two-component system PprAB. PLoS Pathog. 2012, 8, e1003052. [Google Scholar] [CrossRef]
  616. Cue, D.; Lei, M.G.; Lee, C.Y. Activation of sarX by Rbf is required for biofilm formation and icaADBC expression in Staphylococcus aureus. J. Bacteriol. 2013, 195, 1515–1524. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  617. Rowe, S.E.; Campbell, C.; Lowry, C.; O’Donnell, S.T.; Olson, M.E.; Lindgren, J.K.; Waters, E.M.; Fey, P.D.; O’Gara, J.P. AraC-type regulator Rbf controls the Staphylococcus epidermidis biofilm phenotype by negatively regulating the icaADBC repressor SarR. J. Bacteriol. 2016, 198, 2914–2924. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  618. Cue, D.; Lei, M.G.; Luong, T.T.; Kuechenmeister, L.; Dunman, P.M.; O’Donnell, S.; Rowe, S.; O’Gara, J.P.; Lee, C.Y. Rbf promotes biofilm formation by Staphylococcus aureus via repression of icaR, a negative regulator of icaADBC. J. Bacteriol. 2009, 191, 6363–6373. [Google Scholar] [CrossRef] [Green Version]
  619. Ferrières, L.; Clarke, D.J. The RcsC sensor kinase is required for normal biofilm formation in Escherichia coli K-12 and controls the expression of a regulon in.n response to growth on a solid surface. Mol. Microbiol. 2003, 50, 1665–1682. [Google Scholar] [CrossRef]
  620. Oropeza, R.; Salgado-Bravo, R.; Calva, E. Deletion analysis of RcsC reveals a novel signalling pathway controlling poly-N-acetylglucosamine synthesis and biofilm formation in Escherichia coli. Microbiology 2015, 161, 903–913. [Google Scholar] [CrossRef]
  621. Latasa, C.; García, B.; Echeverz, M.; Toledo-Arana, A.; Valle, J.; Campoy, S.; García-del Portillo, F.; Solano, C.; Lasa, I. Salmonella biofilm development depends on the phosphorylation status of RcsB. J. Bacteriol. 2012, 194, 3708–3722. [Google Scholar] [CrossRef] [Green Version]
  622. Wall, E.A.; Majdalani, N.; Gottesman, S. IgaA negatively regulates the Rcs phosphorelay via contact with the RcsD phosphotransfer protein. PLoS Genet. 2020, 16, e1008610. [Google Scholar] [CrossRef] [PubMed]
  623. Mikkelsen, H.; Ball, G.; Giraud, C.; Filloux, A. Expression of Pseudomonas aeruginosa CupD fimbrial genes is antagonistically controlled by RcsB and the EAL-containing PvrR response regulators. PLoS ONE 2009, 4, e6018. [Google Scholar] [CrossRef] [PubMed]
  624. Nicastro, G.G.; Boechat, A.L.; Abe, C.M.; Kaihami, G.H.; Baldini, R.L. Pseudomonas aeruginosa PA14 cupD transcription is activated by the RcsB response regulator, but repressed by its putative cognate sensor RcsC. FEMS Microbiol. Lett. 2009, 301, 115–123. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  625. Moscoso, J.A.; Mikkelsen, H.; Heeb, S.; Williams, P.; Filloux, A. The Pseudomonas aeruginosa sensor RetS switches type III and type VI secretion via c-di-GMP signalling. Environ. Microbiol. 2011, 13, 3128–3138. [Google Scholar] [CrossRef] [PubMed]
  626. Mukherjee, S.; Moustafa, D.A.; Stergioula, V.; Smith, C.D.; Goldberg, J.B.; Bassler, B.L. The PqsE and RhlR proteins are an autoinducer synthase-receptor pair that control virulence and biofilm development in Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. USA 2018, 115, E9411–E9418. [Google Scholar] [CrossRef] [Green Version]
  627. Mukherjee, S.; Moustafa, D.; Smith, C.D.; Goldberg, J.B.; Bassler, B.L. The RhlR quorum-sensing receptor controls Pseudomonas aeruginosa pathogenesis and biofilm development independently of its canonical homoserine lactone autoinducer. PLoS Pathog. 2017, 13, e1006504. [Google Scholar] [CrossRef] [Green Version]
  628. Kulasekara, H.D.; Ventre, I.; Kulasekara, B.R.; Lazdunski, A.; Filloux, A.; Lory, S. A novel two-component system controls the expression of Pseudomonas aeruginosa fimbrial cup genes. Mol. Microbiol. 2005, 55, 368–380. [Google Scholar] [CrossRef]
  629. Rao, F.; Yang, Y.; Qi, Y.; Liang, Z.X. Catalytic mechanism of cyclic di-GMP-specific phosphodiesterase: A study of the EAL domain-containing RocR from Pseudomonas aeruginosa. J. Bacteriol. 2008, 190, 3622–3631. [Google Scholar] [CrossRef] [Green Version]
  630. Mootz, J.M.; Benson, M.A.; Heim, C.E.; Crosby, H.A.; Kavanaugh, J.S.; Dunman, P.M.; Kielian, T.; Torres, V.J.; Horswill, A.R. Rot is a key regulator of Staphylococcus aureus biofilm formation. Mol. Microbiol. 2015, 96, 388–404. [Google Scholar] [CrossRef] [Green Version]
  631. Hengge, R. The two-component network and the general stress sigma factor RpoS (sigma S) in Escherichia coli. Adv. Exp. Med. Biol. 2008, 631, 40–53. [Google Scholar] [CrossRef]
  632. Battesti, A.; Majdalani, N.; Gottesman, S. The RpoS-mediated general stress response in Escherichia coli. Annu. Rev. Microbiol. 2011, 65, 189–213. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  633. Adams, J.L.; McLean, R.J. Impact of rpoS deletion on Escherichia coli biofilms. Appl. Environ. Microbiol. 1999, 65, 4285–4287. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  634. Ito, A.; May, T.; Kawata, K.; Okabe, S. Significance of rpoS during maturation of Escherichia coli biofilms. Biotechnol. Bioeng. 2008, 99, 1462–1471. [Google Scholar] [CrossRef]
  635. Corona-Izquierdo, F.P.; Membrillo-Hernández, J. A mutation in rpoS enhances biofilm formation in Escherichia coli during exponential phase of growth. FEMS Microbiol. Lett. 2002, 211, 105–110. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  636. Uhlich, G.A.; Chen, C.Y.; Cottrell, B.J.; Hofmann, C.S.; Dudley, E.G.; Strobaugh, T.P.; Nguyen, L.H. Phage insertion in mlrA and variations in rpoS limit curli expression and biofilm formation in Escherichia coli serotype O157: H7. Microbiology 2013, 159, 1586–1596. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  637. Murakami, K.; Ono, T.; Viducic, D.; Kayama, S.; Mori, M.; Hirota, K.; Nemoto, K.; Miyake, Y. Role for rpoS gene of Pseudomonas aeruginosa in antibiotic tolerance. FEMS Microbiol. Lett. 2005, 242, 161–167. [Google Scholar] [CrossRef] [Green Version]
  638. Kuchma, S.L.; Connolly, J.P.; O’Toole, G.A. A three-component regulatory system regulates biofilm maturation and type III secretion in Pseudomonas aeruginosa. J. Bacteriol. 2005, 187, 1441–1454. [Google Scholar] [CrossRef] [Green Version]
  639. Benson, M.A.; Lilo, S.; Nygaard, T.; Voyich, J.M.; Torres, V.J. Rot and SaeRS cooperate to activate expression of the staphylococcal superantigen-like exoproteins. J. Bacteriol. 2012, 194, 4355–4365. [Google Scholar] [CrossRef] [Green Version]
  640. Lou, Q.; Zhu, T.; Hu, J.; Ben, H.; Yang, J.; Yu, F.; Liu, J.; Wu, Y.; Fischer, A.; Francois, P.; et al. Role of the SaeRS two-component regulatory system in Staphylococcus epidermidis autolysis and biofilm formation. BMC Microbiol. 2011, 11, 146. [Google Scholar] [CrossRef] [Green Version]
  641. Petrova, O.E.; Gupta, K.; Liao, J.; Goodwine, J.S.; Sauer, K. Divide and conquer: The Pseudomonas aeruginosa two-component hybrid SagS enables biofilm formation and recalcitrance of biofilm cells to antimicrobial agents via distinct regulatory circuits. Environ. Microbiol. 2017, 19, 2005–2024. [Google Scholar] [CrossRef] [Green Version]
  642. Dingemans, J.; Poudyal, B.; Sondermann, H.; Sauer, K. The Yin and Yang of SagS: Distinct residues in the HmsP domain of SagS independently regulate biofilm formation and biofilm drug tolerance. mSphere 2018, 3, e00192-18. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  643. Poudyal, B.; Sauer, K. The ABC of biofilm drug tolerance: The MerR-like regulator BrlR is an activator of ABC transport systems, with PA1874-77 contributing to the tolerance of Pseudomonas aeruginosa biofilms to tobramycin. Antimicrob. Agents Chemother. 2018, 62, e01981-17. [Google Scholar] [CrossRef] [PubMed]
  644. Gupta, K.; Marques, C.N.; Petrova, O.E.; Sauer, K. Antimicrobial tolerance of Pseudomonas aeruginosa biofilms is activated during an early developmental stage and requires the two-component hybrid SagS. J. Bacteriol. 2013, 195, 4975–4987. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  645. Oriol, C.; Cengher, L.; Manna, A.C.; Mauro, T.; Pinel-Marie, M.L.; Felden, B.; Cheung, A.; Rouillon, A. Expanding the Staphylococcus aureus SarA regulon to small RNAs. mSystems 2021, 6, e0071321. [Google Scholar] [CrossRef]
  646. Jenul, C.; Horswill, A.R. Regulation of Staphylococcus aureus virulence. Microbiol. Spectr. 2019, 7, GPP3-0031-2018. [Google Scholar] [CrossRef]
  647. Beenken, K.E.; Blevins, J.S.; Smeltzer, M.S. Mutation of sarA in Staphylococcus aureus limits biofilm formation. Infect. Immun. 2003, 71, 4206–4211. [Google Scholar] [CrossRef] [Green Version]
  648. Tsang, L.H.; Cassat, J.E.; Shaw, L.N.; Beenken, K.E.; Smeltzer, M.S. Factors contributing to the biofilm-deficient phenotype of Staphylococcus aureus sarA mutants. PLoS ONE 2008, 3, e3361. [Google Scholar] [CrossRef]
  649. Hao, Z.; Guo, Y.; Rao, L.; Yu, J.; Zhan, Q.; Xu, Y.; Wang, B.; Wu, X.; Yu, F. Deletion of SarX decreases biofilm formation of Staphylococcus aureus in a Polysaccharide Intercellular Adhesin (PIA)-dependent manner by downregulating spa. Infect. Drug Resist. 2021, 14, 2241–2250. [Google Scholar] [CrossRef]
  650. Manna, A.C.; Cheung, A.L. Expression of SarX, a negative regulator of agr and exoprotein synthesis, is activated by MgrA in Staphylococcus aureus. J. Bacteriol. 2006, 188, 4288–4299. [Google Scholar] [CrossRef] [Green Version]
  651. Rowe, S.E.; Mahon, V.; Smith, S.G.; O’Gara, J.P. A novel role for SarX in Staphylococcus epidermidis biofilm regulation. Microbiology 2011, 157, 1042–1049. [Google Scholar] [CrossRef] [Green Version]
  652. Culler, H.F.; Couto, S.C.F.; Higa, J.S.; Ruiz, R.M.; Yang, M.J.; Bueris, V.; Franzolin, M.R.; Sircili, M.P. Role of SdiA on biofilm formation by atypical enteropathogenic Escherichia coli. Genes 2018, 9, 253. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  653. Shimada, K.; Ogasawara, H.; Yamada, K.; Shimura, M.; Kori, A.; Shimada, T.; Yamanaka, Y.; Yamamoto, K.; Ishihama, A. Screening of promoter-specific transcription factors: Multiple regulators for the sdiA gene involved in cell division control and quorum sensing. Microbiology 2013, 159, 2501–2512. [Google Scholar] [CrossRef] [PubMed]
  654. Shimada, T.; Shimada, K.; Matsui, M.; Kitai, Y.; Igarashi, J.; Suga, H.; Ishihama, A. Roles of cell division control factor SdiA: Recognition of quorum sensing signals and modulation of transcription regulation targets. Genes Cells 2014, 19, 405–418. [Google Scholar] [CrossRef]
  655. Lauderdale, K.J.; Boles, B.R.; Cheung, A.L.; Horswill, A.R. Interconnections between Sigma B, agr, and proteolytic activity in Staphylococcus aureus biofilm maturation. Infect. Immun. 2009, 77, 1623–1635. [Google Scholar] [CrossRef] [Green Version]
  656. Chang, Y.M.; Jeng, W.Y.; Ko, T.P.; Yeh, Y.J.; Chen, C.K.; Wang, A.H. Structural study of TcaR and its complexes with multiple antibiotics from Staphylococcus epidermidis. Proc. Natl. Acad. Sci. USA 2010, 107, 8617–8622. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  657. Jefferson, K.K.; Pier, D.B.; Goldmann, D.A.; Pier, G.B. The teicoplanin-associated locus regulator (TcaR) and the intercellular adhesin locus regulator (IcaR) are transcriptional inhibitors of the ica locus in Staphylococcus aureus. J. Bacteriol. 2004, 186, 2449–2456. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  658. Brandenberger, M.; Tschierske, M.; Giachino, P.; Wada, A.; Berger-Bächi, B. Inactivation of a novel three-cistronic operon tcaR-tcaA-tcaB increases teicoplanin resistance in Staphylococcus aureus. Biochim. Biophys. Acta 2000, 1523, 135–139. [Google Scholar] [CrossRef]
  659. Römling, U.; Galperin, M.Y.; Gomelsky, M. Cyclic di-GMP: The first 25 years of a universal bacterial second messenger. Microbiol. Mol. Biol. Rev. 2013, 77, 1–52. [Google Scholar] [CrossRef] [Green Version]
  660. Jenal, U.; Reinders, A.; Lori, C. Cyclic di-GMP: Second messenger extraordinaire. Nat. Rev. Microbiol. 2017, 15, 271–284. [Google Scholar] [CrossRef] [Green Version]
  661. Aline Dias da, P.; Nathalia Marins de, A.; Gabriel Guarany de, A.; Robson Francisco de, S.; Cristiane Rodrigues, G. The world of cyclic dinucleotides in bacterial behavior. Molecules 2020, 25, 2462. [Google Scholar] [CrossRef]
  662. Yoon, S.H.; Waters, C.M. The ever-expanding world of bacterial cyclic oligonucleotide second messengers. Curr. Opin. Microbiol. 2021, 60, 96–103. [Google Scholar] [CrossRef] [PubMed]
  663. Srivastava, D.; Waters, C.M. A tangled web: Regulatory connections between quorum sensing and cyclic Di-GMP. J. Bacteriol. 2012, 194, 4485–4493. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  664. Smith, K.D.; Lipchock, S.V.; Strobel, S.A. Structural and biochemical characterization of linear dinucleotide analogues bound to the c-di-GMP-I aptamer. Biochemistry 2012, 51, 425–432. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  665. Hengge, R. Principles of c-di-GMP signalling in bacteria. Nat. Rev. Microbiol. 2009, 7, 263–273. [Google Scholar] [CrossRef]
  666. Borlee, B.R.; Goldman, A.D.; Murakami, K.; Samudrala, R.; Wozniak, D.J.; Parsek, M.R. Pseudomonas aeruginosa uses a cyclic-di-GMP-regulated adhesin to reinforce the biofilm extracellular matrix. Mol. Microbiol. 2010, 75, 827–842. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  667. Reichhardt, C.; Jacobs, H.M.; Matwichuk, M.; Wong, C.; Wozniak, D.J.; Parsek, M.R. The versatile Pseudomonas aeruginosa biofilm matrix protein CdrA promotes aggregation through different extracellular exopolysaccharide interactions. J. Bacteriol. 2020, 202, e00216-20. [Google Scholar] [CrossRef] [PubMed]
  668. Merighi, M.; Lee, V.T.; Hyodo, M.; Hayakawa, Y.; Lory, S. The second messenger bis-(3′–5′)-cyclic-GMP and its PilZ domain-containing receptor Alg44 are required for alginate biosynthesis in Pseudomonas aeruginosa. Mol. Microbiol. 2007, 65, 876–895. [Google Scholar] [CrossRef]
  669. Maunders, E.; Welch, M. Matrix exopolysaccharides; the sticky side of biofilm formation. FEMS Microbiol. Lett. 2017, 364, fnx120. [Google Scholar] [CrossRef] [Green Version]
  670. Bianco, C.M.; Fröhlich, K.S.; Vanderpool, C.K. Bacterial Cyclopropane Fatty Acid Synthase mRNA is targeted by activating and repressing small RNAs. J. Bacteriol. 2019, 201, e00461-19. [Google Scholar] [CrossRef] [Green Version]
  671. Schoenfelder, S.M.K.; Lange, C.; Prakash, S.A.; Marincola, G.; Lerch, M.F.; Wencker, F.D.R.; Förstner, K.U.; Sharma, C.M.; Ziebuhr, W. The small non-coding RNA RsaE influences extracellular matrix composition in Staphylococcus epidermidis biofilm communities. PLoS Pathog. 2019, 15, e1007618. [Google Scholar] [CrossRef] [Green Version]
  672. Lerch, M.F.; Schoenfelder, S.M.K.; Marincola, G.; Wencker, F.D.R.; Eckart, M.; Förstner, K.U.; Sharma, C.M.; Thormann, K.M.; Kucklick, M.; Engelmann, S.; et al. A non-coding RNA from the intercellular adhesion (ica) locus of Staphylococcus epidermidis controls polysaccharide intercellular adhesion (PIA)-mediated biofilm formation. Mol. Microbiol. 2019, 111, 1571–1591. [Google Scholar] [CrossRef] [PubMed]
  673. Miller, C.L.; Romero, M.; Karna, S.L.; Chen, T.; Heeb, S.; Leung, K.P. RsmW, Pseudomonas aeruginosa small non-coding RsmA-binding RNA upregulated in biofilm versus planktonic growth conditions. BMC Microbiol. 2016, 16, 155. [Google Scholar] [CrossRef] [PubMed]
  674. Burrowes, E.; Baysse, C.; Adams, C.; O’Gara, F. Influence of the regulatory protein RsmA on cellular functions in Pseudomonas aeruginosa PAO1, as revealed by transcriptome analysis. Microbiology 2006, 152, 405–418. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  675. Allsopp, L.P.; Wood, T.E.; Howard, S.A.; Maggiorelli, F.; Nolan, L.M.; Wettstadt, S.; Filloux, A. RsmA and AmrZ orchestrate the assembly of all three type VI secretion systems in Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. USA 2017, 114, 7707–7712. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  676. Berk, V.; Fong, J.C.; Dempsey, G.T.; Develioglu, O.N.; Zhuang, X.; Liphardt, J.; Yildiz, F.H.; Chu, S. Molecular architecture and assembly principles of Vibrio cholerae biofilms. Science 2012, 337, 236–239. [Google Scholar] [CrossRef] [Green Version]
  677. Beyhan, S.; Bilecen, K.; Salama, S.R.; Casper-Lindley, C.; Yildiz, F.H. Regulation of rugosity and biofilm formation in Vibrio cholerae: Comparison of VpsT and VpsR regulons and epistasis analysis of vpsT, vpsR, and hapR. J. Bacteriol. 2007, 189, 388–402. [Google Scholar] [CrossRef] [Green Version]
  678. Hsieh, M.L.; Waters, C.M.; Hinton, D.M. VpsR directly activates transcription of multiple biofilm genes in Vibrio cholerae. J. Bacteriol. 2020, 202, e00234-20. [Google Scholar] [CrossRef]
  679. Chakrabortty, T.; Roy Chowdhury, S.; Ghosh, B.; Sen, U. Crystal structure of VpsR revealed novel dimeric architecture and c-di-GMP binding site: Mechanistic implications in oligomerization, ATPase activity and DNA binding. J. Mol. Biol. 2022, 434, 167354. [Google Scholar] [CrossRef]
  680. Krasteva, P.V.; Fong, J.C.; Shikuma, N.J.; Beyhan, S.; Navarro, M.V.; Yildiz, F.H.; Sondermann, H. Vibrio cholerae VpsT regulates matrix production and motility by directly sensing cyclic di-GMP. Science 2010, 327, 866–868. [Google Scholar] [CrossRef] [Green Version]
  681. Matter, L.B.; Ares, M.A.; Abundes-Gallegos, J.; Cedillo, M.L.; Yáñez, J.A.; Martínez-Laguna, Y.; De la Cruz, M.A.; Girón, J.A. The CpxRA stress response system regulates virulence features of avian pathogenic Escherichia coli. Environ. Microbiol. 2018, 20, 3363–3377. [Google Scholar] [CrossRef]
  682. Pamp, S.J.; Tolker-Nielsen, T. Multiple roles of biosurfactants in structural biofilm development by Pseudomonas aeruginosa. J. Bacteriol. 2007, 189, 2531–2539. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  683. Tolker-Nielsen, T. Biofilm development. Microbiol. Spectr. 2015, 3, Mb-0001-2014. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  684. Das, T.; Kutty, S.K.; Tavallaie, R.; Ibugo, A.I.; Panchompoo, J.; Sehar, S.; Aldous, L.; Yeung, A.W.; Thomas, S.R.; Kumar, N.; et al. Phenazine virulence factor binding to extracellular DNA is important for Pseudomonas aeruginosa biofilm formation. Sci. Rep. 2015, 5, 8398. [Google Scholar] [CrossRef] [PubMed]
  685. Davenport, P.W.; Griffin, J.L.; Welch, M. Quorum sensing is accompanied by global metabolic changes in the opportunistic human pathogen Pseudomonas aeruginosa. J. Bacteriol. 2015, 197, 2072–2082. [Google Scholar] [CrossRef] [Green Version]
  686. Liu, Z.; Hossain, S.S.; Morales Moreira, Z.; Haney, C.H. Putrescine and its metabolic precursor arginine promote biofilm and c-di-GMP synthesis in Pseudomonas aeruginosa. J. Bacteriol. 2021, 204, Jb0029721. [Google Scholar] [CrossRef]
  687. Chen, G.; Gan, J.; Yang, C.; Zuo, Y.; Peng, J.; Li, M.; Huo, W.; Xie, Y.; Zhang, Y.; Wang, T.; et al. The SiaA/B/C/D signaling network regulates biofilm formation in Pseudomonas aeruginosa. EMBO J. 2020, 39, e103412. [Google Scholar] [CrossRef]
  688. Bjarnsholt, T.; Tolker-Nielsen, T.; Høiby, N.; Givskov, M. Interference of Pseudomonas aeruginosa signalling and biofilm formation for infection control. Expert Rev. Mol. Med. 2010, 12, e11. [Google Scholar] [CrossRef]
  689. Yan, S.; Wu, G. Can biofilm be reversed through quorum sensing in Pseudomonas aeruginosa? Front. Microbiol. 2019, 10, 1582. [Google Scholar] [CrossRef] [Green Version]
  690. Rampioni, G.; Pustelny, C.; Fletcher, M.P.; Wright, V.J.; Bruce, M.; Rumbaugh, K.P.; Heeb, S.; Cámara, M.; Williams, P. Transcriptomic analysis reveals a global alkyl-quinolone-independent regulatory role for PqsE in facilitating the environmental adaptation of Pseudomonas aeruginosa to plant and animal hosts. Environ. Microbiol. 2010, 12, 1659–1673. [Google Scholar] [CrossRef] [Green Version]
  691. Kay, E.; Humair, B.; Dénervaud, V.; Riedel, K.; Spahr, S.; Eberl, L.; Valverde, C.; Haas, D. Two GacA-dependent small RNAs modulate the quorum-sensing response in Pseudomonas aeruginosa. J. Bacteriol. 2006, 188, 6026–6033. [Google Scholar] [CrossRef] [Green Version]
  692. Bordi, C.; Lamy, M.C.; Ventre, I.; Termine, E.; Hachani, A.; Fillet, S.; Roche, B.; Bleves, S.; Méjean, V.; Lazdunski, A.; et al. Regulatory RNAs and the HptB/RetS signalling pathways fine-tune Pseudomonas aeruginosa pathogenesis. Mol. Microbiol. 2010, 76, 1427–1443. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  693. Colley, B.; Dederer, V.; Carnell, M.; Kjelleberg, S.; Rice, S.A.; Klebensberger, J. SiaA/D Interconnects c-di-GMP and RsmA signaling to coordinate cellular aggregation of Pseudomonas aeruginosa in response to environmental conditions. Front. Microbiol. 2016, 7, 179. [Google Scholar] [CrossRef] [PubMed]
  694. Davies, J.A.; Harrison, J.J.; Marques, L.L.; Foglia, G.R.; Stremick, C.A.; Storey, D.G.; Turner, R.J.; Olson, M.E.; Ceri, H. The GacS sensor kinase controls phenotypic reversion of small colony variants isolated from biofilms of Pseudomonas aeruginosa PA14. FEMS Microbiol. Ecol. 2007, 59, 32–46. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  695. Petrova, O.E.; Schurr, J.R.; Schurr, M.J.; Sauer, K. Microcolony formation by the opportunistic pathogen Pseudomonas aeruginosa requires pyruvate and pyruvate fermentation. Mol. Microbiol. 2012, 86, 819–835. [Google Scholar] [CrossRef] [Green Version]
  696. Katharios-Lanwermeyer, S.; O’Toole, G.A. Biofilm maintenance as an active process: Evidence that biofilms work hard to stay put. J. Bacteriol. 2022, 204, e0058721. [Google Scholar] [CrossRef]
  697. McCarthy, R.R.; Valentini, M.; Filloux, A. Contribution of Cyclic di-GMP in the control of Type III and Type VI secretion in Pseudomonas aeruginosa. Methods Mol. Biol. 2017, 1657, 213–224. [Google Scholar] [CrossRef]
  698. Sivaneson, M.; Mikkelsen, H.; Ventre, I.; Bordi, C.; Filloux, A. Two-component regulatory systems in Pseudomonas aeruginosa: An intricate network mediating fimbrial and efflux pump gene expression. Mol. Microbiol. 2011, 79, 1353–1366. [Google Scholar] [CrossRef] [Green Version]
  699. Nguyen, H.T.T.; Nguyen, T.H.; Otto, M. The staphylococcal exopolysaccharide PIA—Biosynthesis and role in biofilm formation, colonization, and infection. Comput. Struct. Biotechnol. J. 2020, 18, 3324–3334. [Google Scholar] [CrossRef]
  700. O’Neill, E.; Pozzi, C.; Houston, P.; Humphreys, H.; Robinson, D.A.; Loughman, A.; Foster, T.J.; O’Gara, J.P. A novel Staphylococcus aureus biofilm phenotype mediated by the fibronectin-binding proteins, FnBPA and FnBPB. J. Bacteriol. 2008, 190, 3835–3850. [Google Scholar] [CrossRef] [Green Version]
  701. Foster, T.J.; Geoghegan, J.A.; Ganesh, V.K.; Höök, M. Adhesion, invasion and evasion: The many functions of the surface proteins of Staphylococcus aureus. Nat. Rev. Microbiol. 2014, 12, 49–62. [Google Scholar] [CrossRef] [Green Version]
  702. McCourt, J.; O’Halloran, D.P.; McCarthy, H.; O’Gara, J.P.; Geoghegan, J.A. Fibronectin-binding proteins are required for biofilm formation by community-associated methicillin-resistant Staphylococcus aureus strain LAC. FEMS Microbiol. Lett. 2014, 353, 157–164. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  703. Herman-Bausier, P.; El-Kirat-Chatel, S.; Foster, T.J.; Geoghegan, J.A.; Dufrêne, Y.F. Staphylococcus aureus Fibronectin-Binding Protein A mediates cell-cell adhesion through low-affinity homophilic bonds. mBio 2015, 6, e00413-15. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  704. Corrigan, R.M.; Rigby, D.; Handley, P.; Foster, T.J. The role of Staphylococcus aureus surface protein SasG in adherence and biofilm formation. Microbiology 2007, 153, 2435–2446. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  705. Yonemoto, K.; Chiba, A.; Sugimoto, S.; Sato, C.; Saito, M.; Kinjo, Y.; Marumo, K.; Mizunoe, Y. Redundant and distinct roles of secreted protein Eap and cell wall-anchored protein SasG in biofilm formation and pathogenicity of Staphylococcus aureus. Infect. Immun. 2019, 87, e00894-18. [Google Scholar] [CrossRef] [Green Version]
  706. Formosa-Dague, C.; Speziale, P.; Foster, T.J.; Geoghegan, J.A.; Dufrêne, Y.F. Zinc-dependent mechanical properties of Staphylococcus aureus biofilm-forming surface protein SasG. Proc. Natl. Acad. Sci. USA 2016, 113, 410–415. [Google Scholar] [CrossRef] [Green Version]
  707. Valle, J.; Fang, X.; Lasa, I. Revisiting Bap multidomain protein: More than sticking bacteria together. Front. Microbiol. 2020, 11, 613581. [Google Scholar] [CrossRef]
  708. Taglialegna, A.; Navarro, S.; Ventura, S.; Garnett, J.A.; Matthews, S.; Penades, J.R.; Lasa, I.; Valle, J. Staphylococcal Bap proteins build amyloid scaffold biofilm matrices in response to environmental signals. PLoS Pathog. 2016, 12, e1005711. [Google Scholar] [CrossRef] [Green Version]
  709. Merino, N.; Toledo-Arana, A.; Vergara-Irigaray, M.; Valle, J.; Solano, C.; Calvo, E.; Lopez, J.A.; Foster, T.J.; Penadés, J.R.; Lasa, I. Protein A-mediated multicellular behavior in Staphylococcus aureus. J. Bacteriol. 2009, 191, 832–843. [Google Scholar] [CrossRef] [Green Version]
  710. Boles, B.R.; Horswill, A.R. Agr-mediated dispersal of Staphylococcus aureus biofilms. PLoS Pathog. 2008, 4, e1000052. [Google Scholar] [CrossRef]
  711. Periasamy, S.; Joo, H.S.; Duong, A.C.; Bach, T.H.; Tan, V.Y.; Chatterjee, S.S.; Cheung, G.Y.; Otto, M. How Staphylococcus aureus biofilms develop their characteristic structure. Proc. Natl. Acad. Sci. USA 2012, 109, 1281–1286. [Google Scholar] [CrossRef] [Green Version]
  712. Yarwood, J.M.; McCormick, J.K.; Schlievert, P.M. Identification of a novel two-component regulatory system that acts in global regulation of virulence factors of Staphylococcus aureus. J. Bacteriol. 2001, 183, 1113–1123. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  713. Bayles, K.W. The biological role of death and lysis in biofilm development. Nat. Rev. Microbiol. 2007, 5, 721–726. [Google Scholar] [CrossRef] [PubMed]
  714. Sadykov, M.R.; Bayles, K.W. The control of death and lysis in staphylococcal biofilms: A coordination of physiological signals. Curr. Opin. Microbiol. 2012, 15, 211–215. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  715. Grande, R.; Nistico, L.; Sambanthamoorthy, K.; Longwell, M.; Iannitelli, A.; Cellini, L.; Di Stefano, A.; Hall Stoodley, L.; Stoodley, P. Temporal expression of agrB, cidA, and alsS in the early development of Staphylococcus aureus UAMS-1 biofilm formation and the structural role of extracellular DNA and carbohydrates. Pathog. Dis. 2014, 70, 414–422. [Google Scholar] [CrossRef] [Green Version]
  716. Ranjit, D.K.; Endres, J.L.; Bayles, K.W. Staphylococcus aureus CidA and LrgA proteins exhibit holin-like properties. J. Bacteriol. 2011, 193, 2468–2476. [Google Scholar] [CrossRef] [Green Version]
  717. Balestrino, D.; Ghigo, J.M.; Charbonnel, N.; Haagensen, J.A.; Forestier, C. The characterization of functions involved in the establishment and maturation of Klebsiella pneumoniae in vitro biofilm reveals dual roles for surface exopolysaccharides. Environ. Microbiol. 2008, 10, 685–701. [Google Scholar] [CrossRef]
  718. Alcántar-Curiel, M.D.; Blackburn, D.; Saldaña, Z.; Gayosso-Vázquez, C.; Iovine, N.M.; De la Cruz, M.A.; Girón, J.A. Multi-functional analysis of Klebsiella pneumoniae fimbrial types in adherence and biofilm formation. Virulence 2013, 4, 129–138. [Google Scholar] [CrossRef] [Green Version]
  719. Vuotto, C.; Longo, F.; Pascolini, C.; Donelli, G.; Balice, M.P.; Libori, M.F.; Tiracchia, V.; Salvia, A.; Varaldo, P.E. Biofilm formation and antibiotic resistance in Klebsiella pneumoniae urinary strains. J. Appl. Microbiol. 2017, 123, 1003–1018. [Google Scholar] [CrossRef]
  720. Chen, K.M.; Chiang, M.K.; Wang, M.; Ho, H.C.; Lu, M.C.; Lai, Y.C. The role of pgaC in Klebsiella pneumoniae virulence and biofilm formation. Microb. Pathog. 2014, 77, 89–99. [Google Scholar] [CrossRef]
  721. Peng, D.; Li, X.; Liu, P.; Zhou, X.; Luo, M.; Su, K.; Chen, S.; Zhang, Z.; He, Q.; Qiu, J.; et al. Transcriptional regulation of galF by RcsAB affects capsular polysaccharide formation in Klebsiella pneumoniae NTUH-K2044. Microbiol. Res. 2018, 216, 70–78. [Google Scholar] [CrossRef]
  722. Boddicker, J.D.; Anderson, R.A.; Jagnow, J.; Clegg, S. Signature-tagged mutagenesis of Klebsiella pneumoniae to identify genes that influence biofilm formation on extracellular matrix material. Infect. Immun. 2006, 74, 4590–4597. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  723. Hennequin, C.; Forestier, C. oxyR, a LysR-type regulator involved in Klebsiella pneumoniae mucosal and abiotic colonization. Infect. Immun. 2009, 77, 5449–5457. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  724. Sharma, D.; Misba, L.; Khan, A.U. Antibiotics versus biofilm: An emerging battleground in microbial communities. Antimicrob. Resist. Infect. Control. 2019, 8, 76. [Google Scholar] [CrossRef] [PubMed]
  725. Mah, T.F. Biofilm-specific antibiotic resistance. Future Microbiol. 2012, 7, 1061–1072. [Google Scholar] [CrossRef] [Green Version]
  726. Ito, A.; Taniuchi, A.; May, T.; Kawata, K.; Okabe, S. Increased antibiotic resistance of Escherichia coli in mature biofilms. Appl. Environ. Microbiol. 2009, 75, 4093–4100. [Google Scholar] [CrossRef] [Green Version]
  727. Orazi, G.; O’Toole, G.A. "It Takes a Village": Mechanisms underlying antimicrobial recalcitrance of polymicrobial biofilms. J. Bacteriol. 2019, 202, e00530-19. [Google Scholar] [CrossRef]
  728. Soto, S.M. Role of efflux pumps in the antibiotic resistance of bacteria embedded in a biofilm. Virulence 2013, 4, 223–229. [Google Scholar] [CrossRef] [Green Version]
  729. Garnett, J.A.; Matthews, S. Interactions in bacterial biofilm development: A structural perspective. Curr. Protein Pept. Sci. 2012, 13, 739–755. [Google Scholar] [CrossRef] [Green Version]
  730. Lebeaux, D.; Ghigo, J.M.; Beloin, C. Biofilm-related infections: Bridging the gap between clinical management and fundamental aspects of recalcitrance toward antibiotics. Microbiol. Mol. Biol. Rev. 2014, 78, 510–543. [Google Scholar] [CrossRef] [Green Version]
  731. Shenkutie, A.M.; Yao, M.Z.; Siu, G.K.; Wong, B.K.C.; Leung, P.H. Biofilm-induced antibiotic resistance in clinical Acinetobacter baumannii isolates. Antibiotics 2020, 9, 817. [Google Scholar] [CrossRef]
  732. Bowler, P.; Murphy, C.; Wolcott, R. Biofilm exacerbates antibiotic resistance: Is this a current oversight in antimicrobial stewardship? Antimicrob. Resist. Infect. Control. 2020, 9, 162. [Google Scholar] [CrossRef] [PubMed]
  733. Anderl, J.N.; Franklin, M.J.; Stewart, P.S. Role of antibiotic penetration limitation in Klebsiella pneumoniae biofilm resistance to ampicillin and ciprofloxacin. Antimicrob. Agents Chemother. 2000, 44, 1818–1824. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  734. Lynch, S.V.; Dixon, L.; Benoit, M.R.; Brodie, E.L.; Keyhan, M.; Hu, P.; Ackerley, D.F.; Andersen, G.L.; Matin, A. Role of the rapA gene in controlling antibiotic resistance of Escherichia coli biofilms. Antimicrob. Agents Chemother. 2007, 51, 3650–3658. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  735. Singh, S.; Datta, S.; Narayanan, K.B.; Rajnish, K.N. Bacterial exo-polysaccharides in biofilms: Role in antimicrobial resistance and treatments. J. Genet. Eng. Biotechnol 2021, 19, 140. [Google Scholar] [CrossRef] [PubMed]
  736. Vega, N.M.; Allison, K.R.; Samuels, A.N.; Klempner, M.S.; Collins, J.J. Salmonella typhimurium intercepts Escherichia coli signaling to enhance antibiotic tolerance. Proc. Natl. Acad. Sci. USA 2013, 110, 14420–14425. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  737. Harriott, M.M.; Noverr, M.C. Candida albicans and Staphylococcus aureus form polymicrobial biofilms: Effects on antimicrobial resistance. Antimicrob. Agents Chemother. 2009, 53, 3914–3922. [Google Scholar] [CrossRef] [Green Version]
  738. Kean, R.; Rajendran, R.; Haggarty, J.; Townsend, E.M.; Short, B.; Burgess, K.E.; Lang, S.; Millington, O.; Mackay, W.G.; Williams, C.; et al. Candida albicans mycofilms support Staphylococcus aureus colonization and enhances miconazole resistance in dual-species interactions. Front. Microbiol. 2017, 8, 258. [Google Scholar] [CrossRef] [Green Version]
  739. Tseng, B.S.; Zhang, W.; Harrison, J.J.; Quach, T.P.; Song, J.L.; Penterman, J.; Singh, P.K.; Chopp, D.L.; Packman, A.I.; Parsek, M.R. The extracellular matrix protects Pseudomonas aeruginosa biofilms by limiting the penetration of tobramycin. Environ. Microbiol. 2013, 15, 2865–2878. [Google Scholar] [CrossRef] [Green Version]
  740. Hentzer, M.; Teitzel, G.M.; Balzer, G.J.; Heydorn, A.; Molin, S.; Givskov, M.; Parsek, M.R. Alginate overproduction affects Pseudomonas aeruginosa biofilm structure and function. J. Bacteriol. 2001, 183, 5395–5401. [Google Scholar] [CrossRef] [Green Version]
  741. Teitzel, G.M.; Parsek, M.R. Heavy metal resistance of biofilm and planktonic Pseudomonas aeruginosa. Appl. Environ. Microbiol. 2003, 69, 2313–2320. [Google Scholar] [CrossRef] [Green Version]
  742. Johnson, L.; Horsman, S.R.; Charron-Mazenod, L.; Turnbull, A.L.; Mulcahy, H.; Surette, M.G.; Lewenza, S. Extracellular DNA-induced antimicrobial peptide resistance in Salmonella enterica serovar Typhimurium. BMC Microbiol. 2013, 13, 115. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  743. Soh, E.Y.; Smith, F.; Gimenez, M.R.; Yang, L.; Vejborg, R.M.; Fletcher, M.; Halliday, N.; Bleves, S.; Heeb, S.; Cámara, M.; et al. Disruption of the Pseudomonas aeruginosa Tat system perturbs PQS-dependent quorum sensing and biofilm maturation through lack of the Rieske cytochrome bc1 sub-unit. PLoS Pathog. 2021, 17, e1009425. [Google Scholar] [CrossRef] [PubMed]
  744. Beebout, C.J.; Eberly, A.R.; Werby, S.H.; Reasoner, S.A.; Brannon, J.R.; De, S.; Fitzgerald, M.J.; Huggins, M.M.; Clayton, D.B.; Cegelski, L.; et al. Respiratory heterogeneity shapes biofilm formation and host colonization in uropathogenic Escherichia coli. mBio 2019, 10, e02400-18. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  745. Nadell, C.D.; Drescher, K.; Foster, K.R. Spatial structure, cooperation and competition in biofilms. Nat. Rev. Microbiol. 2016, 14, 589–600. [Google Scholar] [CrossRef] [PubMed]
  746. Stewart, P.S.; Zhang, T.; Xu, R.; Pitts, B.; Walters, M.C.; Roe, F.; Kikhney, J.; Moter, A. Reaction-diffusion theory explains hypoxia and heterogeneous growth within microbial biofilms associated with chronic infections. NPJ Biofilms Microbiomes 2016, 2, 16012. [Google Scholar] [CrossRef]
  747. Walters, M.C., 3rd; Roe, F.; Bugnicourt, A.; Franklin, M.J.; Stewart, P.S. Contributions of antibiotic penetration, oxygen limitation, and low metabolic activity to tolerance of Pseudomonas aeruginosa biofilms to ciprofloxacin and tobramycin. Antimicrob. Agents Chemother. 2003, 47, 317–323. [Google Scholar] [CrossRef] [Green Version]
  748. Chung, H.S.; Yao, Z.; Goehring, N.W.; Kishony, R.; Beckwith, J.; Kahne, D. Rapid beta-lactam-induced lysis requires successful assembly of the cell division machinery. Proc. Natl. Acad. Sci. USA 2009, 106, 21872–21877. [Google Scholar] [CrossRef] [Green Version]
  749. Martínez, J.L.; Rojo, F. Metabolic regulation of antibiotic resistance. FEMS Microbiol. Rev. 2011, 35, 768–789. [Google Scholar] [CrossRef]
  750. Levin, B.R.; Rozen, D.E. Non-inherited antibiotic resistance. Nat. Rev. Microbiol. 2006, 4, 556–562. [Google Scholar] [CrossRef]
  751. Waters, E.M.; Rowe, S.E.; O’Gara, J.P.; Conlon, B.P. Convergence of Staphylococcus aureus persister and biofilm research: Can biofilms be defined as communities of adherent persister cells? PLoS Pathog. 2016, 12, e1006012. [Google Scholar] [CrossRef]
  752. Nguyen, D.; Joshi-Datar, A.; Lepine, F.; Bauerle, E.; Olakanmi, O.; Beer, K.; McKay, G.; Siehnel, R.; Schafhauser, J.; Wang, Y.; et al. Active starvation responses mediate antibiotic tolerance in biofilms and nutrient-limited bacteria. Science 2011, 334, 982–986. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  753. Bernier, S.P.; Lebeaux, D.; DeFrancesco, A.S.; Valomon, A.; Soubigou, G.; Coppée, J.Y.; Ghigo, J.M.; Beloin, C. Starvation, together with the SOS response, mediates high biofilm-specific tolerance to the fluoroquinolone ofloxacin. PLoS Genet. 2013, 9, e1003144. [Google Scholar] [CrossRef] [Green Version]
  754. Ma, D.; Mandell, J.B.; Donegan, N.P.; Cheung, A.L.; Ma, W.; Rothenberger, S.; Shanks, R.M.Q.; Richardson, A.R.; Urish, K.L. The toxin-antitoxin MazEF drives Staphylococcus aureus biofilm formation, antibiotic tolerance, and chronic infection. mBio 2019, 10, e01658-19. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  755. Tiwari, P.; Arora, G.; Singh, M.; Kidwai, S.; Narayan, O.P.; Singh, R. MazF ribonucleases promote Mycobacterium tuberculosis drug tolerance and virulence in guinea pigs. Nat. Commun. 2015, 6, 6059. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  756. Zhang, Y.; Zhang, J.; Hoeflich, K.P.; Ikura, M.; Qing, G.; Inouye, M. MazF cleaves cellular mRNAs specifically at ACA to block protein synthesis in Escherichia coli. Mol. Cell 2003, 12, 913–923. [Google Scholar] [CrossRef]
  757. Al-Attar, S.; Yu, Y.; Pinkse, M.; Hoeser, J.; Friedrich, T.; Bald, D.; de Vries, S. Cytochrome bd displays significant quinol peroxidase activity. Sci. Rep. 2016, 6, 27631. [Google Scholar] [CrossRef] [Green Version]
  758. Beebout, C.J.; Sominsky, L.A.; Eberly, A.R.; Van Horn, G.T.; Hadjifrangiskou, M. Cytochrome bd promotes Escherichia coli biofilm antibiotic tolerance by regulating accumulation of noxious chemicals. NPJ Biofilms Microbiomes 2021, 7, 35. [Google Scholar] [CrossRef]
  759. Hall, C.W.; Hinz, A.J.; Gagnon, L.B.; Zhang, L.; Nadeau, J.P.; Copeland, S.; Saha, B.; Mah, T.F. Pseudomonas aeruginosa biofilm antibiotic resistance gene ndvB expression requires the RpoS stationary-phase sigma factor. Appl. Environ. Microbiol. 2018, 84, e02762-17. [Google Scholar] [CrossRef] [Green Version]
  760. Schellhorn, H.E. Elucidating the function of the RpoS regulon. Future Microbiol. 2014, 9, 497–507. [Google Scholar] [CrossRef]
  761. Lloyd, M.G.; Vossler, J.L.; Nomura, C.T.; Moffat, J.F. Blocking RpoN reduces virulence of Pseudomonas aeruginosa isolated from cystic fibrosis patients and increases antibiotic sensitivity in a laboratory strain. Sci. Rep. 2019, 9, 6677. [Google Scholar] [CrossRef] [Green Version]
  762. Bagge, N.; Hentzer, M.; Andersen, J.B.; Ciofu, O.; Givskov, M.; Høiby, N. Dynamics and spatial distribution of beta-lactamase expression in Pseudomonas aeruginosa biofilms. Antimicrob. Agents Chemother. 2004, 48, 1168–1174. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  763. Bagge, N.; Schuster, M.; Hentzer, M.; Ciofu, O.; Givskov, M.; Greenberg, E.P.; Høiby, N. Pseudomonas aeruginosa biofilms exposed to imipenem exhibit changes in global gene expression and beta-lactamase and alginate production. Antimicrob. Agents Chemother. 2004, 48, 1175–1187. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  764. Huszczynski, S.M.; Lam, J.S.; Khursigara, C.M. The role of Pseudomonas aeruginosa lipopolysaccharide in bacterial pathogenesis and physiology. Pathogens 2019, 9, 6. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  765. Simpson, B.W.; Trent, M.S. Pushing the envelope: LPS modifications and their consequences. Nat. Rev. Microbiol. 2019, 17, 403–416. [Google Scholar] [CrossRef] [PubMed]
  766. Zhang, L.; Hinz, A.J.; Nadeau, J.P.; Mah, T.F. Pseudomonas aeruginosa tssC1 links type VI secretion and biofilm-specific antibiotic resistance. J. Bacteriol. 2011, 193, 5510–5513. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  767. Dale, J.L.; Cagnazzo, J.; Phan, C.Q.; Barnes, A.M.; Dunny, G.M. Multiple roles for Enterococcus faecalis glycosyltransferases in biofilm-associated antibiotic resistance, cell envelope integrity, and conjugative transfer. Antimicrob. Agents Chemother. 2015, 59, 4094–4105. [Google Scholar] [CrossRef] [Green Version]
  768. Greene, C.; Vadlamudi, G.; Newton, D.; Foxman, B.; Xi, C. The influence of biofilm formation and multidrug resistance on environmental survival of clinical and environmental isolates of Acinetobacter baumannii. Am. J. Infect. Control. 2016, 44, e65–e71. [Google Scholar] [CrossRef]
  769. Bardbari, A.M.; Arabestani, M.R.; Karami, M.; Keramat, F.; Alikhani, M.Y.; Bagheri, K.P. Correlation between ability of biofilm formation with their responsible genes and MDR patterns in clinical and environmental Acinetobacter baumannii isolates. Microb. Pathog. 2017, 108, 122–128. [Google Scholar] [CrossRef]
  770. Shin, J.H.; Lee, H.W.; Kim, S.M.; Kim, J. Proteomic analysis of Acinetobacter baumannii in biofilm and planktonic growth mode. J. Microbiol. 2009, 47, 728–735. [Google Scholar] [CrossRef]
  771. Gillis, R.J.; White, K.G.; Choi, K.H.; Wagner, V.E.; Schweizer, H.P.; Iglewski, B.H. Molecular basis of azithromycin-resistant Pseudomonas aeruginosa biofilms. Antimicrob. Agents Chemother. 2005, 49, 3858–3867. [Google Scholar] [CrossRef] [Green Version]
  772. Zhang, L.; Mah, T.F. Involvement of a novel efflux system in biofilm-specific resistance to antibiotics. J. Bacteriol. 2008, 190, 4447–4452. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  773. Molin, S.; Tolker-Nielsen, T. Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure. Curr. Opin. Biotechnol 2003, 14, 255–261. [Google Scholar] [CrossRef]
  774. Baugh, S.; Phillips, C.R.; Ekanayaka, A.S.; Piddock, L.J.; Webber, M.A. Inhibition of multidrug efflux as a strategy to prevent biofilm formation. J. Antimicrob. Chemother. 2014, 69, 673–681. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  775. Reza, A.; Sutton, J.M.; Rahman, K.M. Effectiveness of efflux pump inhibitors as biofilm disruptors and resistance breakers in gram-negative (ESKAPEE) bacteria. Antibiotics 2019, 8, 229. [Google Scholar] [CrossRef] [Green Version]
  776. Dawan, J.; Li, Y.; Lu, F.; He, X.; Ahn, J. Role of efflux pump-mediated antibiotic resistance in quorum sensing-regulated biofilm formation by Salmonella Typhimurium. Pathogens 2022, 11, 147. [Google Scholar] [CrossRef]
  777. He, X.; Ahn, J. Differential gene expression in planktonic and biofilm cells of multiple antibiotic-resistant Salmonella Typhimurium and Staphylococcus aureus. FEMS Microbiol. Lett. 2011, 325, 180–188. [Google Scholar] [CrossRef] [Green Version]
  778. Waite, R.D.; Papakonstantinopoulou, A.; Littler, E.; Curtis, M.A. Transcriptome analysis of Pseudomonas aeruginosa growth: Comparison of gene expression in planktonic cultures and developing and mature biofilms. J. Bacteriol. 2005, 187, 6571–6576. [Google Scholar] [CrossRef] [Green Version]
  779. Hirakata, Y.; Srikumar, R.; Poole, K.; Gotoh, N.; Suematsu, T.; Kohno, S.; Kamihira, S.; Hancock, R.E.; Speert, D.P. Multidrug efflux systems play an important role in the invasiveness of Pseudomonas aeruginosa. J. Exp. Med. 2002, 196, 109–118. [Google Scholar] [CrossRef] [Green Version]
  780. Buckley, A.M.; Webber, M.A.; Cooles, S.; Randall, L.P.; La Ragione, R.M.; Woodward, M.J.; Piddock, L.J. The AcrAB-TolC efflux system of Salmonella enterica serovar Typhimurium plays a role in pathogenesis. Cell Microbiol. 2006, 8, 847–856. [Google Scholar] [CrossRef]
  781. Subhadra, B.; Surendran, S.; Lim, B.R.; Yim, J.S.; Kim, D.H.; Woo, K.; Kim, H.J.; Oh, M.H.; Choi, C.H. Regulation of the AcrAB efflux system by the quorum-sensing regulator AnoR in Acinetobacter nosocomialis. J. Microbiol. 2020, 58, 507–518. [Google Scholar] [CrossRef]
  782. Subhadra, B.; Kim, J.; Kim, D.H.; Woo, K.; Oh, M.H.; Choi, C.H. Local repressor AcrR regulates AcrAB efflux pump required for biofilm formation and virulence in Acinetobacter nosocomialis. Front. Cell Infect. Microbiol. 2018, 8, 270. [Google Scholar] [CrossRef] [PubMed]
  783. Padilla, E.; Llobet, E.; Doménech-Sánchez, A.; Martínez-Martínez, L.; Bengoechea, J.A.; Albertí, S. Klebsiella pneumoniae AcrAB efflux pump contributes to antimicrobial resistance and virulence. Antimicrob. Agents Chemother. 2010, 54, 177–183. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  784. Bialek, S.; Lavigne, J.P.; Chevalier, J.; Marcon, E.; Leflon-Guibout, V.; Davin, A.; Moreau, R.; Pagès, J.M.; Nicolas-Chanoine, M.H. Membrane efflux and influx modulate both multidrug resistance and virulence of Klebsiella pneumoniae in a Caenorhabditis elegans model. Antimicrob. Agents Chemother. 2010, 54, 4373–4378. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  785. Coudeyras, S.; Nakusi, L.; Charbonnel, N.; Forestier, C. A tripartite efflux pump involved in gastrointestinal colonization by Klebsiella pneumoniae confers a tolerance response to inorganic acid. Infect. Immun. 2008, 76, 4633–4641. [Google Scholar] [CrossRef] [Green Version]
  786. Singh, S.; Kalia, N.P.; Joshi, P.; Kumar, A.; Sharma, P.R.; Kumar, A.; Bharate, S.B.; Khan, I.A. Boeravinone B, A novel dual inhibitor of NorA bacterial efflux pump of Staphylococcus aureus and human P-Glycoprotein, reduces the biofilm formation and intracellular invasion of bacteria. Front. Microbiol. 2017, 8, 1868. [Google Scholar] [CrossRef]
  787. Abd El-Baky, R.M.; Sandle, T.; John, J.; Abuo-Rahma, G.E.A.; Hetta, H.F. A novel mechanism of action of ketoconazole: Inhibition of the NorA efflux pump system and biofilm formation in multidrug-resistant Staphylococcus aureus. Infect. Drug Resist. 2019, 12, 1703–1718. [Google Scholar] [CrossRef] [Green Version]
  788. Hirakata, Y.; Kondo, A.; Hoshino, K.; Yano, H.; Arai, K.; Hirotani, A.; Kunishima, H.; Yamamoto, N.; Hatta, M.; Kitagawa, M.; et al. Efflux pump inhibitors reduce the invasiveness of Pseudomonas aeruginosa. Int. J. Antimicrob. Agents 2009, 34, 343–346. [Google Scholar] [CrossRef]
  789. Banerjee, S.; Sionov, R.V.; Feldman, M.; Smoum, R.; Mechoulam, R.; Steinberg, D. Anandamide alters the membrane properties, halts the cell division and prevents drug efflux in multidrug resistant Staphylococcus aureus. Sci. Rep. 2021, 11, 8690. [Google Scholar] [CrossRef]
  790. Henson, K.E.; Yim, J.; Smith, J.R.; Sakoulas, G.; Rybak, M.J. β-Lactamase inhibitors enhance the synergy between β-Lactam antibiotics and daptomycin against methicillin-resistant Staphylococcus aureus. Antimicrob. Agents Chemother. 2017, 61, e01564-16. [Google Scholar] [CrossRef] [Green Version]
  791. Worthington, R.J.; Melander, C. Combination approaches to combat multidrug-resistant bacteria. Trends Biotechnol. 2013, 31, 177–184. [Google Scholar] [CrossRef] [Green Version]
  792. Annunziato, G. Strategies to overcome antimicrobial resistance (AMR) making use of non-essential target inhibitors: A review. Int. J. Mol. Sci. 2019, 20, 5844. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  793. Zhou, L.; Zhang, Y.; Ge, Y.; Zhu, X.; Pan, J. Regulatory mechanisms and promising applications of quorum sensing-inhibiting agents in control of bacterial biofilm formation. Front. Microbiol. 2020, 11, 589640. [Google Scholar] [CrossRef] [PubMed]
  794. Rémy, B.; Mion, S.; Plener, L.; Elias, M.; Chabrière, E.; Daudé, D. Interference in Bacterial quorum sensing: A biopharmaceutical perspective. Front. Pharmacol. 2018, 9, 203. [Google Scholar] [CrossRef] [PubMed]
  795. Nadar, S.; Khan, T.; Patching, S.G.; Omri, A. Development of antibiofilm therapeutics strategies to overcome antimicrobial drug resistance. Microorganisms 2022, 10, 303. [Google Scholar] [CrossRef]
  796. Silber, N.; Matos de Opitz, C.L.; Mayer, C.; Sass, P. Cell division protein FtsZ: From structure and mechanism to antibiotic target. Future Microbiol. 2020, 15, 801–831. [Google Scholar] [CrossRef]
  797. Naclerio, G.A.; Sintim, H.O. Multiple ways to kill bacteria via inhibiting novel cell wall or membrane targets. Future Med. Chem. 2020, 12, 1253–1279. [Google Scholar] [CrossRef]
  798. Farha, M.A.; Leung, A.; Sewell, E.W.; D’Elia, M.A.; Allison, S.E.; Ejim, L.; Pereira, P.M.; Pinho, M.G.; Wright, G.D.; Brown, E.D. Inhibition of WTA synthesis blocks the cooperative action of PBPs and sensitizes MRSA to β-lactams. ACS Chem. Biol. 2013, 8, 226–233. [Google Scholar] [CrossRef]
  799. Munguia, J.; Nizet, V. Pharmacological targeting of the host-pathogen interaction: Alternatives to classical antibiotics to combat drug-resistant superbugs. Trends Pharmacol. Sci. 2017, 38, 473–488. [Google Scholar] [CrossRef] [Green Version]
  800. Douafer, H.; Andrieu, V.; Phanstiel, O.t.; Brunel, J.M. Antibiotic adjuvants: Make antibiotics great again! J. Med. Chem. 2019, 62, 8665–8681. [Google Scholar] [CrossRef]
  801. Sharma, N.; Chhillar, A.K.; Dahiya, S.; Choudhary, P.; Punia, A.; Gulia, P. Antibiotic adjuvants: A promising approach to combat multidrug resistant bacteria. Curr. Drug Targets 2021, 22, 1334–1345. [Google Scholar] [CrossRef]
  802. Wright, G.D. Antibiotic adjuvants: Rescuing antibiotics from resistance. Trends Microbiol. 2016, 24, 862–871. [Google Scholar] [CrossRef] [PubMed]
  803. Appendino, G.; Gibbons, S.; Giana, A.; Pagani, A.; Grassi, G.; Stavri, M.; Smith, E.; Rahman, M.M. Antibacterial cannabinoids from Cannabis sativa: A structure-activity study. J. Nat. Prod. 2008, 71, 1427–1430. [Google Scholar] [CrossRef] [PubMed]
  804. Blaskovich, M.A.T.; Kavanagh, A.M.; Elliott, A.G.; Zhang, B.; Ramu, S.; Amado, M.; Lowe, G.J.; Hinton, A.O.; Pham, D.M.T.; Zuegg, J.; et al. The antimicrobial potential of cannabidiol. Commun. Biol. 2021, 4, 7. [Google Scholar] [CrossRef] [PubMed]
  805. Sionov, R.V.; Steinberg, D. Anti-microbial activity of phytocannabinoids and endocannabinoids in the light of their physiological and pathophysiological roles. Biomedicines 2022, 10, 631. [Google Scholar] [CrossRef]
  806. Hussein, M.; Allobawi, R.; Levou, I.; Blaskovich, M.A.T.; Rao, G.G.; Li, J.; Velkov, T. Mechanisms underlying synergistic killing of polymyxin b in combination with cannabidiol against Acinetobacter baumannii: A metabolomic study. Pharmaceutics 2022, 14, 786. [Google Scholar] [CrossRef] [PubMed]
  807. Abichabki, N.; Zacharias, L.V.; Moreira, N.C.; Bellissimo-Rodrigues, F.; Moreira, F.L.; Benzi, J.R.L.; Ogasawara, T.M.C.; Ferreira, J.C.; Ribeiro, C.M.; Pavan, F.R.; et al. Potential cannabidiol (CBD) repurposing as antibacterial and promising therapy of CBD plus polymyxin B (PB) against PB-resistant gram-negative bacilli. Sci. Rep. 2022, 12, 6454. [Google Scholar] [CrossRef]
  808. Grimsey, E.M.; Piddock, L.J.V. Do phenothiazines possess antimicrobial and efflux inhibitory properties? FEMS Microbiol. Rev. 2019, 43, 577–590. [Google Scholar] [CrossRef]
  809. Ejim, L.; Farha, M.A.; Falconer, S.B.; Wildenhain, J.; Coombes, B.K.; Tyers, M.; Brown, E.D.; Wright, G.D. Combinations of antibiotics and nonantibiotic drugs enhance antimicrobial efficacy. Nat. Chem. Biol. 2011, 7, 348–350. [Google Scholar] [CrossRef]
  810. Vargiu, A.V.; Ruggerone, P.; Opperman, T.J.; Nguyen, S.T.; Nikaido, H. Molecular mechanism of MBX2319 inhibition of Escherichia coli AcrB multidrug efflux pump and comparison with other inhibitors. Antimicrob. Agents Chemother. 2014, 58, 6224–6234. [Google Scholar] [CrossRef] [Green Version]
  811. Hu, Y.; Coates, A. Zidovudine enhances activity of carbapenems against NDM-1-producing Enterobacteriaceae. J. Antimicrob. Chemother. 2021, 76, 2302–2305. [Google Scholar] [CrossRef]
  812. Torres, N.S.; Abercrombie, J.J.; Srinivasan, A.; Lopez-Ribot, J.L.; Ramasubramanian, A.K.; Leung, K.P. Screening a commercial library of pharmacologically active small molecules against Staphylococcus aureus biofilms. Antimicrob. Agents Chemother. 2016, 60, 5663–5672. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  813. Peyclit, L.; Baron, S.A.; Hadjadj, L.; Rolain, J.M. In vitro screening of a 1280 FDA-Approved drugs library against multidrug-resistant and extensively drug-resistant bacteria. Antibiotics 2022, 11, 291. [Google Scholar] [CrossRef] [PubMed]
  814. Ayerbe-Algaba, R.; Gil-Marqués, M.L.; Jiménez-Mejías, M.E.; Sánchez-Encinales, V.; Parra-Millán, R.; Pachón-Ibáñez, M.E.; Pachón, J.; Smani, Y. Synergistic activity of niclosamide in combination with colistin against colistin-susceptible and colistin-resistant Acinetobacter baumannii and Klebsiella pneumoniae. Front. Cell Infect. Microbiol. 2018, 8, 348. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  815. Domalaon, R.; De Silva, P.M.; Kumar, A.; Zhanel, G.G.; Schweizer, F. The Anthelmintic drug niclosamide synergizes with colistin and reverses colistin resistance in Gram-negative Bacilli. Antimicrob. Agents Chemother. 2019, 63, e02574-18. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  816. Ayerbe-Algaba, R.; Gil-Marqués, M.L.; Miró-Canturri, A.; Parra-Millán, R.; Pachón-Ibáñez, M.E.; Jiménez-Mejías, M.E.; Pachón, J.; Smani, Y. The anthelmintic oxyclozanide restores the activity of colistin against colistin-resistant Gram-negative bacilli. Int. J. Antimicrob. Agents 2019, 54, 507–512. [Google Scholar] [CrossRef]
  817. Domalaon, R.; Okunnu, O.; Zhanel, G.G.; Schweizer, F. Synergistic combinations of anthelmintic salicylanilides oxyclozanide, rafoxanide, and closantel with colistin eradicates multidrug-resistant colistin-resistant Gram-negative bacilli. J. Antibiot. 2019, 72, 605–616. [Google Scholar] [CrossRef]
  818. Anju, V.T.; Busi, S.; Ranganathan, S.; Ampasala, D.R.; Kumar, S.; Suchiang, K.; Kumavath, R.; Dyavaiah, M. Sesamin and sesamolin rescues Caenorhabditis elegans from Pseudomonas aeruginosa infection through the attenuation of quorum sensing regulated virulence factors. Microb. Pathog. 2021, 155, 104912. [Google Scholar] [CrossRef]
  819. Burt, S.A.; Ojo-Fakunle, V.T.; Woertman, J.; Veldhuizen, E.J. The natural antimicrobial carvacrol inhibits quorum sensing in Chromobacterium violaceum and reduces bacterial biofilm formation at sub-lethal concentrations. PLoS ONE 2014, 9, e93414. [Google Scholar] [CrossRef] [Green Version]
  820. Shang, D.; Han, X.; Du, W.; Kou, Z.; Jiang, F. Trp-Containing antibacterial peptides impair quorum sensing and biofilm development in multidrug-resistant Pseudomonas aeruginosa and exhibit synergistic effects with antibiotics. Front. Microbiol. 2021, 12, 611009. [Google Scholar] [CrossRef]
  821. Huang, Y.; Chen, Y.; Zhang, L.H. The roles of microbial cell-cell chemical communication systems in the modulation of antimicrobial resistance. Antibiotics 2020, 9, 779. [Google Scholar] [CrossRef]
  822. King, A.; Blackledge, M.S. Evaluation of small molecule kinase inhibitors as novel antimicrobial and antibiofilm agents. Chem. Biol. Drug Des. 2021, 98, 1038–1064. [Google Scholar] [CrossRef] [PubMed]
  823. Jakobsen, T.H.; Warming, A.N.; Vejborg, R.M.; Moscoso, J.A.; Stegger, M.; Lorenzen, F.; Rybtke, M.; Andersen, J.B.; Petersen, R.; Andersen, P.S.; et al. A broad range quorum sensing inhibitor working through sRNA inhibition. Sci. Rep. 2017, 7, 9857. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  824. Jakobsen, T.H.; van Gennip, M.; Phipps, R.K.; Shanmugham, M.S.; Christensen, L.D.; Alhede, M.; Skindersoe, M.E.; Rasmussen, T.B.; Friedrich, K.; Uthe, F.; et al. Ajoene, a sulfur-rich molecule from garlic, inhibits genes controlled by quorum sensing. Antimicrob. Agents Chemother. 2012, 56, 2314–2325. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  825. Xu, Z.; Zhang, H.; Yu, H.; Dai, Q.; Xiong, J.; Sheng, H.; Qiu, J.; Jiang, L.; Peng, J.; He, X.; et al. Allicin inhibits Pseudomonas aeruginosa virulence by suppressing the rhl and pqs quorum-sensing systems. Can. J. Microbiol. 2019, 65, 563–574. [Google Scholar] [CrossRef] [Green Version]
  826. Luo, J.; Dong, B.; Wang, K.; Cai, S.; Liu, T.; Cheng, X.; Lei, D.; Chen, Y.; Li, Y.; Kong, J.; et al. Baicalin inhibits biofilm formation, attenuates the quorum sensing-controlled virulence and enhances Pseudomonas aeruginosa clearance in a mouse peritoneal implant infection model. PLoS ONE 2017, 12, e0176883. [Google Scholar] [CrossRef] [Green Version]
  827. Liu, T.; Luo, J.; Bi, G.; Du, Z.; Kong, J.; Chen, Y. Antibacterial synergy between linezolid and baicalein against methicillin-resistant Staphylococcus aureus biofilm in vivo. Microb. Pathog. 2020, 147, 104411. [Google Scholar] [CrossRef]
  828. Zhang, P.; Guo, Q.; Wei, Z.; Yang, Q.; Guo, Z.; Shen, L.; Duan, K.; Chen, L. Baicalin represses type three secretion system of Pseudomonas aeruginosa through PQS System. Molecules 2021, 26, 1497. [Google Scholar] [CrossRef]
  829. Peng, L.Y.; Yuan, M.; Wu, Z.M.; Song, K.; Zhang, C.L.; An, Q.; Xia, F.; Yu, J.L.; Yi, P.F.; Fu, B.D.; et al. Anti-bacterial activity of baicalin against APEC through inhibition of quorum sensing and inflammatory responses. Sci. Rep. 2019, 9, 4063. [Google Scholar] [CrossRef]
  830. Abinaya, M.; Gayathri, M. Inhibition of biofilm formation, quorum sensing activity and molecular docking study of isolated 3, 5, 7-Trihydroxyflavone from Alstonia scholaris leaf against P.aeruginosa. Bioorg. Chem. 2019, 87, 291–301. [Google Scholar] [CrossRef]
  831. Xu, C.; Wang, F.; Huang, F.; Yang, M.; He, D.; Deng, L. Targeting effect of berberine on type I fimbriae of Salmonella Typhimurium and its effective inhibition of biofilm. Appl. Microbiol. Biotechnol. 2021, 105, 1563–1573. [Google Scholar] [CrossRef]
  832. Sun, T.; Li, X.D.; Hong, J.; Liu, C.; Zhang, X.L.; Zheng, J.P.; Xu, Y.J.; Ou, Z.Y.; Zheng, J.L.; Yu, D.J. Inhibitory effect of two traditional Chinese medicine monomers, berberine and matrine, on the quorum sensing system of antimicrobial-resistant Escherichia coli. Front. Microbiol. 2019, 10, 2584. [Google Scholar] [CrossRef] [PubMed]
  833. Rajkumari, J.; Borkotoky, S.; Murali, A.; Suchiang, K.; Mohanty, S.K.; Busi, S. Attenuation of quorum sensing controlled virulence factors and biofilm formation in Pseudomonas aeruginosa by pentacyclic triterpenes, betulin and betulinic acid. Microb. Pathog. 2018, 118, 48–60. [Google Scholar] [CrossRef] [PubMed]
  834. O’Loughlin, C.T.; Miller, L.C.; Siryaporn, A.; Drescher, K.; Semmelhack, M.F.; Bassler, B.L. A quorum-sensing inhibitor blocks Pseudomonas aeruginosa virulence and biofilm formation. Proc. Natl. Acad. Sci. USA 2013, 110, 17981–17986. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  835. Huang, Z.X.; Yu, J.H.; Xu, X.J.; Xu, X.F.; Zeng, T.; Lin, J.; Chen, W.M. Cajaninstilbene acid analogues as novel quorum sensing and biofilm inhibitors of Pseudomonas aeruginosa. Microb. Pathog. 2020, 148, 104414. [Google Scholar] [CrossRef] [PubMed]
  836. Aqawi, M.; Gallily, R.; Sionov, R.V.; Zaks, B.; Friedman, M.; Steinberg, D. Cannabigerol prevents quorum sensing and biofilm formation of Vibrio harveyi. Front. Microbiol. 2020, 11, 858. [Google Scholar] [CrossRef]
  837. Aqawi, M.; Sionov, R.V.; Gallily, R.; Friedman, M.; Steinberg, D. Anti-bacterial properties of cannabigerol toward Streptococcus mutans. Front. Microbiol. 2021, 12, 656471. [Google Scholar] [CrossRef]
  838. Aqawi, M.; Sionov, R.V.; Gallily, R.; Friedman, M.; Steinberg, D. Anti-biofilm activity of cannabigerol against Streptococcus mutans. Microorganisms 2021, 9, 2031. [Google Scholar] [CrossRef]
  839. Farha, M.A.; El-Halfawy, O.M.; Gale, R.T.; MacNair, C.R.; Carfrae, L.A.; Zhang, X.; Jentsch, N.G.; Magolan, J.; Brown, E.D. Uncovering the hidden antibiotic potential of Cannabis. ACS Infect. Dis. 2020, 6, 338–346. [Google Scholar] [CrossRef]
  840. Selvaraj, A.; Valliammai, A.; Muthuramalingam, P.; Priya, A.; Suba, M.; Ramesh, M.; Karutha Pandian, S. Carvacrol targets SarA and CrtM of methicillin-resistant Staphylococcus aureus to mitigate biofilm formation and staphyloxanthin synthesis: An in vitro and in vivo approach. ACS Omega 2020, 5, 31100–31114. [Google Scholar] [CrossRef]
  841. Pesingi, P.V.; Singh, B.R.; Pesingi, P.K.; Bhardwaj, M.; Singh, S.V.; Kumawat, M.; Sinha, D.K.; Gandham, R.K. MexAB-OprM efflux pump of Pseudomonas aeruginosa offers resistance to carvacrol: A herbal antimicrobial agent. Front. Microbiol. 2019, 10, 2664. [Google Scholar] [CrossRef]
  842. Tapia-Rodriguez, M.R.; Bernal-Mercado, A.T.; Gutierrez-Pacheco, M.M.; Vazquez-Armenta, F.J.; Hernandez-Mendoza, A.; Gonzalez-Aguilar, G.A.; Martinez-Tellez, M.A.; Nazzaro, F.; Ayala-Zavala, J.F. Virulence of Pseudomonas aeruginosa exposed to carvacrol: Alterations of the quorum sensing at enzymatic and gene levels. J. Cell Commun. Signal. 2019, 13, 531–537. [Google Scholar] [CrossRef] [PubMed]
  843. Rajkumari, J.; Borkotoky, S.; Murali, A.; Suchiang, K.; Mohanty, S.K.; Busi, S. Cinnamic acid attenuates quorum sensing associated virulence factors and biofilm formation in Pseudomonas aeruginosa PAO1. Biotechnol. Lett. 2018, 40, 1087–1100. [Google Scholar] [CrossRef] [PubMed]
  844. Jantaruk, P.; Pabuprapap, W.; Nakaew, A.; Kunthalert, D.; Suksamrarn, A. 4-methoxybenzalacetone, the cinnamic acid analog as a potential quorum sensing inhibitor against Chromobacterium violaceum and Pseudomonas aeruginosa. World J. Microbiol. Biotechnol. 2021, 37, 153. [Google Scholar] [CrossRef] [PubMed]
  845. Topa, S.H.; Palombo, E.A.; Kingshott, P.; Blackall, L.L. Activity of cinnamaldehyde on quorum sensing and biofilm susceptibility to antibiotics in Pseudomonas aeruginosa. Microorganisms 2020, 8, 455. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  846. Topa, S.H.; Subramoni, S.; Palombo, E.A.; Kingshott, P.; Rice, S.A.; Blackall, L.L. Cinnamaldehyde disrupts biofilm formation and swarming motility of Pseudomonas aeruginosa. Microbiology 2018, 164, 1087–1097. [Google Scholar] [CrossRef]
  847. Ali, I.A.A.; Matinlinna, J.P.; Lévesque, C.M.; Neelakantan, P. Trans-Cinnamaldehyde attenuates Enterococcus faecalis virulence and inhibits biofilm formation. Antibiotics 2021, 10, 702. [Google Scholar] [CrossRef]
  848. Amalaradjou, M.A.; Narayanan, A.; Baskaran, S.A.; Venkitanarayanan, K. Antibiofilm effect of trans-cinnamaldehyde on uropathogenic Escherichia coli. J. Urol. 2010, 184, 358–363. [Google Scholar] [CrossRef]
  849. Amalaradjou, M.A.; Narayanan, A.; Venkitanarayanan, K. Trans-cinnamaldehyde decreases attachment and invasion of uropathogenic Escherichia coli in urinary tract epithelial cells by modulating virulence gene expression. J. Urol. 2011, 185, 1526–1531. [Google Scholar] [CrossRef]
  850. Jia, P.; Xue, Y.J.; Duan, X.J.; Shao, S.H. Effect of cinnamaldehyde on biofilm formation and sarA expression by methicillin-resistant Staphylococcus aureus. Lett. Appl. Microbiol. 2011, 53, 409–416. [Google Scholar] [CrossRef]
  851. Albano, M.; Crulhas, B.P.; Alves, F.C.B.; Pereira, A.F.M.; Andrade, B.; Barbosa, L.N.; Furlanetto, A.; Lyra, L.; Rall, V.L.M.; Júnior, A.F. Antibacterial and anti-biofilm activities of cinnamaldehyde against S. epidermidis. Microb. Pathog. 2019, 126, 231–238. [Google Scholar] [CrossRef]
  852. D’Angelo, F.; Baldelli, V.; Halliday, N.; Pantalone, P.; Polticelli, F.; Fiscarelli, E.; Williams, P.; Visca, P.; Leoni, L.; Rampioni, G. Identification of FDA-approved drugs as antivirulence agents targeting the pqs quorum-sensing system of Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 2018, 62, e01296-18. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  853. Bahari, S.; Zeighami, H.; Mirshahabi, H.; Roudashti, S.; Haghi, F. Inhibition of Pseudomonas aeruginosa quorum sensing by subinhibitory concentrations of curcumin with gentamicin and azithromycin. J. Glob. Antimicrob. Resist. 2017, 10, 21–28. [Google Scholar] [CrossRef] [PubMed]
  854. Shukla, A.; Shukla, G.; Parmar, P.; Patel, B.; Goswami, D.; Saraf, M. Exemplifying the next generation of antibiotic susceptibility intensifiers of phytochemicals by LasR-mediated quorum sensing inhibition. Sci. Rep. 2021, 11, 22421. [Google Scholar] [CrossRef] [PubMed]
  855. Shukla, A.; Parmar, P.; Rao, P.; Goswami, D.; Saraf, M. Twin peaks: Presenting the antagonistic molecular interplay of curcumin with LasR and LuxR quorum sensing pathways. Curr. Microbiol. 2020, 77, 1800–1810. [Google Scholar] [CrossRef] [PubMed]
  856. Roudashti, S.; Zeighami, H.; Mirshahabi, H.; Bahari, S.; Soltani, A.; Haghi, F. Synergistic activity of sub-inhibitory concentrations of curcumin with ceftazidime and ciprofloxacin against Pseudomonas aeruginosa quorum sensing related genes and virulence traits. World J. Microbiol. Biotechnol. 2017, 33, 50. [Google Scholar] [CrossRef]
  857. Raorane, C.J.; Lee, J.H.; Kim, Y.G.; Rajasekharan, S.K.; García-Contreras, R.; Lee, J. Antibiofilm and antivirulence efficacies of flavonoids and curcumin against Acinetobacter baumannii. Front. Microbiol. 2019, 10, 990. [Google Scholar] [CrossRef]
  858. Hu, P.; Huang, P.; Chen, W.M. Curcumin inhibits the Sortase A activity of the Streptococcus mutans UA159. Appl. Biochem. Biotechnol. 2013, 171, 396–402. [Google Scholar] [CrossRef]
  859. Wang, S.; Kim, M.C.; Kang, O.H.; Kwon, D.Y. The mechanism of bisdemethoxycurcumin enhances conventional antibiotics against methicillin-resistant Staphylococcus aureus. Int. J. Mol. Sci. 2020, 21, 7945. [Google Scholar] [CrossRef]
  860. El-Ganiny, A.M.; Gad, A.I.; El-Sayed, M.A.; Shaldam, M.A.; Abbas, H.A. The promising anti-virulence activity of candesartan, domperidone, and miconazole on Staphylococcus aureus. Braz. J. Microbiol. 2022, 53, 1–18. [Google Scholar] [CrossRef]
  861. Zhao, C.; Zheng, H.; Zhou, L.; Ji, H.; Zhao, L.; Yu, W.; Gong, Q. Falcarindiol isolated from Notopterygium incisum inhibits the quorum sensing of Pseudomonas aeruginosa. Molecules 2021, 26, 5896. [Google Scholar] [CrossRef]
  862. Paczkowski, J.E.; Mukherjee, S.; McCready, A.R.; Cong, J.P.; Aquino, C.J.; Kim, H.; Henke, B.R.; Smith, C.D.; Bassler, B.L. Flavonoids suppress Pseudomonas aeruginosa virulence through allosteric inhibition of quorum-sensing receptors. J. Biol. Chem. 2017, 292, 4064–4076. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  863. Vandeputte, O.M.; Kiendrebeogo, M.; Rajaonson, S.; Diallo, B.; Mol, A.; El Jaziri, M.; Baucher, M. Identification of catechin as one of the flavonoids from Combretum albiflorum bark extract that reduces the production of quorum-sensing-controlled virulence factors in Pseudomonas aeruginosa PAO1. Appl. Environ. Microbiol. 2010, 76, 243–253. [Google Scholar] [CrossRef] [Green Version]
  864. Vandeputte, O.M.; Kiendrebeogo, M.; Rasamiravaka, T.; Stévigny, C.; Duez, P.; Rajaonson, S.; Diallo, B.; Mol, A.; Baucher, M.; El Jaziri, M. The flavanone naringenin reduces the production of quorum sensing-controlled virulence factors in Pseudomonas aeruginosa PAO1. Microbiology 2011, 157, 2120–2132. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  865. Vikram, A.; Jayaprakasha, G.K.; Jesudhasan, P.R.; Pillai, S.D.; Patil, B.S. Suppression of bacterial cell-cell signalling, biofilm formation and type III secretion system by citrus flavonoids. J. Appl. Microbiol. 2010, 109, 515–527. [Google Scholar] [CrossRef] [PubMed]
  866. Kadirvel, M.; Fanimarvasti, F.; Forbes, S.; McBain, A.; Gardiner, J.M.; Brown, G.D.; Freeman, S. Inhibition of quorum sensing and biofilm formation in Vibrio harveyi by 4-fluoro-DPD; a novel potent inhibitor of signalling. Chem. Commun. 2014, 50, 5000–5002. [Google Scholar] [CrossRef]
  867. Shukla, A.; Parmar, P.; Patel, B.; Goswami, D.; Saraf, M. Breaking bad: Better call gingerol for improving antibiotic susceptibility of Pseudomonas aeruginosa by inhibiting multiple quorum sensing pathways. Microbiol. Res. 2021, 252, 126863. [Google Scholar] [CrossRef]
  868. Kim, H.S.; Lee, S.H.; Byun, Y.; Park, H.D. 6-Gingerol reduces Pseudomonas aeruginosa biofilm formation and virulence via quorum sensing inhibition. Sci. Rep. 2015, 5, 8656. [Google Scholar] [CrossRef]
  869. Hentzer, M.; Riedel, K.; Rasmussen, T.B.; Heydorn, A.; Andersen, J.B.; Parsek, M.R.; Rice, S.A.; Eberl, L.; Molin, S.; Høiby, N.; et al. Inhibition of quorum sensing in Pseudomonas aeruginosa biofilm bacteria by a halogenated furanone compound. Microbiology 2002, 148, 87–102. [Google Scholar] [CrossRef] [Green Version]
  870. Christensen, L.D.; van Gennip, M.; Jakobsen, T.H.; Alhede, M.; Hougen, H.P.; Høiby, N.; Bjarnsholt, T.; Givskov, M. Synergistic antibacterial efficacy of early combination treatment with tobramycin and quorum-sensing inhibitors against Pseudomonas aeruginosa in an intraperitoneal foreign-body infection mouse model. J. Antimicrob. Chemother. 2012, 67, 1198–1206. [Google Scholar] [CrossRef] [Green Version]
  871. Zhang, Y.; Lin, Y.; Zhang, X.; Chen, L.; Xu, C.; Liu, S.; Cao, J.; Zheng, X.; Jia, H.; Chen, L.; et al. Combining colistin with furanone C-30 rescues colistin resistance of Gram-negative bacteria in vitro and in vivo. Microbiol. Spectr. 2021, 9, e0123121. [Google Scholar] [CrossRef]
  872. Ren, D.; Sims, J.J.; Wood, T.K. Inhibition of biofilm formation and swarming of Escherichia coli by (5Z)-4-bromo-5-(bromomethylene)-3-butyl-2(5H)-furanone. Environ. Microbiol. 2001, 3, 731–736. [Google Scholar] [CrossRef] [PubMed]
  873. Ren, D.; Bedzyk, L.A.; Ye, R.W.; Thomas, S.M.; Wood, T.K. Differential gene expression shows natural brominated furanones interfere with the autoinducer-2 bacterial signaling system of Escherichia coli. Biotechnol. Bioeng. 2004, 88, 630–642. [Google Scholar] [CrossRef] [PubMed]
  874. Zhao, J.; Cheng, W.; He, X.; Liu, Y.; Li, J.; Sun, J.; Li, J.; Wang, F.; Gao, Y. Association of furanone C-30 with biofilm formation & antibiotic resistance in Pseudomonas aeruginosa. Indian J. Med. Res. 2018, 147, 400–406. [Google Scholar] [CrossRef] [PubMed]
  875. Lillicrap, A.; Macken, A.; Wennberg, A.C.; Grung, M.; Rundberget, J.T.; Fredriksen, L.; Scheie, A.A.; Benneche, T.; d’Auriac, M.A. Environmental fate and effects of novel quorum sensing inhibitors that can control biofilm formation. Chemosphere 2016, 164, 52–58. [Google Scholar] [CrossRef]
  876. Defoirdt, T.; Benneche, T.; Brackman, G.; Coenye, T.; Sorgeloos, P.; Scheie, A.A. A quorum sensing-disrupting brominated thiophenone with a promising therapeutic potential to treat luminescent vibriosis. PLoS ONE 2012, 7, e41788. [Google Scholar] [CrossRef] [Green Version]
  877. Lönn-Stensrud, J.; Naemi, A.O.; Benneche, T.; Petersen, F.C.; Scheie, A.A. Thiophenones inhibit Staphylococcus epidermidis biofilm formation at nontoxic concentrations. FEMS Immunol. Med. Microbiol. 2012, 65, 326–334. [Google Scholar] [CrossRef] [Green Version]
  878. Opoku-Temeng, C.; Onyedibe, K.I.; Aryal, U.K.; Sintim, H.O. Proteomic analysis of bacterial response to a 4-hydroxybenzylidene indolinone compound, which re-sensitizes bacteria to traditional antibiotics. J. Proteom. 2019, 202, 103368. [Google Scholar] [CrossRef]
  879. Opoku-Temeng, C.; Dayal, N.; Miller, J.; Sintim, H.O. Hydroxybenzylidene-indolinones, c-di-AMP synthase inhibitors, have antibacterial and anti-biofilm activities and also re-sensitize resistant bacteria to methicillin and vancomycin. RSC Adv. 2017, 7, 8288–8294. [Google Scholar] [CrossRef] [Green Version]
  880. Geng, Y.F.; Yang, C.; Zhang, Y.; Tao, S.N.; Mei, J.; Zhang, X.C.; Sun, Y.J.; Zhao, B.T. An innovative role for luteolin as a natural quorum sensing inhibitor in Pseudomonas aeruginosa. Life Sci. 2021, 274, 119325. [Google Scholar] [CrossRef]
  881. Ma, Y.; Shi, Q.; He, Q.; Chen, G. Metabolomic insights into the inhibition mechanism of methyl N-methylanthranilate: A novel quorum sensing inhibitor and antibiofilm agent against Pseudomonas aeruginosa. Int. J. Food Microbiol. 2021, 358, 109402. [Google Scholar] [CrossRef]
  882. Calfee, M.W.; Coleman, J.P.; Pesci, E.C. Interference with Pseudomonas quinolone signal synthesis inhibits virulence factor expression by Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. USA 2001, 98, 11633–11637. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  883. Balamurugan, P.; Praveen Krishna, V.; Bharath, D.; Lavanya, R.; Vairaprakash, P.; Adline Princy, S. Staphylococcus aureus quorum regulator SarA targeted compound, 2-[(Methylamino)methyl]phenol inhibits biofilm and down-regulates virulence genes. Front. Microbiol. 2017, 8, 1290. [Google Scholar] [CrossRef] [PubMed]
  884. Hwang, H.J.; Choi, H.; Hong, S.; Moon, H.R.; Lee, J.H. Antipathogenic compounds that are effective at very low concentrations and have both antibiofilm and antivirulence effects against Pseudomonas aeruginosa. Microbiol. Spectr. 2021, 9, e0024921. [Google Scholar] [CrossRef] [PubMed]
  885. Tang, K.; Su, Y.; Brackman, G.; Cui, F.; Zhang, Y.; Shi, X.; Coenye, T.; Zhang, X.H. MomL, a novel marine-derived N-acyl homoserine lactonase from Muricauda olearia. Appl. Environ. Microbiol. 2015, 81, 774–782. [Google Scholar] [CrossRef] [Green Version]
  886. Zhang, J.; Wang, J.; Feng, T.; Du, R.; Tian, X.; Wang, Y.; Zhang, X.H. Heterologous expression of the marine-derived quorum quenching enzyme MomL can expand the antibacterial spectrum of Bacillus brevis. Mar. Drugs 2019, 17, 128. [Google Scholar] [CrossRef] [Green Version]
  887. Hnamte, S.; Parasuraman, P.; Ranganathan, S.; Ampasala, D.R.; Reddy, D.; Kumavath, R.N.; Suchiang, K.; Mohanty, S.K.; Busi, S. Mosloflavone attenuates the quorum sensing controlled virulence phenotypes and biofilm formation in Pseudomonas aeruginosa PAO1: In vitro, in vivo and in silico approach. Microb. Pathog. 2019, 131, 128–134. [Google Scholar] [CrossRef]
  888. Imperi, F.; Massai, F.; Ramachandran Pillai, C.; Longo, F.; Zennaro, E.; Rampioni, G.; Visca, P.; Leoni, L. New life for an old drug: The anthelmintic drug niclosamide inhibits Pseudomonas aeruginosa quorum sensing. Antimicrob. Agents Chemother. 2013, 57, 996–1005. [Google Scholar] [CrossRef] [Green Version]
  889. Baldelli, V.; D’Angelo, F.; Pavoncello, V.; Fiscarelli, E.V.; Visca, P.; Rampioni, G.; Leoni, L. Identification of FDA-approved antivirulence drugs targeting the Pseudomonas aeruginosa quorum sensing effector protein PqsE. Virulence 2020, 11, 652–668. [Google Scholar] [CrossRef]
  890. Soukarieh, F.; Mashabi, A.; Richardson, W.; Oton, E.V.; Romero, M.; Roberston, S.N.; Grossman, S.; Sou, T.; Liu, R.; Halliday, N.; et al. Design and evaluation of new Quinazolin-4(3H)-one derived PqsR antagonists as quorum sensing quenchers in Pseudomonas aeruginosa. ACS Infect. Dis. 2021, 7, 2666–2685. [Google Scholar] [CrossRef]
  891. Yang, D.; Hao, S.; Zhao, L.; Shi, F.; Ye, G.; Zou, Y.; Song, X.; Li, L.; Yin, Z.; He, X.; et al. Paeonol attenuates quorum-sensing regulated virulence and biofilm formation in Pseudomonas aeruginosa. Front. Microbiol. 2021, 12, 692474. [Google Scholar] [CrossRef]
  892. Wenderska, I.B.; Chong, M.; McNulty, J.; Wright, G.D.; Burrows, L.L. Palmitoyl-DL-carnitine is a multitarget inhibitor of Pseudomonas aeruginosa biofilm development. Chembiochem 2011, 12, 2759–2766. [Google Scholar] [CrossRef] [PubMed]
  893. Kalia, M.; Yadav, V.K.; Singh, P.K.; Sharma, D.; Narvi, S.S.; Agarwal, V. Exploring the impact of parthenolide as anti-quorum sensing and anti-biofilm agent against Pseudomonas aeruginosa. Life Sci. 2018, 199, 96–103. [Google Scholar] [CrossRef] [PubMed]
  894. Chifiriuc, M.C.; Diţu, L.M.; Banu, O.; Bleotu, C.; Drăcea, O.; Bucur, M.; Larion, C.; Israil, A.M.; Lazăr, V. Subinhibitory concentrations of phenyl lactic acid interfere with the expression of virulence factors in Staphylococcus aureus and Pseudomonas aeruginosa clinical strains. Roum Arch. Microbiol. Immunol. 2009, 68, 27–33. [Google Scholar] [PubMed]
  895. Furiga, A.; Lajoie, B.; El Hage, S.; Baziard, G.; Roques, C. Impairment of Pseudomonas aeruginosa biofilm resistance to antibiotics by combining the drugs with a new quorum-sensing inhibitor. Antimicrob. Agents Chemother. 2015, 60, 1676–1686. [Google Scholar] [CrossRef] [Green Version]
  896. Grossman, S.; Soukarieh, F.; Richardson, W.; Liu, R.; Mashabi, A.; Emsley, J.; Williams, P.; Cámara, M.; Stocks, M.J. Novel quinazolinone inhibitors of the Pseudomonas aeruginosa quorum sensing transcriptional regulator PqsR. Eur. J. Med. Chem. 2020, 208, 112778. [Google Scholar] [CrossRef]
  897. Vipin, C.; Saptami, K.; Fida, F.; Mujeeburahiman, M.; Rao, S.S.; Arun, A.B.; Rekha, P.D. Potential synergistic activity of quercetin with antibiotics against multidrug-resistant clinical strains of Pseudomonas aeruginosa. PLoS ONE 2020, 15, e0241304. [Google Scholar] [CrossRef]
  898. Siriwong, S.; Teethaisong, Y.; Thumanu, K.; Dunkhunthod, B.; Eumkeb, G. The synergy and mode of action of quercetin plus amoxicillin against amoxicillin-resistant Staphylococcus epidermidis. BMC Pharmacol. Toxicol. 2016, 17, 39. [Google Scholar] [CrossRef] [Green Version]
  899. Amin, M.U.; Khurram, M.; Khattak, B.; Khan, J. Antibiotic additive and synergistic action of rutin, morin and quercetin against methicillin resistant Staphylococcus aureus. BMC Complement. Altern. Med. 2015, 15, 59. [Google Scholar] [CrossRef] [Green Version]
  900. Qu, S.; Dai, C.; Shen, Z.; Tang, Q.; Wang, H.; Zhai, B.; Zhao, L.; Hao, Z. Mechanism of synergy between tetracycline and quercetin against antibiotic resistant Escherichia coli. Front. Microbiol. 2019, 10, 2536. [Google Scholar] [CrossRef] [Green Version]
  901. Zhou, J.W.; Chen, T.T.; Tan, X.J.; Sheng, J.Y.; Jia, A.Q. Can the quorum sensing inhibitor resveratrol function as an aminoglycoside antibiotic accelerant against Pseudomonas aeruginosa? Int. J. Antimicrob. Agents 2018, 52, 35–41. [Google Scholar] [CrossRef]
  902. Chen, T.; Sheng, J.; Fu, Y.; Li, M.; Wang, J.; Jia, A.Q. (1)H NMR-based global metabolic studies of Pseudomonas aeruginosa upon exposure of the quorum sensing inhibitor Resveratrol. J. Proteome Res. 2017, 16, 824–830. [Google Scholar] [CrossRef] [PubMed]
  903. Qin, N.; Tan, X.; Jiao, Y.; Liu, L.; Zhao, W.; Yang, S.; Jia, A. RNA-Seq-based transcriptome analysis of methicillin-resistant Staphylococcus aureus biofilm inhibition by ursolic acid and resveratrol. Sci. Rep. 2014, 4, 5467. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  904. Cho, H.S.; Lee, J.H.; Cho, M.H.; Lee, J. Red wines and flavonoids diminish Staphylococcus aureus virulence with anti-biofilm and anti-hemolytic activities. Biofouling 2015, 31, 1–11. [Google Scholar] [CrossRef] [PubMed]
  905. Mikalauskas, A.; Parkins, M.D.; Poole, K. Rifampicin potentiation of aminoglycoside activity against cystic fibrosis isolates of Pseudomonas aeruginosa. J. Antimicrob. Chemother. 2017, 72, 3349–3352. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  906. Poole, K.; Gilmour, C.; Farha, M.A.; Mullen, E.; Lau, C.H.; Brown, E.D. Potentiation of aminoglycoside activity in Pseudomonas aeruginosa by targeting the AmgRS envelope stress-responsive two-component system. Antimicrob. Agents Chemother. 2016, 60, 3509–3518. [Google Scholar] [CrossRef] [Green Version]
  907. Yadav, M.K.; Park, S.W.; Chae, S.W.; Song, J.J. Sinefungin, a natural nucleoside analogue of S-adenosylmethionine, inhibits Streptococcus pneumoniae biofilm growth. BioMed. Res. Int. 2014, 2014, 156987. [Google Scholar] [CrossRef] [Green Version]
  908. Mahdally, N.H.; George, R.F.; Kashef, M.T.; Al-Ghobashy, M.; Murad, F.E.; Attia, A.S. Staquorsin: A novel Staphylococcus aureus Agr-mediated quorum sensing inhibitor impairing virulence in vivo without notable resistance development. Front. Microbiol. 2021, 12, 700494. [Google Scholar] [CrossRef]
  909. Narendrakumar, L.; Theresa, M.; Krishnankutty Chandrika, S.; Thomas, S. Tryptanthrin, a potential biofilm inhibitor against toxigenic Vibrio cholerae, modulating the global quorum sensing regulator, LuxO. Biofouling 2019, 35, 1093–1103. [Google Scholar] [CrossRef]
  910. Shang, D.; Liu, Y.; Jiang, F.; Ji, F.; Wang, H.; Han, X. Synergistic antibacterial activity of designed Trp-containing antibacterial peptides in combination with antibiotics against multidrug-resistant Staphylococcus epidermidis. Front. Microbiol. 2019, 10, 2719. [Google Scholar] [CrossRef] [Green Version]
  911. Nicol, M.; Alexandre, S.; Luizet, J.B.; Skogman, M.; Jouenne, T.; Salcedo, S.P.; Dé, E. Unsaturated fatty acids affect quorum sensing communication system and inhibit motility and biofilm formation of Acinetobacter baumannii. Int. J. Mol. Sci. 2018, 19, 214. [Google Scholar] [CrossRef] [Green Version]
  912. Kim, H.S.; Cha, E.; Ham, S.Y.; Park, J.H.; Nam, S.; Kwon, H.; Byun, Y.; Park, H.D. Linoleic acid inhibits Pseudomonas aeruginosa biofilm formation by activating diffusible signal factor-mediated quorum sensing. Biotechnol. Bioeng. 2021, 118, 82–93. [Google Scholar] [CrossRef] [PubMed]
  913. Kumar, P.; Lee, J.H.; Beyenal, H.; Lee, J. Fatty acids as antibiofilm and antivirulence agents. Trends Microbiol. 2020, 28, 753–768. [Google Scholar] [CrossRef] [PubMed]
  914. Davies, D.G.; Marques, C.N. A fatty acid messenger is responsible for inducing dispersion in microbial biofilms. J. Bacteriol. 2009, 191, 1393–1403. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  915. Kim, Y.G.; Lee, J.H.; Raorane, C.J.; Oh, S.T.; Park, J.G.; Lee, J. Herring oil and omega fatty acids inhibit Staphylococcus aureus biofilm formation and virulence. Front. Microbiol. 2018, 9, 1241. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  916. Gupta, A.; Cheepurupalli, L.; Vigneswaran, S.; Singh Rathore, S.; Suma Mohan, S.; Ramakrishnan, J. In vitro and in silico investigation of caprylic acid effect on multi drug resistant (MDR) Klebsiella pneumoniae biofilm. J. Biomol. Struct. Dyn. 2020, 38, 616–624. [Google Scholar] [CrossRef] [PubMed]
  917. Beavers, W.N.; Munneke, M.J.; Stackhouse, A.R.; Freiberg, J.A.; Skaar, E.P. Host polyunsaturated fatty acids potentiate aminoglycoside killing of Staphylococcus aureus. Microbiol. Spectr. 2022, 10, e0276721. [Google Scholar] [CrossRef]
  918. Beavers, W.N.; Monteith, A.J.; Amarnath, V.; Mernaugh, R.L.; Roberts, L.J., 2nd; Chazin, W.J.; Davies, S.S.; Skaar, E.P. Arachidonic acid kills Staphylococcus aureus through a lipid peroxidation mechanism. mBio 2019, 10, e01333-19. [Google Scholar] [CrossRef] [Green Version]
  919. Herndon, J.L.; Peters, R.E.; Hofer, R.N.; Simmons, T.B.; Symes, S.J.; Giles, D.K. Exogenous polyunsaturated fatty acids (PUFAs) promote changes in growth, phospholipid composition, membrane permeability and virulence phenotypes in Escherichia coli. BMC Microbiol. 2020, 20, 305. [Google Scholar] [CrossRef]
  920. Yuyama, K.T.; Rohde, M.; Molinari, G.; Stadler, M.; Abraham, W.R. Unsaturated fatty acids control biofilm formation of Staphylococcus aureus and other Gram-positive bacteria. Antibiotics 2020, 9, 788. [Google Scholar] [CrossRef]
  921. Parsons, J.B.; Yao, J.; Frank, M.W.; Jackson, P.; Rock, C.O. Membrane disruption by antimicrobial fatty acids releases low-molecular-weight proteins from Staphylococcus aureus. J. Bacteriol. 2012, 194, 5294–5304. [Google Scholar] [CrossRef] [Green Version]
  922. Kumar, L.; Chhibber, S.; Kumar, R.; Kumar, M.; Harjai, K. Zingerone silences quorum sensing and attenuates virulence of Pseudomonas aeruginosa. Fitoterapia 2015, 102, 84–95. [Google Scholar] [CrossRef] [PubMed]
  923. Kumar, L.; Chhibber, S.; Harjai, K. Zingerone inhibit biofilm formation and improve antibiofilm efficacy of ciprofloxacin against Pseudomonas aeruginosa PAO1. Fitoterapia 2013, 90, 73–78. [Google Scholar] [CrossRef] [PubMed]
  924. Okada, A.; Igarashi, M.; Okajima, T.; Kinoshita, N.; Umekita, M.; Sawa, R.; Inoue, K.; Watanabe, T.; Doi, A.; Martin, A.; et al. Walkmycin B targets WalK (YycG), a histidine kinase essential for bacterial cell growth. J. Antibiot. 2010, 63, 89–94. [Google Scholar] [CrossRef] [PubMed]
  925. Givskov, M.; de Nys, R.; Manefield, M.; Gram, L.; Maximilien, R.; Eberl, L.; Molin, S.; Steinberg, P.D.; Kjelleberg, S. Eukaryotic interference with homoserine lactone-mediated prokaryotic signalling. J. Bacteriol. 1996, 178, 6618–6622. [Google Scholar] [CrossRef] [Green Version]
  926. Manefield, M.; de Nys, R.; Naresh, K.; Roger, R.; Givskov, M.; Peter, S.; Kjelleberg, S. Evidence that halogenated furanones from Delisea pulchra inhibit acylated homoserine lactone (AHL)-mediated gene expression by displacing the AHL signal from its receptor protein. Microbiology 1999, 145 Pt 2, 283–291. [Google Scholar] [CrossRef] [Green Version]
  927. Borges, A.; Abreu, A.C.; Dias, C.; Saavedra, M.J.; Borges, F.; Simões, M. New perspectives on the use of phytochemicals as an emergent strategy to control bacterial infections including biofilms. Molecules 2016, 21, 877. [Google Scholar] [CrossRef]
  928. Bouyahya, A.; Chamkhi, I.; Balahbib, A.; Rebezov, M.; Shariati, M.A.; Wilairatana, P.; Mubarak, M.S.; Benali, T.; El Omari, N. Mechanisms, anti-quorum-sensing actions, and clinical trials of medicinal plant bioactive compounds against bacteria: A comprehensive review. Molecules 2022, 27, 1484. [Google Scholar] [CrossRef]
  929. Liu, Y.C.; Hussain, F.; Negm, O.; Pavia, A.; Halliday, N.; Dubern, J.F.; Singh, S.; Muntaka, S.; Wheldon, L.; Luckett, J.; et al. Contribution of the alkylquinolone quorum-sensing system to the interaction of Pseudomonas aeruginosa with bronchial epithelial cells. Front. Microbiol. 2018, 9, 3018. [Google Scholar] [CrossRef]
  930. Bredenbruch, F.; Nimtz, M.; Wray, V.; Morr, M.; Müller, R.; Häussler, S. Biosynthetic pathway of Pseudomonas aeruginosa 4-hydroxy-2-alkylquinolines. J. Bacteriol. 2005, 187, 3630–3635. [Google Scholar] [CrossRef] [Green Version]
  931. Soheili, V.; Tajani, A.S.; Ghodsi, R.; Bazzaz, B.S.F. Anti-PqsR compounds as next-generation antibacterial agents against Pseudomonas aeruginosa: A review. Eur. J. Med. Chem. 2019, 172, 26–35. [Google Scholar] [CrossRef]
  932. Pustelny, C.; Albers, A.; Büldt-Karentzopoulos, K.; Parschat, K.; Chhabra, S.R.; Cámara, M.; Williams, P.; Fetzner, S. Dioxygenase-mediated quenching of quinolone-dependent quorum sensing in Pseudomonas aeruginosa. Chem. Biol. 2009, 16, 1259–1267. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  933. Lesic, B.; Lépine, F.; Déziel, E.; Zhang, J.; Zhang, Q.; Padfield, K.; Castonguay, M.H.; Milot, S.; Stachel, S.; Tzika, A.A.; et al. Inhibitors of pathogen intercellular signals as selective anti-infective compounds. PLoS Pathog. 2007, 3, 1229–1239. [Google Scholar] [CrossRef] [PubMed]
  934. Storz, M.P.; Maurer, C.K.; Zimmer, C.; Wagner, N.; Brengel, C.; de Jong, J.C.; Lucas, S.; Müsken, M.; Häussler, S.; Steinbach, A.; et al. Validation of PqsD as an anti-biofilm target in Pseudomonas aeruginosa by development of small-molecule inhibitors. J. Am. Chem. Soc. 2012, 134, 16143–16146. [Google Scholar] [CrossRef] [PubMed]
  935. Rasmussen, T.B.; Bjarnsholt, T.; Skindersoe, M.E.; Hentzer, M.; Kristoffersen, P.; Köte, M.; Nielsen, J.; Eberl, L.; Givskov, M. Screening for quorum-sensing inhibitors (QSI) by use of a novel genetic system, the QSI selector. J. Bacteriol. 2005, 187, 1799–1814. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  936. Bjarnsholt, T.; Jensen, P.; Rasmussen, T.B.; Christophersen, L.; Calum, H.; Hentzer, M.; Hougen, H.P.; Rygaard, J.; Moser, C.; Eberl, L.; et al. Garlic blocks quorum sensing and promotes rapid clearing of pulmonary Pseudomonas aeruginosa infections. Microbiology 2005, 151, 3873–3880. [Google Scholar] [CrossRef] [Green Version]
  937. El-Sayed, N.R.; Samir, R.; Jamil, M.A.-H.L.; Ramadan, M.A. Olive leaf extract modulates quorum sensing genes and biofilm formation in multi-drug resistant Pseudomonas aeruginosa. Antibiotics 2020, 9, 526. [Google Scholar] [CrossRef]
  938. Song, Z.; Kong, K.F.; Wu, H.; Maricic, N.; Ramalingam, B.; Priestap, H.; Schneper, L.; Quirke, J.M.; Høiby, N.; Mathee, K. Panax ginseng has anti-infective activity against opportunistic pathogen Pseudomonas aeruginosa by inhibiting quorum sensing, a bacterial communication process critical for establishing infection. Phytomedicine 2010, 17, 1040–1046. [Google Scholar] [CrossRef] [Green Version]
  939. Cordes, T.; Michelucci, A.; Hiller, K. Itaconic acid: The surprising role of an industrial compound as a mammalian antimicrobial metabolite. Annu. Rev. Nutr. 2015, 35, 451–473. [Google Scholar] [CrossRef]
  940. Ho, D.K.; De Rossi, C.; Loretz, B.; Murgia, X.; Lehr, C.M. Itaconic acid increases the efficacy of tobramycin against Pseudomonas aeruginosa biofilms. Pharmaceutics 2020, 12, 691. [Google Scholar] [CrossRef]
  941. Mishra, R.; Panda, A.K.; De Mandal, S.; Shakeel, M.; Bisht, S.S.; Khan, J. Natural anti-biofilm agents: Strategies to control biofilm-forming pathogens. Front. Microbiol. 2020, 11, 566325. [Google Scholar] [CrossRef]
  942. Schneewind, O.; Missiakas, D. Sortases, surface proteins, and their roles in Staphylococcus aureus disease and vaccine development. Microbiol. Spectr. 2019, 7, PSIB-0004-2018. [Google Scholar] [CrossRef] [PubMed]
  943. Parrino, B.; Carbone, D.; Cascioferro, S.; Pecoraro, C.; Giovannetti, E.; Deng, D.; Di Sarno, V.; Musella, S.; Auriemma, G.; Cusimano, M.G.; et al. 1,2,4-Oxadiazole topsentin analogs as staphylococcal biofilm inhibitors targeting the bacterial transpeptidase sortase A. Eur. J. Med. Chem 2021, 209, 112892. [Google Scholar] [CrossRef] [PubMed]
  944. Wallock-Richards, D.J.; Marles-Wright, J.; Clarke, D.J.; Maitra, A.; Dodds, M.; Hanley, B.; Campopiano, D.J. Molecular basis of Streptococcus mutans sortase A inhibition by the flavonoid natural product trans-chalcone. Chem. Commun. 2015, 51, 10483–10485. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  945. Wang, J.; Shi, Y.; Jing, S.; Dong, H.; Wang, D.; Wang, T. Astilbin inhibits the activity of Sortase A from Streptococcus mutans. Molecules 2019, 24, 465. [Google Scholar] [CrossRef] [Green Version]
  946. Nitulescu, G.; Margina, D.; Zanfirescu, A.; Olaru, O.T.; Nitulescu, G.M. Targeting bacterial sortases in search of anti-virulence therapies with low risk of resistance development. Pharmaceuticals 2021, 14, 415. [Google Scholar] [CrossRef]
  947. Alharthi, S.; Alavi, S.E.; Moyle, P.M.; Ziora, Z.M. Sortase A (SrtA) inhibitors as an alternative treatment for superbug infections. Drug Discov. Today 2021, 26, 2164–2172. [Google Scholar] [CrossRef]
  948. Thappeta, K.R.V.; Zhao, L.N.; Nge, C.E.; Crasta, S.; Leong, C.Y.; Ng, V.; Kanagasundaram, Y.; Fan, H.; Ng, S.B. In-silico identified new natural Sortase A inhibitors disrupt S. aureus biofilm formation. Int. J. Mol. Sci. 2020, 21, 8601. [Google Scholar] [CrossRef]
  949. Wang, L.; Wang, G.; Qu, H.; Wang, K.; Jing, S.; Guan, S.; Su, L.; Li, Q.; Wang, D. Taxifolin, an inhibitor of Sortase A, interferes with the adhesion of methicillin-resistant Staphylococcus aureus. Front. Microbiol. 2021, 12, 686864. [Google Scholar] [CrossRef]
  950. Khan, F.; Pham, D.T.N.; Oloketuyi, S.F.; Manivasagan, P.; Oh, J.; Kim, Y.M. Chitosan and their derivatives: Antibiofilm drugs against pathogenic bacteria. Colloids Surf. B Biointerfaces 2020, 185, 110627. [Google Scholar] [CrossRef]
  951. Li, R.; Yuan, X.; Wei, J.; Zhang, X.; Cheng, G.; Wang, Z.A.; Du, Y. Synthesis and evaluation of a chitosan oligosaccharide-streptomycin conjugate against Pseudomonas aeruginosa biofilms. Mar. Drugs 2019, 17, 43. [Google Scholar] [CrossRef] [Green Version]
  952. Zhang, A.; Mu, H.; Zhang, W.; Cui, G.; Zhu, J.; Duan, J. Chitosan coupling makes microbial biofilms susceptible to antibiotics. Sci. Rep. 2013, 3, 3364. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  953. Shang, Y.; Guo, J.; Zhao, Y.; Chen, J.; Meng, Q.; Qu, D.; Zheng, J.; Yu, Z.; Wu, Y.; Deng, Q. Clemastine inhibits the biofilm and hemolytic of Staphylococcus aureus through the GdpP Protein. Microbiol. Spectr. 2022, 10, e0054121. [Google Scholar] [CrossRef] [PubMed]
  954. Tkachenko, A.G.; Kashevarova, N.M.; Sidorov, R.Y.; Nesterova, L.Y.; Akhova, A.V.; Tsyganov, I.V.; Vaganov, V.Y.; Shipilovskikh, S.A.; Rubtsov, A.E.; Malkov, A.V. A synthetic diterpene analogue inhibits mycobacterial persistence and biofilm formation by targeting (p)ppGpp synthetases. Cell Chem. Biol. 2021, 28, 1420–1432.e1429. [Google Scholar] [CrossRef] [PubMed]
  955. Arita-Morioka, K.I.; Yamanaka, K.; Mizunoe, Y.; Tanaka, Y.; Ogura, T.; Sugimoto, S. Inhibitory effects of Myricetin derivatives on curli-dependent biofilm formation in Escherichia coli. Sci. Rep. 2018, 8, 8452. [Google Scholar] [CrossRef] [Green Version]
  956. Hengge, R. Targeting bacterial biofilms by the green tea polyphenol EGCG. Molecules 2019, 24, 2403. [Google Scholar] [CrossRef] [Green Version]
  957. Schneider-Rayman, M.; Steinberg, D.; Sionov, R.V.; Friedman, M.; Shalish, M. Effect of epigallocatechin gallate on dental biofilm of Streptococcus mutans: An in vitro study. BMC Oral Health 2021, 21, 447. [Google Scholar] [CrossRef]
  958. Yadav, M.K.; Chae, S.W.; Im, G.J.; Chung, J.W.; Song, J.J. Eugenol: A phyto-compound effective against methicillin-resistant and methicillin-sensitive Staphylococcus aureus clinical strain biofilms. PLoS ONE 2015, 10, e0119564. [Google Scholar] [CrossRef] [Green Version]
  959. Xia, W.; Li, N.; Shan, H.; Lin, Y.; Yin, F.; Yu, X.; Zhou, Z. Gallium porphyrin and gallium nitrate reduce the high vancomycin tolerance of MRSA biofilms by promoting extracellular DNA-dependent biofilm dispersion. ACS Infect. Dis. 2021, 7, 2565–2582. [Google Scholar] [CrossRef]
  960. Kang, D.; Revtovich, A.V.; Deyanov, A.E.; Kirienko, N.V. Pyoverdine inhibitors and gallium nitrate synergistically affect Pseudomonas aeruginosa. mSphere 2021, 6, e0040121. [Google Scholar] [CrossRef]
  961. Kaneko, Y.; Thoendel, M.; Olakanmi, O.; Britigan, B.E.; Singh, P.K. The transition metal gallium disrupts Pseudomonas aeruginosa iron metabolism and has antimicrobial and antibiofilm activity. J. Clin. Investig. 2007, 117, 877–888. [Google Scholar] [CrossRef]
  962. Minandri, F.; Bonchi, C.; Frangipani, E.; Imperi, F.; Visca, P. Promises and failures of gallium as an antibacterial agent. Future Microbiol. 2014, 9, 379–397. [Google Scholar] [CrossRef] [PubMed]
  963. Li, F.; Liu, F.; Huang, K.; Yang, S. Advancement of gallium and gallium-based compounds as antimicrobial agents. Front. Bioeng. Biotechnol. 2022, 10, 827960. [Google Scholar] [CrossRef] [PubMed]
  964. Tseng, S.P.; Hung, W.C.; Huang, C.Y.; Lin, Y.S.; Chan, M.Y.; Lu, P.L.; Lin, L.; Sheu, J.H. 5-Episinuleptolide decreases the expression of the extracellular matrix in early biofilm formation of multi-drug resistant Acinetobacter baumannii. Mar. Drugs 2016, 14, 143. [Google Scholar] [CrossRef] [PubMed]
  965. Vijayakumar, K.; Thirunanasambandham, R. 5-Hydroxymethylfurfural inhibits Acinetobacter baumannii biofilms: An in vitro study. Arch. Microbiol. 2021, 203, 673–682. [Google Scholar] [CrossRef] [PubMed]
  966. Ming, D.; Wang, D.; Cao, F.; Xiang, H.; Mu, D.; Cao, J.; Li, B.; Zhong, L.; Dong, X.; Zhong, X.; et al. Kaempferol inhibits the primary attachment phase of biofilm formation in Staphylococcus aureus. Front. Microbiol. 2017, 8, 2263. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  967. Gao, L.; Tang, Z.; Li, T.; Wang, J. Combination of kaempferol and azithromycin attenuates Staphylococcus aureus-induced osteomyelitis via anti-biofilm effects and by inhibiting the phosphorylation of ERK1/2 and SAPK. Pathog. Dis. 2021, 79, ftab048. [Google Scholar] [CrossRef]
  968. Sivaranjani, M.; Srinivasan, R.; Aravindraja, C.; Karutha Pandian, S.; Veera Ravi, A. Inhibitory effect of α-mangostin on Acinetobacter baumannii biofilms—An in vitro study. Biofouling 2018, 34, 579–593. [Google Scholar] [CrossRef]
  969. She, P.; Wang, Y.; Luo, Z.; Chen, L.; Tan, R.; Wang, Y.; Wu, Y. Meloxicam inhibits biofilm formation and enhances antimicrobial agents efficacy by Pseudomonas aeruginosa. Microbiologyopen 2018, 7, e00545. [Google Scholar] [CrossRef] [Green Version]
  970. Soheili, V.; Bazzaz, B.S.; Abdollahpour, N.; Hadizadeh, F. Investigation of Pseudomonas aeruginosa quorum-sensing signaling system for identifying multiple inhibitors using molecular docking and structural analysis methodology. Microb. Pathog. 2015, 89, 73–78. [Google Scholar] [CrossRef]
  971. Guan, X.N.; Zhang, T.; Yang, T.; Dong, Z.; Yang, S.; Lan, L.; Gan, J.; Yang, C.G. Covalent Sortase A inhibitor ML346 prevents Staphylococcus aureus infection of Galleria mellonella. RSC Med. Chem. 2022, 13, 138–149. [Google Scholar] [CrossRef]
  972. Selvaraj, A.; Jayasree, T.; Valliammai, A.; Pandian, S.K. Myrtenol attenuates MRSA biofilm and virulence by suppressing sarA expression dynamism. Front. Microbiol. 2019, 10, 2027. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  973. Selvaraj, A.; Valliammai, A.; Sivasankar, C.; Suba, M.; Sakthivel, G.; Pandian, S.K. Antibiofilm and antivirulence efficacy of myrtenol enhances the antibiotic susceptibility of Acinetobacter baumannii. Sci. Rep. 2020, 10, 21975. [Google Scholar] [CrossRef] [PubMed]
  974. Wang, L.; Jing, S.; Qu, H.; Wang, K.; Jin, Y.; Ding, Y.; Yang, L.; Yu, H.; Shi, Y.; Li, Q.; et al. Orientin mediates protection against MRSA-induced pneumonia by inhibiting Sortase A. Virulence 2021, 12, 2149–2161. [Google Scholar] [CrossRef] [PubMed]
  975. Yadav, M.K.; Go, Y.Y.; Chae, S.W.; Song, J.J. The small molecule DAM inhibitor, pyrimidinedione, disrupts Streptococcus pneumoniae biofilm growth in vitro. PLoS ONE 2015, 10, e0139238. [Google Scholar] [CrossRef] [PubMed]
  976. Abirami, G.; Durgadevi, R.; Velmurugan, P.; Ravi, A.V. Gene expressing analysis indicates the role of Pyrogallol as a novel antibiofilm and antivirulence agent against Acinetobacter baumannii. Arch. Microbiol. 2021, 203, 251–260. [Google Scholar] [CrossRef] [PubMed]
  977. Lee, J.H.; Park, J.H.; Cho, H.S.; Joo, S.W.; Cho, M.H.; Lee, J. Anti-biofilm activities of quercetin and tannic acid against Staphylococcus aureus. Biofouling 2013, 29, 491–499. [Google Scholar] [CrossRef]
  978. Dong, G.; Liu, H.; Yu, X.; Zhang, X.; Lu, H.; Zhou, T.; Cao, J. Antimicrobial and anti-biofilm activity of tannic acid against Staphylococcus aureus. Nat. Prod. Res. 2018, 32, 2225–2228. [Google Scholar] [CrossRef]
  979. Payne, D.E.; Martin, N.R.; Parzych, K.R.; Rickard, A.H.; Underwood, A.; Boles, B.R. Tannic acid inhibits Staphylococcus aureus surface colonization in an IsaA-dependent manner. Infect. Immun. 2013, 81, 496–504. [Google Scholar] [CrossRef] [Green Version]
  980. Kang, X.; Ma, Q.; Wang, G.; Li, N.; Mao, Y.; Wang, X.; Wang, Y.; Wang, G. Potential mechanisms of quercetin influence the ClfB protein during biofilm formation of Staphylococcus aureus. Front. Pharmacol. 2022, 13, 825489. [Google Scholar] [CrossRef]
  981. Lidor, O.; Al-Quntar, A.; Pesci, E.C.; Steinberg, D. Mechanistic analysis of a synthetic inhibitor of the Pseudomonas aeruginosa LasI quorum-sensing signal synthase. Sci. Rep. 2015, 5, 16569. [Google Scholar] [CrossRef] [Green Version]
  982. Feldman, M.; Al-Quntar, A.; Polacheck, I.; Friedman, M.; Steinberg, D. Therapeutic potential of thiazolidinedione-8 as an antibiofilm agent against Candida albicans. PLoS ONE 2014, 9, e93225. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  983. Stegenga, M.E.; Florquin, S.; de Vos, A.F.; van der Poll, T. The thiazolidinedione ciglitazone reduces bacterial outgrowth and early inflammation during Streptococcus pneumoniae pneumonia in mice. Crit. Care Med. 2009, 37, 614–618. [Google Scholar] [CrossRef] [PubMed]
  984. Brackman, G.; Al Quntar, A.A.; Enk, C.D.; Karalic, I.; Nelis, H.J.; Van Calenbergh, S.; Srebnik, M.; Coenye, T. Synthesis and evaluation of thiazolidinedione and dioxazaborocane analogues as inhibitors of AI-2 quorum sensing in Vibrio harveyi. Bioorg. Med. Chem. 2013, 21, 660–667. [Google Scholar] [CrossRef] [PubMed]
  985. Ren, D.; Zuo, R.; González Barrios, A.F.; Bedzyk, L.A.; Eldridge, G.R.; Pasmore, M.E.; Wood, T.K. Differential gene expression for investigation of Escherichia coli biofilm inhibition by plant extract ursolic acid. Appl. Environ. Microbiol. 2005, 71, 4022–4034. [Google Scholar] [CrossRef] [Green Version]
  986. Sycz, Z.; Tichaczek-Goska, D.; Wojnicz, D. Anti-planktonic and anti-biofilm properties of pentacyclic triterpenes-asiatic acid and ursolic acid as promising antibacterial future pharmaceuticals. Biomolecules 2022, 12, 98. [Google Scholar] [CrossRef]
  987. Nait Chabane, Y.; Mlouka, M.B.; Alexandre, S.; Nicol, M.; Marti, S.; Pestel-Caron, M.; Vila, J.; Jouenne, T.; Dé, E. Virstatin inhibits biofilm formation and motility of Acinetobacter baumannii. BMC Microbiol. 2014, 14, 62. [Google Scholar] [CrossRef] [Green Version]
  988. Hung, D.T.; Shakhnovich, E.A.; Pierson, E.; Mekalanos, J.J. Small-molecule inhibitor of Vibrio cholerae virulence and intestinal colonization. Science 2005, 310, 670–674. [Google Scholar] [CrossRef]
  989. Oh, M.H.; Choi, C.H. Role of LuxIR Homologue AnoIR in Acinetobacter nosocomialis and the effect of virstatin on the expression of anoR gene. J. Microbiol. Biotechnol. 2015, 25, 1390–1400. [Google Scholar] [CrossRef]
  990. Kim, H.R.; Shin, D.S.; Jang, H.I.; Eom, Y.B. Anti-biofilm and anti-virulence effects of zerumbone against Acinetobacter baumannii. Microbiology 2020, 166, 717–726. [Google Scholar] [CrossRef]
  991. Monteiro, K.L.C.; de Aquino, T.M.; Mendonça Junior, F.J.B. An update on Staphylococcus aureus NorA efflux pump inhibitors. Curr. Top. Med. Chem. 2020, 20, 2168–2185. [Google Scholar] [CrossRef]
  992. Wang, Y.; Venter, H.; Ma, S. Efflux pump inhibitors: A novel approach to combat efflux-mediated drug resistance in bacteria. Curr. Drug Targets 2016, 17, 702–719. [Google Scholar] [CrossRef] [PubMed]
  993. Waditzer, M.; Bucar, F. Flavonoids as inhibitors of bacterial efflux pumps. Molecules 2021, 26, 6904. [Google Scholar] [CrossRef] [PubMed]
  994. Gonçalves, B.M.F.; Cardoso, D.S.P.; Ferreira, M.J.U. Overcoming multidrug resistance: Flavonoid and terpenoid nitrogen-containing derivatives as ABC transporter modulators. Molecules 2020, 25, 3364. [Google Scholar] [CrossRef] [PubMed]
  995. Bhattacharyya, T.; Sharma, A.; Akhter, J.; Pathania, R. The small molecule IITR08027 restores the antibacterial activity of fluoroquinolones against multidrug-resistant Acinetobacter baumannii by efflux inhibition. Int. J. Antimicrob. Agents 2017, 50, 219–226. [Google Scholar] [CrossRef] [PubMed]
  996. Grimsey, E.M.; Fais, C.; Marshall, R.L.; Ricci, V.; Ciusa, M.L.; Stone, J.W.; Ivens, A.; Malloci, G.; Ruggerone, P.; Vargiu, A.V.; et al. Chlorpromazine and Amitriptyline are substrates and inhibitors of the AcrB multidrug efflux pump. mBio 2020, 11, e00465-20. [Google Scholar] [CrossRef]
  997. Tegos, G.P.; Haynes, M.; Strouse, J.J.; Khan, M.M.; Bologa, C.G.; Oprea, T.I.; Sklar, L.A. Microbial efflux pump inhibition: Tactics and strategies. Curr. Pharm. Des. 2011, 17, 1291–1302. [Google Scholar] [CrossRef] [Green Version]
  998. Fernebro, J. Fighting bacterial infections-future treatment options. Drug Resist. Updat. 2011, 14, 125–139. [Google Scholar] [CrossRef]
  999. Malléa, M.; Mahamoud, A.; Chevalier, J.; Alibert-Franco, S.; Brouant, P.; Barbe, J.; Pagès, J.M. Alkylaminoquinolines inhibit the bacterial antibiotic efflux pump in multidrug-resistant clinical isolates. Biochem. J. 2003, 376, 801–805. [Google Scholar] [CrossRef] [Green Version]
  1000. Tambat, R.; Jangra, M.; Mahey, N.; Chandal, N.; Kaur, M.; Chaudhary, S.; Verma, D.K.; Thakur, K.G.; Raje, M.; Jachak, S.; et al. Microbe-derived indole metabolite demonstrates potent multidrug efflux pump inhibition in Staphylococcus aureus. Front. Microbiol. 2019, 10, 2153. [Google Scholar] [CrossRef]
  1001. Fontaine, F.; Héquet, A.; Voisin-Chiret, A.S.; Bouillon, A.; Lesnard, A.; Cresteil, T.; Jolivalt, C.; Rault, S. Boronic species as promising inhibitors of the Staphylococcus aureus NorA efflux pump: Study of 6-substituted pyridine-3-boronic acid derivatives. Eur. J. Med. Chem. 2015, 95, 185–198. [Google Scholar] [CrossRef]
  1002. Giorgini, G.; Mangiaterra, G.; Cedraro, N.; Laudadio, E.; Sabbatini, G.; Cantarini, M.; Minnelli, C.; Mobbili, G.; Frangipani, E.; Biavasco, F.; et al. Berberine derivatives as Pseudomonas aeruginosa MexXY-OprM inhibitors: Activity and in silico insights. Molecules 2021, 26, 6644. [Google Scholar] [CrossRef] [PubMed]
  1003. Laudadio, E.; Cedraro, N.; Mangiaterra, G.; Citterio, B.; Mobbili, G.; Minnelli, C.; Bizzaro, D.; Biavasco, F.; Galeazzi, R. Natural alkaloid berberine activity against Pseudomonas aeruginosa MexXY-mediated aminoglycoside resistance: In silico and in vitro studies. J. Nat. Prod. 2019, 82, 1935–1944. [Google Scholar] [CrossRef] [PubMed]
  1004. Kalia, N.P.; Mahajan, P.; Mehra, R.; Nargotra, A.; Sharma, J.P.; Koul, S.; Khan, I.A. Capsaicin, a novel inhibitor of the NorA efflux pump, reduces the intracellular invasion of Staphylococcus aureus. J. Antimicrob. Chemother. 2012, 67, 2401–2408. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  1005. Dos Santos Barbosa, C.R.; Scherf, J.R.; de Freitas, T.S.; de Menezes, I.R.A.; Pereira, R.L.S.; Dos Santos, J.F.S.; de Jesus, S.S.P.; Lopes, T.P.; de Sousa Silveira, Z.; de Morais Oliveira-Tintino, C.D.; et al. Effect of carvacrol and thymol on NorA efflux pump inhibition in multidrug-resistant (MDR) Staphylococcus aureus strains. J. Bioenerg. Biomembr. 2021, 53, 489–498. [Google Scholar] [CrossRef] [PubMed]
  1006. Siriyong, T.; Srimanote, P.; Chusri, S.; Yingyongnarongkul, B.E.; Suaisom, C.; Tipmanee, V.; Voravuthikunchai, S.P. Conessine as a novel inhibitor of multidrug efflux pump systems in Pseudomonas aeruginosa. BMC Complement. Altern. Med. 2017, 17, 405. [Google Scholar] [CrossRef] [PubMed]
  1007. Siriyong, T.; Voravuthikunchai, S.P.; Coote, P.J. Steroidal alkaloids and conessine from the medicinal plant Holarrhena antidysenterica restore antibiotic efficacy in a Galleria mellonella model of multidrug-resistant Pseudomonas aeruginosa infection. BMC Complement. Altern. Med. 2018, 18, 285. [Google Scholar] [CrossRef] [Green Version]
  1008. Yoshida, K.; Nakayama, K.; Ohtsuka, M.; Kuru, N.; Yokomizo, Y.; Sakamoto, A.; Takemura, M.; Hoshino, K.; Kanda, H.; Nitanai, H.; et al. MexAB-OprM specific efflux pump inhibitors in Pseudomonas aeruginosa. Part 7: Highly soluble and in vivo active quaternary ammonium analogue D13-9001, a potential preclinical candidate. Bioorg. Med. Chem. 2007, 15, 7087–7097. [Google Scholar] [CrossRef]
  1009. Feldman, M.; Smoum, R.; Mechoulam, R.; Steinberg, D. Potential combinations of endocannabinoid/endocannabinoid-like compounds and antibiotics against methicillin-resistant Staphylococcus aureus. PLoS ONE 2020, 15, e0231583. [Google Scholar] [CrossRef] [Green Version]
  1010. Feldman, M.; Smoum, R.; Mechoulam, R.; Steinberg, D. Antimicrobial potential of endocannabinoid and endocannabinoid-like compounds against methicillin-resistant Staphylococcus aureus. Sci. Rep. 2018, 8, 17696. [Google Scholar] [CrossRef]
  1011. Muniz, D.F.; Dos Santos Barbosa, C.R.; de Menezes, I.R.A.; de Sousa, E.O.; Pereira, R.L.S.; Júnior, J.T.C.; Pereira, P.S.; de Matos, Y.; da Costa, R.H.S.; de Morais Oliveira-Tintino, C.D.; et al. In vitro and in silico inhibitory effects of synthetic and natural eugenol derivatives against the NorA efflux pump in Staphylococcus aureus. Food Chem. 2021, 337, 127776. [Google Scholar] [CrossRef]
  1012. Gupta, V.K.; Gaur, R.; Sharma, A.; Akther, J.; Saini, M.; Bhakuni, R.S.; Pathania, R. A novel bi-functional chalcone inhibits multi-drug resistant Staphylococcus aureus and potentiates the activity of fluoroquinolones. Bioorg. Chem. 2019, 83, 214–225. [Google Scholar] [CrossRef] [PubMed]
  1013. Opperman, T.J.; Kwasny, S.M.; Kim, H.S.; Nguyen, S.T.; Houseweart, C.; D’Souza, S.; Walker, G.C.; Peet, N.P.; Nikaido, H.; Bowlin, T.L. Characterization of a novel pyranopyridine inhibitor of the AcrAB efflux pump of Escherichia coli. Antimicrob. Agents Chemother. 2014, 58, 722–733. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  1014. Poole, K.; Gilmour, C.; Farha, M.A.; Parkins, M.D.; Klinoski, R.; Brown, E.D. Meropenem potentiation of aminoglycoside activity against Pseudomonas aeruginosa: Involvement of the MexXY-OprM multidrug efflux system. J. Antimicrob. Chemother. 2018, 73, 1247–1255. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  1015. Baiomy, A.A.; Shaker, G.H.; Abbas, H.A. Sensitizing multi drug resistant Staphylococcus aureus isolated from surgical site infections to antimicrobials by efflux pump inhibitors. Afr. Health Sci. 2020, 20, 1632–1645. [Google Scholar] [CrossRef]
  1016. Thamilselvan, G.; Sarveswari, H.B.; Vasudevan, S.; Stanley, A.; Shanmugam, K.; Vairaprakash, P.; Solomon, A.P. Development of an antibiotic resistance breaker to resensitize drug-resistant Staphylococcus aureus: In silico and in vitro approach. Front. Cell Infect. Microbiol. 2021, 11, 700198. [Google Scholar] [CrossRef]
  1017. Kinana, A.D.; Vargiu, A.V.; May, T.; Nikaido, H. Aminoacyl β-naphthylamides as substrates and modulators of AcrB multidrug efflux pump. Proc. Natl. Acad. Sci. USA 2016, 113, 1405–1410. [Google Scholar] [CrossRef] [Green Version]
  1018. Sabatini, S.; Kaatz, G.W.; Rossolini, G.M.; Brandini, D.; Fravolini, A. From phenothiazine to 3-phenyl-1,4-benzothiazine derivatives as inhibitors of the Staphylococcus aureus NorA multidrug efflux pump. J. Med. Chem. 2008, 51, 4321–4330. [Google Scholar] [CrossRef]
  1019. Bailey, A.M.; Paulsen, I.T.; Piddock, L.J. RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB, which is inhibited by chlorpromazine. Antimicrob. Agents Chemother. 2008, 52, 3604–3611. [Google Scholar] [CrossRef] [Green Version]
  1020. Kristiansen, J.E.; Mortensen, I.; Nissen, B. Membrane stabilizers inhibit potassium efflux from Staphylococcus aureus strain No. U2275. Biochim. Biophys. Acta 1982, 685, 379–382. [Google Scholar] [CrossRef]
  1021. Kaczor, A.; Witek, K.; Podlewska, S.; Sinou, V.; Czekajewska, J.; Żesławska, E.; Doroz-Płonka, A.; Lubelska, A.; Latacz, G.; Nitek, W.; et al. Molecular insights into an antibiotic enhancer action of new morpholine-containing 5-arylideneimidazolones in the fight against MDR bacteria. Int. J. Mol. Sci. 2021, 22, 2062. [Google Scholar] [CrossRef]
  1022. Casalone, E.; Vignolini, T.; Braconi, L.; Gardini, L.; Capitanio, M.; Pavone, F.S.; Giovannelli, L.; Dei, S.; Teodori, E. Characterization of substituted piperazines able to reverse MDR in Escherichia coli strains overexpressing resistance-nodulation-cell division (RND) efflux pumps. J. Antimicrob. Chemother. 2021, 77, 413–424. [Google Scholar] [CrossRef]
  1023. Sangwan, P.L.; Koul, J.L.; Koul, S.; Reddy, M.V.; Thota, N.; Khan, I.A.; Kumar, A.; Kalia, N.P.; Qazi, G.N. Piperine analogs as potent Staphylococcus aureus NorA efflux pump inhibitors. Bioorg. Med. Chem. 2008, 16, 9847–9857. [Google Scholar] [CrossRef]
  1024. Mahey, N.; Tambat, R.; Chandal, N.; Verma, D.K.; Thakur, K.G.; Nandanwar, H. Repurposing approved drugs as fluoroquinolone potentiators to overcome efflux pump resistance in Staphylococcus aureus. Microbiol. Spectr. 2021, 9, e0095121. [Google Scholar] [CrossRef]
  1025. Neyfakh, A.A.; Borsch, C.M.; Kaatz, G.W. Fluoroquinolone resistance protein NorA of Staphylococcus aureus is a multidrug efflux transporter. Antimicrob. Agents Chemother. 1993, 37, 128–129. [Google Scholar] [CrossRef] [Green Version]
  1026. Gibbons, S.; Udo, E.E. The effect of reserpine, a modulator of multidrug efflux pumps, on the in vitro activity of tetracycline against clinical isolates of methicillin resistant Staphylococcus aureus (MRSA) possessing the tet(K) determinant. Phytother. Res. 2000, 14, 139–140. [Google Scholar] [CrossRef]
  1027. Parai, D.; Banerjee, M.; Dey, P.; Chakraborty, A.; Islam, E.; Mukherjee, S.K. Effect of reserpine on Pseudomonas aeruginosa quorum sensing mediated virulence factors and biofilm formation. Biofouling 2018, 34, 320–334. [Google Scholar] [CrossRef]
  1028. Parai, D.; Banerjee, M.; Dey, P.; Mukherjee, S.K. Reserpine attenuates biofilm formation and virulence of Staphylococcus aureus. Microb. Pathog. 2020, 138, 103790. [Google Scholar] [CrossRef]
  1029. Singkham-In, U.; Higgins, P.G.; Wannigama, D.L.; Hongsing, P.; Chatsuwan, T. Rescued chlorhexidine activity by resveratrol against carbapenem-resistant Acinetobacter baumannii via down-regulation of AdeB efflux pump. PLoS ONE 2020, 15, e0243082. [Google Scholar] [CrossRef]
  1030. Hwang, D.; Lim, Y.H. Resveratrol controls Escherichia coli growth by inhibiting the AcrAB-TolC efflux pump. FEMS Microbiol. Lett. 2019, 366, fnz030. [Google Scholar] [CrossRef]
  1031. Vestergaard, M.; Roshanak, S.; Ingmer, H. Targeting the ATP synthase in Staphylococcus aureus small colony variants, Streptococcus pyogenes and pathogenic fungi. Antibiotics 2021, 10, 376. [Google Scholar] [CrossRef]
  1032. Liu, L.; Beck, C.; Nøhr-Meldgaard, K.; Peschel, A.; Kretschmer, D.; Ingmer, H.; Vestergaard, M. Inhibition of the ATP synthase sensitizes Staphylococcus aureus towards human antimicrobial peptides. Sci. Rep. 2020, 10, 11391. [Google Scholar] [CrossRef]
  1033. Vestergaard, M.; Nøhr-Meldgaard, K.; Bojer, M.S.; Krogsgård Nielsen, C.; Meyer, R.L.; Slavetinsky, C.; Peschel, A.; Ingmer, H. Inhibition of the ATP synthase eliminates the intrinsic resistance of Staphylococcus aureus towards polymyxins. mBio 2017, 8, e01114-17. [Google Scholar] [CrossRef] [Green Version]
  1034. Pereira, P.S.; Lima, M.; Neto, P.P.M.; Oliveira-Tintino, C.D.M.; Tintino, S.R.; Menezes, I.R.A.; de Oliveira, J.F.; Marchand, P.; Coutinho, H.D.M.; Rodrigues, M.D.D.; et al. Thiazolidinedione and thiazole derivatives potentiate norfloxacin activity against NorA efflux pump over expression in Staphylococcus aureus 1199B strains. Bioorg. Med. Chem. 2019, 27, 3797–3804. [Google Scholar] [CrossRef]
  1035. Feldman, M.; Ginsburg, I.; Al-Quntar, A.; Steinberg, D. Thiazolidinedione-8 alters symbiotic relationship in C. albicans-S. mutans dual species biofilm. Front. Microbiol. 2016, 7, 140. [Google Scholar] [CrossRef] [Green Version]
  1036. Froes, T.Q.; Chaves, B.T.; Mendes, M.S.; Ximenes, R.M.; da Silva, I.M.; da Silva, P.B.G.; de Albuquerque, J.F.C.; Castilho, M.S. Synthesis and biological evaluation of thiazolidinedione derivatives with high ligand efficiency to P. aeruginosa PhzS. J. Enzyme Inhib. Med. Chem. 2021, 36, 1217–1229. [Google Scholar] [CrossRef]
  1037. Smith, E.C.; Kaatz, G.W.; Seo, S.M.; Wareham, N.; Williamson, E.M.; Gibbons, S. The phenolic diterpene totarol inhibits multidrug efflux pump activity in Staphylococcus aureus. Antimicrob. Agents Chemother. 2007, 51, 4480–4483. [Google Scholar] [CrossRef] [Green Version]
  1038. Piddock, L.J.; Garvey, M.I.; Rahman, M.M.; Gibbons, S. Natural and synthetic compounds such as trimethoprim behave as inhibitors of efflux in Gram-negative bacteria. J. Antimicrob. Chemother. 2010, 65, 1215–1223. [Google Scholar] [CrossRef] [Green Version]
  1039. Gupta, S.; Cohen, K.A.; Winglee, K.; Maiga, M.; Diarra, B.; Bishai, W.R. Efflux inhibition with verapamil potentiates bedaquiline in Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 2014, 58, 574–576. [Google Scholar] [CrossRef] [Green Version]
  1040. Viveiros, M.; Amaral, L. Enhancement of antibiotic activity against poly-drug resistant Mycobacterium tuberculosis by phenothiazines. Int. J. Antimicrob. Agents 2001, 17, 225–228. [Google Scholar] [CrossRef]
  1041. Kaatz, G.W.; Moudgal, V.V.; Seo, S.M.; Kristiansen, J.E. Phenothiazines and thioxanthenes inhibit multidrug efflux pump activity in Staphylococcus aureus. Antimicrob. Agents Chemother. 2003, 47, 719–726. [Google Scholar] [CrossRef] [Green Version]
  1042. Brown, S.; Xia, G.; Luhachack, L.G.; Campbell, J.; Meredith, T.C.; Chen, C.; Winstel, V.; Gekeler, C.; Irazoqui, J.E.; Peschel, A.; et al. Methicillin resistance in Staphylococcus aureus requires glycosylated wall teichoic acids. Proc. Natl. Acad. Sci. USA 2012, 109, 18909–18914. [Google Scholar] [CrossRef] [Green Version]
  1043. Campbell, J.; Singh, A.K.; Santa Maria, J.P., Jr.; Kim, Y.; Brown, S.; Swoboda, J.G.; Mylonakis, E.; Wilkinson, B.J.; Walker, S. Synthetic lethal compound combinations reveal a fundamental connection between wall teichoic acid and peptidoglycan biosyntheses in Staphylococcus aureus. ACS Chem. Biol. 2011, 6, 106–116. [Google Scholar] [CrossRef] [Green Version]
  1044. Wang, H.; Gill, C.J.; Lee, S.H.; Mann, P.; Zuck, P.; Meredith, T.C.; Murgolo, N.; She, X.; Kales, S.; Liang, L.; et al. Discovery of wall teichoic acid inhibitors as potential anti-MRSA β-lactam combination agents. Chem. Biol. 2013, 20, 272–284. [Google Scholar] [CrossRef] [Green Version]
  1045. Kohler, T.; Weidenmaier, C.; Peschel, A. Wall teichoic acid protects Staphylococcus aureus against antimicrobial fatty acids from human skin. J. Bacteriol. 2009, 191, 4482–4484. [Google Scholar] [CrossRef] [Green Version]
  1046. Weidenmaier, C.; Kokai-Kun, J.F.; Kristian, S.A.; Chanturiya, T.; Kalbacher, H.; Gross, M.; Nicholson, G.; Neumeister, B.; Mond, J.J.; Peschel, A. Role of teichoic acids in Staphylococcus aureus nasal colonization, a major risk factor in nosocomial infections. Nat. Med. 2004, 10, 243–245. [Google Scholar] [CrossRef]
  1047. Weidenmaier, C.; Kokai-Kun, J.F.; Kulauzovic, E.; Kohler, T.; Thumm, G.; Stoll, H.; Götz, F.; Peschel, A. Differential roles of sortase-anchored surface proteins and wall teichoic acid in Staphylococcus aureus nasal colonization. Int. J. Med. Microbiol. 2008, 298, 505–513. [Google Scholar] [CrossRef]
  1048. Weidenmaier, C.; Peschel, A.; Xiong, Y.Q.; Kristian, S.A.; Dietz, K.; Yeaman, M.R.; Bayer, A.S. Lack of wall teichoic acids in Staphylococcus aureus leads to reduced interactions with endothelial cells and to attenuated virulence in a rabbit model of endocarditis. J. Infect. Dis. 2005, 191, 1771–1777. [Google Scholar] [CrossRef] [Green Version]
  1049. van Dalen, R.; Peschel, A.; van Sorge, N.M. Wall teichoic acid in Staphylococcus aureus host interaction. Trends Microbiol. 2020, 28, 985–998. [Google Scholar] [CrossRef]
  1050. Frankel, M.B.; Schneewind, O. Determinants of murein hydrolase targeting to cross-wall of Staphylococcus aureus peptidoglycan. J. Biol. Chem. 2012, 287, 10460–10471. [Google Scholar] [CrossRef] [Green Version]
  1051. Schlag, M.; Biswas, R.; Krismer, B.; Kohler, T.; Zoll, S.; Yu, W.; Schwarz, H.; Peschel, A.; Götz, F. Role of staphylococcal wall teichoic acid in targeting the major autolysin Atl. Mol. Microbiol. 2010, 75, 864–873. [Google Scholar] [CrossRef]
  1052. Kajimura, J.; Fujiwara, T.; Yamada, S.; Suzawa, Y.; Nishida, T.; Oyamada, Y.; Hayashi, I.; Yamagishi, J.; Komatsuzawa, H.; Sugai, M. Identification and molecular characterization of an N-acetylmuramyl-L-alanine amidase Sle1 involved in cell separation of Staphylococcus aureus. Mol. Microbiol. 2005, 58, 1087–1101. [Google Scholar] [CrossRef]
  1053. Tiwari, K.B.; Gatto, C.; Walker, S.; Wilkinson, B.J. Exposure of Staphylococcus aureus to Targocil blocks translocation of the major autolysin Atl across the membrane, resulting in a significant decrease in autolysis. Antimicrob. Agents Chemother. 2018, 62, e00323-18. [Google Scholar] [CrossRef] [Green Version]
  1054. Thalsø-Madsen, I.; Torrubia, F.R.; Xu, L.; Petersen, A.; Jensen, C.; Frees, D. The Sle1 cell wall amidase is essential for β-Lactam resistance in community-acquired methicillin-resistant Staphylococcus aureus USA300. Antimicrob. Agents Chemother. 2019, 64, e01931-19. [Google Scholar] [CrossRef] [Green Version]
  1055. Liu, Q.; Wang, X.; Qin, J.; Cheng, S.; Yeo, W.S.; He, L.; Ma, X.; Liu, X.; Li, M.; Bae, T. The ATP-dependent protease ClpP inhibits biofilm formation by regulating Agr and cell wall hydrolase Sle1 in Staphylococcus aureus. Front. Cell Infect. Microbiol. 2017, 7, 181. [Google Scholar] [CrossRef]
  1056. Brown, S.; Santa Maria, J.P., Jr.; Walker, S. Wall teichoic acids of gram-positive bacteria. Annu. Rev. Microbiol. 2013, 67, 313–336. [Google Scholar] [CrossRef] [Green Version]
  1057. Neuhaus, F.C.; Baddiley, J. A continuum of anionic charge: Structures and functions of D-alanyl-teichoic acids in gram-positive bacteria. Microbiol. Mol. Biol. Rev. 2003, 67, 686–723. [Google Scholar] [CrossRef] [Green Version]
  1058. Mann, P.A.; Müller, A.; Wolff, K.A.; Fischmann, T.; Wang, H.; Reed, P.; Hou, Y.; Li, W.; Müller, C.E.; Xiao, J.; et al. Chemical genetic analysis and functional characterization of Staphylococcal wall teichoic acid 2-epimerases reveals unconventional antibiotic drug targets. PLoS Pathog. 2016, 12, e1005585. [Google Scholar] [CrossRef]
  1059. Reichmann, N.T.; Cassona, C.P.; Gründling, A. Revised mechanism of D-alanine incorporation into cell wall polymers in Gram-positive bacteria. Microbiology 2013, 159, 1868–1877. [Google Scholar] [CrossRef]
  1060. Coupri, D.; Verneuil, N.; Hartke, A.; Liebaut, A.; Lequeux, T.; Pfund, E.; Budin-Verneuil, A. Inhibition of D-alanylation of teichoic acids overcomes resistance of methicillin-resistant Staphylococcus aureus. J. Antimicrob. Chemother. 2021, 76, 2778–2786. [Google Scholar] [CrossRef]
  1061. Kovács, M.; Halfmann, A.; Fedtke, I.; Heintz, M.; Peschel, A.; Vollmer, W.; Hakenbeck, R.; Brückner, R. A functional dlt operon, encoding proteins required for incorporation of d-alanine in teichoic acids in gram-positive bacteria, confers resistance to cationic antimicrobial peptides in Streptococcus pneumoniae. J. Bacteriol. 2006, 188, 5797–5805. [Google Scholar] [CrossRef] [Green Version]
  1062. Mechler, L.; Bonetti, E.J.; Reichert, S.; Flötenmeyer, M.; Schrenzel, J.; Bertram, R.; François, P.; Götz, F. Daptomycin tolerance in the Staphylococcus aureus pitA6 mutant is due to upregulation of the dlt operon. Antimicrob. Agents Chemother. 2016, 60, 2684–2691. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  1063. Lee, K.; Campbell, J.; Swoboda, J.G.; Cuny, G.D.; Walker, S. Development of improved inhibitors of wall teichoic acid biosynthesis with potent activity against Staphylococcus aureus. Bioorg. Med. Chem. Lett. 2010, 20, 1767–1770. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  1064. Suzuki, T.; Swoboda, J.G.; Campbell, J.; Walker, S.; Gilmore, M.S. In vitro antimicrobial activity of wall teichoic acid biosynthesis inhibitors against Staphylococcus aureus isolates. Antimicrob. Agents Chemother. 2011, 55, 767–774. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  1065. Campbell, J.; Singh, A.K.; Swoboda, J.G.; Gilmore, M.S.; Wilkinson, B.J.; Walker, S. An antibiotic that inhibits a late step in wall teichoic acid biosynthesis induces the cell wall stress stimulon in Staphylococcus aureus. Antimicrob. Agents Chemother. 2012, 56, 1810–1820. [Google Scholar] [CrossRef] [Green Version]
  1066. Farha, M.A.; Czarny, T.L.; Myers, C.L.; Worrall, L.J.; French, S.; Conrady, D.G.; Wang, Y.; Oldfield, E.; Strynadka, N.C.; Brown, E.D. Antagonism screen for inhibitors of bacterial cell wall biogenesis uncovers an inhibitor of undecaprenyl diphosphate synthase. Proc. Natl. Acad. Sci. USA 2015, 112, 11048–11053. [Google Scholar] [CrossRef] [Green Version]
  1067. Naclerio, G.A.; Onyedibe, K.I.; Sintim, H.O. Lipoteichoic acid biosynthesis inhibitors as potent inhibitors of S. aureus and E. faecalis growth and biofilm formation. Molecules 2020, 25, 2277. [Google Scholar] [CrossRef]
  1068. Lee, S.H.; Wang, H.; Labroli, M.; Koseoglu, S.; Zuck, P.; Mayhood, T.; Gill, C.; Mann, P.; Sher, X.; Ha, S.; et al. TarO-specific inhibitors of wall teichoic acid biosynthesis restore β-lactam efficacy against methicillin-resistant Staphylococci. Sci. Transl. Med. 2016, 8, 329ra32. [Google Scholar] [CrossRef]
  1069. Zhu, X.; Liu, D.; Singh, A.K.; Drolia, R.; Bai, X.; Tenguria, S.; Bhunia, A.K. Tunicamycin mediated inhibition of wall teichoic acid affects Staphylococcus aureus and Listeria monocytogenes cell morphology, biofilm formation and virulence. Front. Microbiol. 2018, 9, 1352. [Google Scholar] [CrossRef]
  1070. Pinho, M.G.; Filipe, S.R.; de Lencastre, H.; Tomasz, A. Complementation of the essential peptidoglycan transpeptidase function of penicillin-binding protein 2 (PBP2) by the drug resistance protein PBP2A in Staphylococcus aureus. J. Bacteriol. 2001, 183, 6525–6531. [Google Scholar] [CrossRef] [Green Version]
  1071. Hamilton, S.M.; Alexander, J.A.N.; Choo, E.J.; Basuino, L.; da Costa, T.M.; Severin, A.; Chung, M.; Aedo, S.; Strynadka, N.C.J.; Tomasz, A.; et al. High-level resistance of Staphylococcus aureus to β-Lactam antibiotics mediated by Penicillin-Binding Protein 4 (PBP4). Antimicrob. Agents Chemother. 2017, 61, e02727-16. [Google Scholar] [CrossRef] [Green Version]
  1072. Lee, S.H.; Jarantow, L.W.; Wang, H.; Sillaots, S.; Cheng, H.; Meredith, T.C.; Thompson, J.; Roemer, T. Antagonism of chemical genetic interaction networks resensitize MRSA to β-lactam antibiotics. Chem. Biol. 2011, 18, 1379–1389. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  1073. Pinho, M.G.; Errington, J. Dispersed mode of Staphylococcus aureus cell wall synthesis in the absence of the division machinery. Mol. Microbiol. 2003, 50, 871–881. [Google Scholar] [CrossRef] [PubMed]
  1074. Otero, L.H.; Rojas-Altuve, A.; Llarrull, L.I.; Carrasco-López, C.; Kumarasiri, M.; Lastochkin, E.; Fishovitz, J.; Dawley, M.; Hesek, D.; Lee, M.; et al. How allosteric control of Staphylococcus aureus penicillin binding protein 2a enables methicillin resistance and physiological function. Proc. Natl. Acad. Sci. USA 2013, 110, 16808–16813. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  1075. Acebrón, I.; Chang, M.; Mobashery, S.; Hermoso, J.A. The allosteric site for the nascent cell wall in Penicillin-Binding Protein 2a: An Achilles’ heel of methicillin-resistant Staphylococcus aureus. Curr. Med. Chem. 2015, 22, 1678–1686. [Google Scholar] [CrossRef] [Green Version]
  1076. García-Fernández, E.; Koch, G.; Wagner, R.M.; Fekete, A.; Stengel, S.T.; Schneider, J.; Mielich-Süss, B.; Geibel, S.; Markert, S.M.; Stigloher, C.; et al. Membrane microdomain disassembly inhibits MRSA antibiotic resistance. Cell 2017, 171, 1354–1367.e1320. [Google Scholar] [CrossRef] [PubMed]
  1077. Falagas, M.E.; Makris, G.C.; Matthaiou, D.K.; Rafailidis, P.I. Statins for infection and sepsis: A systematic review of the clinical evidence. J. Antimicrob. Chemother. 2008, 61, 774–785. [Google Scholar] [CrossRef] [Green Version]
  1078. Tralhão, A.F.; Cés de Souza-Dantas, V.; Salluh, J.I.; Póvoa, P.M. Impact of statins in outcomes of septic patients: A systematic review. Postgrad. Med. 2014, 126, 45–58. [Google Scholar] [CrossRef]
  1079. Almog, Y.; Shefer, A.; Novack, V.; Maimon, N.; Barski, L.; Eizinger, M.; Friger, M.; Zeller, L.; Danon, A. Prior statin therapy is associated with a decreased rate of severe sepsis. Circulation 2004, 110, 880–885. [Google Scholar] [CrossRef]
  1080. López-Cortés, L.E.; Gálvez-Acebal, J.; Del Toro, M.D.; Velasco, C.; de Cueto, M.; Caballero, F.J.; Muniain, M.A.; Pascual, A.; Rodríguez-Baño, J. Effect of statin therapy in the outcome of bloodstream infections due to Staphylococcus aureus: A prospective cohort study. PLoS ONE 2013, 8, e82958. [Google Scholar] [CrossRef]
  1081. Casiraghi, A.; Suigo, L.; Valoti, E.; Straniero, V. Targeting bacterial cell division: A binding site-centered approach to the most promising inhibitors of the essential protein FtsZ. Antibiotics 2020, 9, 69. [Google Scholar] [CrossRef] [Green Version]
  1082. Barrows, J.M.; Goley, E.D. FtsZ dynamics in bacterial division: What, how, and why? Curr. Opin. Cell Biol. 2021, 68, 163–172. [Google Scholar] [CrossRef] [PubMed]
  1083. Tan, C.M.; Therien, A.G.; Lu, J.; Lee, S.H.; Caron, A.; Gill, C.J.; Lebeau-Jacob, C.; Benton-Perdomo, L.; Monteiro, J.M.; Pereira, P.M.; et al. Restoring methicillin-resistant Staphylococcus aureus susceptibility to β-lactam antibiotics. Sci. Transl. Med. 2012, 4, 126ra135. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  1084. Erickson, H.P.; Anderson, D.E.; Osawa, M. FtsZ in bacterial cytokinesis: Cytoskeleton and force generator all in one. Microbiol. Mol. Biol. Rev. 2010, 74, 504–528. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  1085. Ferrer-González, E.; Kaul, M.; Parhi, A.K.; LaVoie, E.J.; Pilch, D.S. β-Lactam antibiotics with a high affinity for PBP2 act synergistically with the FtsZ-targeting agent TXA707 against methicillin-resistant Staphylococcus aureus. Antimicrob. Agents Chemother. 2017, 61, e00863-17. [Google Scholar] [CrossRef] [Green Version]
  1086. Ferrer-González, E.; Huh, H.; Al-Tameemi, H.M.; Boyd, J.M.; Lee, S.H.; Pilch, D.S. Impact of FtsZ inhibition on the localization of the penicillin binding proteins in methicillin-resistant Staphylococcus aureus. J. Bacteriol. 2021, 203, e0020421. [Google Scholar] [CrossRef]
  1087. Kaul, M.; Mark, L.; Parhi, A.K.; LaVoie, E.J.; Pilch, D.S. Combining the FtsZ-targeting prodrug TXA709 and the Cephalosporin Cefdinir confers synergy and reduces the frequency of resistance in methicillin-resistant Staphylococcus aureus. Antimicrob. Agents Chemother. 2016, 60, 4290–4296. [Google Scholar] [CrossRef] [Green Version]
  1088. Sun, N.; Ban, L.; Li, M.; Fang, Z.; Li, X.; Yao, W.; Pan, J.; Lu, Y.; Liu, Z.; Wong, W.L. Probing the benzofuroquinolinium derivative as a potent antibacterial agent through the inhibition of FtsZ activity. J. Pharmacol. Sci. 2018, 138, 83–85. [Google Scholar] [CrossRef]
  1089. Domadia, P.N.; Bhunia, A.; Sivaraman, J.; Swarup, S.; Dasgupta, D. Berberine targets assembly of Escherichia coli cell division protein FtsZ. Biochemistry 2008, 47, 3225–3234. [Google Scholar] [CrossRef]
  1090. Li, X.; Song, Y.; Wang, L.; Kang, G.; Wang, P.; Yin, H.; Huang, H. A potential combination therapy of berberine hydrochloride with antibiotics against multidrug-resistant Acinetobacter baumannii. Front. Cell Infect. Microbiol. 2021, 11, 660431. [Google Scholar] [CrossRef]
  1091. Domadia, P.; Swarup, S.; Bhunia, A.; Sivaraman, J.; Dasgupta, D. Inhibition of bacterial cell division protein FtsZ by cinnamaldehyde. Biochem. Pharmacol. 2007, 74, 831–840. [Google Scholar] [CrossRef]
  1092. Wang, S.; Kang, O.H.; Kwon, D.Y. Trans-cinnamaldehyde exhibits synergy with conventional antibiotic against methicillin-resistant Staphylococcus aureus. Int. J. Mol. Sci. 2021, 22, 2752. [Google Scholar] [CrossRef] [PubMed]
  1093. Kot, B.; Sytykiewicz, H.; Sprawka, I.; Witeska, M. Effect of trans-cinnamaldehyde on methicillin-resistant Staphylococcus aureus biofilm formation: Metabolic activity assessment and analysis of the biofilm-associated genes expression. Int. J. Mol. Sci. 2019, 21, 102. [Google Scholar] [CrossRef] [Green Version]
  1094. Kot, B.; Wierzchowska, K.; Grużewska, A.; Lohinau, D. The effects of selected phytochemicals on biofilm formed by five methicillin-resistant Staphylococcus aureus. Nat. Prod. Res. 2018, 32, 1299–1302. [Google Scholar] [CrossRef] [PubMed]
  1095. Fang, Z.; Ban, L.; Li, Y.; Yuan, W.; Liu, Z.; Liu, T.; Li, X.; Wong, K.Y.; Lu, Y.; Sun, N.; et al. A quinoline-based FtsZ inhibitor for the study of antimicrobial activity and synergistic effects with β-lactam antibiotics. J. Pharmacol. Sci. 2018, 137, 283–289. [Google Scholar] [CrossRef] [PubMed]
  1096. Haydon, D.J.; Stokes, N.R.; Ure, R.; Galbraith, G.; Bennett, J.M.; Brown, D.R.; Baker, P.J.; Barynin, V.V.; Rice, D.W.; Sedelnikova, S.E.; et al. An inhibitor of FtsZ with potent and selective anti-staphylococcal activity. Science 2008, 321, 1673–1675. [Google Scholar] [CrossRef] [PubMed]
  1097. Andreu, J.M.; Schaffner-Barbero, C.; Huecas, S.; Alonso, D.; Lopez-Rodriguez, M.L.; Ruiz-Avila, L.B.; Núñez-Ramírez, R.; Llorca, O.; Martín-Galiano, A.J. The antibacterial cell division inhibitor PC190723 is an FtsZ polymer-stabilizing agent that induces filament assembly and condensation. J. Biol. Chem. 2010, 285, 14239–14246. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  1098. Chan, F.Y.; Sun, N.; Leung, Y.C.; Wong, K.Y. Antimicrobial activity of a quinuclidine-based FtsZ inhibitor and its synergistic potential with β-lactam antibiotics. J. Antibiot. 2015, 68, 253–258. [Google Scholar] [CrossRef]
Figure 1. (A). Induction of vancomycin resistance in Staphylococcus aureus by vancomycin. Vancomycin activates the TCS VanRS, which induces the expression of the vanHAX operon responsible for the synthesis of the D-alanyl-D-lactate dipeptide. The D-alanyl–D-lactate dipeptide shows a 1000-fold lower affinity to vancomycin compared to the regular D-alanyl–D-alanine dipeptide, thereby conferring vancomycin resistance. (B). Examples of regulatory mechanisms involved in antibiotic resistance and biofilm formation in Staphylococcus aureus. The expressions of the efflux pumps NorA and AbcA, which confer antibiotic resistance to fluoroquinolones and β-lactams, respectively, are induced by their respective substrates norfloxacin and ampicillin. Additionally, their expression levels are influenced by the ArlRS and Agr TCSs, which both affect the global transcriptional regulator MgrA (also known as NorR). Phosphorylation of MgrA by the PknB serine/theonine kinase leads to increased transcription of norA. The ArlRS and Agr TCSs are regulated by several transcriptional factors (e.g., NorG, Rot, SarA, SarR, SarZ, SigB) as illustrated in the figure. This network of regulatory factors also affects biofilm formation, where AbcA promotes biofilm formation by exporting phenol-soluble modulins (PSMs), and the Agr QS prevents biofilm formation. The Agr QS is explained in more detail in Section 3.3.
Figure 1. (A). Induction of vancomycin resistance in Staphylococcus aureus by vancomycin. Vancomycin activates the TCS VanRS, which induces the expression of the vanHAX operon responsible for the synthesis of the D-alanyl-D-lactate dipeptide. The D-alanyl–D-lactate dipeptide shows a 1000-fold lower affinity to vancomycin compared to the regular D-alanyl–D-alanine dipeptide, thereby conferring vancomycin resistance. (B). Examples of regulatory mechanisms involved in antibiotic resistance and biofilm formation in Staphylococcus aureus. The expressions of the efflux pumps NorA and AbcA, which confer antibiotic resistance to fluoroquinolones and β-lactams, respectively, are induced by their respective substrates norfloxacin and ampicillin. Additionally, their expression levels are influenced by the ArlRS and Agr TCSs, which both affect the global transcriptional regulator MgrA (also known as NorR). Phosphorylation of MgrA by the PknB serine/theonine kinase leads to increased transcription of norA. The ArlRS and Agr TCSs are regulated by several transcriptional factors (e.g., NorG, Rot, SarA, SarR, SarZ, SigB) as illustrated in the figure. This network of regulatory factors also affects biofilm formation, where AbcA promotes biofilm formation by exporting phenol-soluble modulins (PSMs), and the Agr QS prevents biofilm formation. The Agr QS is explained in more detail in Section 3.3.
Microorganisms 10 01239 g001
Figure 2. Induction of antibiotic resistance in Pseudomonas aeruginosa by antibiotics, zinc ions, and low concentrations of extracellular magnesium ions. The expression of the MexXY-OprM efflux pump responsible for multidrug resistance is regulated by several factors including ribosome-targeting antibiotics and the TCSs AmgRS and ParRS. AmgRS is activated by envelope stress, and ParRS is activated by the cationic antimicrobial peptide colistin as well as zinc ions. Moreover, colistin activates other TCSs including CprRS and PmrAB. The latter TCS is also affected by the TCS PhoPQ, which is activated by low extracellular magnesium ion concentrations, and extracellular DNA which sequesters magnesium ions. Extracellular DNA is a central component of Pseudomonas aeruginosa biofilms. The TCSs ParRS, CprRS, and PmrAB induce the translation of the arnBCADTEF operon which is responsible for the L-Ara4N modification of LPS, resulting in resistance to colistin. Additionally, LPS is modified by palmitoylation through PhoPQ-mediated upregulation of pagP, and by PEtN attachments regulated by the ColRS TCS.
Figure 2. Induction of antibiotic resistance in Pseudomonas aeruginosa by antibiotics, zinc ions, and low concentrations of extracellular magnesium ions. The expression of the MexXY-OprM efflux pump responsible for multidrug resistance is regulated by several factors including ribosome-targeting antibiotics and the TCSs AmgRS and ParRS. AmgRS is activated by envelope stress, and ParRS is activated by the cationic antimicrobial peptide colistin as well as zinc ions. Moreover, colistin activates other TCSs including CprRS and PmrAB. The latter TCS is also affected by the TCS PhoPQ, which is activated by low extracellular magnesium ion concentrations, and extracellular DNA which sequesters magnesium ions. Extracellular DNA is a central component of Pseudomonas aeruginosa biofilms. The TCSs ParRS, CprRS, and PmrAB induce the translation of the arnBCADTEF operon which is responsible for the L-Ara4N modification of LPS, resulting in resistance to colistin. Additionally, LPS is modified by palmitoylation through PhoPQ-mediated upregulation of pagP, and by PEtN attachments regulated by the ColRS TCS.
Microorganisms 10 01239 g002
Figure 3. Examples of antibiotic resistance mechanisms induced by bile acids. Bile salts which are secreted into the duodenum, induce the expression of various genes in bacteria that confers antibiotic resistance. Outstanding is the upregulation of efflux pumps such as MexAB-OprM in Pseudomonas aeruginosa, AcrAB-TolC in Enterobacteriaceae and EmrB/QacA in Enterococcus faecalis that confer resistance to multiple antibiotics and antiseptics, as well as to the bile salts themselves. Additionally, the TCSs BasRS and PmrAB are induced in Escherichia coli, resulting in the upregulation of the arnBCADTEF operon responsible for the L-Ara4N modification of LPS. This modification reduces the affinity of colistin/polymyxin B to LPS, with consequent resistance to these drugs.
Figure 3. Examples of antibiotic resistance mechanisms induced by bile acids. Bile salts which are secreted into the duodenum, induce the expression of various genes in bacteria that confers antibiotic resistance. Outstanding is the upregulation of efflux pumps such as MexAB-OprM in Pseudomonas aeruginosa, AcrAB-TolC in Enterobacteriaceae and EmrB/QacA in Enterococcus faecalis that confer resistance to multiple antibiotics and antiseptics, as well as to the bile salts themselves. Additionally, the TCSs BasRS and PmrAB are induced in Escherichia coli, resulting in the upregulation of the arnBCADTEF operon responsible for the L-Ara4N modification of LPS. This modification reduces the affinity of colistin/polymyxin B to LPS, with consequent resistance to these drugs.
Microorganisms 10 01239 g003
Figure 4. Induction of antibiotic resistance by the tryptophan metabolite indole. Indole, which is produced by various gut bacteria including Escherichia coli, induces the expression of various efflux pumps (e.g., AcdD, MdtABC, AcdE, AcrAB-TolC) through activation of TCSs (e.g., BaeSR, CpxAR) or transcriptional regulators (GadX, RamA). The activity of RamA is negatively regulated by RamR.
Figure 4. Induction of antibiotic resistance by the tryptophan metabolite indole. Indole, which is produced by various gut bacteria including Escherichia coli, induces the expression of various efflux pumps (e.g., AcdD, MdtABC, AcdE, AcrAB-TolC) through activation of TCSs (e.g., BaeSR, CpxAR) or transcriptional regulators (GadX, RamA). The activity of RamA is negatively regulated by RamR.
Microorganisms 10 01239 g004
Figure 5. Regulation of AcrAB-TolC efflux pump expression in Gram-negative bacteria. The expression of AcrAB-TolC, which confers multidrug resistance, is regulated by several transcriptional regulators including MarA, RarA, RamA, Rob, AcrR, SidA, and SoxS. MarA, in turn, is regulated by the TCSs CpxAR and QseBC, as well as various antibiotics. MarA reduces the expression of the OmpF porin which is required for the penetration of several antibiotics into the bacteria. RarA is activated by the antibiotic ertapenem. Besides upregulating AcrAB-TolC, RarA increases the expression of the OqxAB multidrug efflux pump. Bile acids and fatty acids increase AcrAB-TolC expression through repression of the Rob transcriptional regulator. SoxS is regulated by SoxR whose activity is influenced by oxidative stress, as well as by the Pseudomonas aeruginosa-produced pyocyanin pigment. In turn, SoxS increases the expression of SodA superoxide dismutase, which is a mechanism to protect the bacteria from oxidative stress. Additionally, SoxR induces the expression of the MexHI-OpmD efflux pump, thus conferring resistance to additional compounds.
Figure 5. Regulation of AcrAB-TolC efflux pump expression in Gram-negative bacteria. The expression of AcrAB-TolC, which confers multidrug resistance, is regulated by several transcriptional regulators including MarA, RarA, RamA, Rob, AcrR, SidA, and SoxS. MarA, in turn, is regulated by the TCSs CpxAR and QseBC, as well as various antibiotics. MarA reduces the expression of the OmpF porin which is required for the penetration of several antibiotics into the bacteria. RarA is activated by the antibiotic ertapenem. Besides upregulating AcrAB-TolC, RarA increases the expression of the OqxAB multidrug efflux pump. Bile acids and fatty acids increase AcrAB-TolC expression through repression of the Rob transcriptional regulator. SoxS is regulated by SoxR whose activity is influenced by oxidative stress, as well as by the Pseudomonas aeruginosa-produced pyocyanin pigment. In turn, SoxS increases the expression of SodA superoxide dismutase, which is a mechanism to protect the bacteria from oxidative stress. Additionally, SoxR induces the expression of the MexHI-OpmD efflux pump, thus conferring resistance to additional compounds.
Microorganisms 10 01239 g005
Figure 6. Regulation of MexAB-OprM multidrug efflux pump expression in Pseudomonas aeruginosa. The expression of the MexAB-OprM efflux pump is positively and negatively regulated by a whole range of transcriptional regulators. Its expression is also affected by bile salts and induced by the AmgRS TCS and CpxR, which is the cognate response regulator of the CpxAR TCS.
Figure 6. Regulation of MexAB-OprM multidrug efflux pump expression in Pseudomonas aeruginosa. The expression of the MexAB-OprM efflux pump is positively and negatively regulated by a whole range of transcriptional regulators. Its expression is also affected by bile salts and induced by the AmgRS TCS and CpxR, which is the cognate response regulator of the CpxAR TCS.
Microorganisms 10 01239 g006
Figure 7. Regulation of the antiholin LrgA–holin CidA system by the small SprX RNA. SprX inhibits the expression of the RNA-binding protein SpoVG, which positively regulates the TCS LytSR. LytSR positively regulates the antiholin LrgA which antagonizes the activity of the holin CidA. SpoVG induces methicillin and oxacillin resistance by promoting cell wall synthesis and inhibiting cell wall degradation. LrgA and CidA affect the response to penicillin by respectively inhibiting or activating murein hydrolase activities. Altogether, the overexpression of SprX results in increased susceptibility to β-lactams.
Figure 7. Regulation of the antiholin LrgA–holin CidA system by the small SprX RNA. SprX inhibits the expression of the RNA-binding protein SpoVG, which positively regulates the TCS LytSR. LytSR positively regulates the antiholin LrgA which antagonizes the activity of the holin CidA. SpoVG induces methicillin and oxacillin resistance by promoting cell wall synthesis and inhibiting cell wall degradation. LrgA and CidA affect the response to penicillin by respectively inhibiting or activating murein hydrolase activities. Altogether, the overexpression of SprX results in increased susceptibility to β-lactams.
Microorganisms 10 01239 g007
Figure 8. Crosstalk of the four QS systems Las, Rhl, Pqs, and Iqs in Pseudomonas aeruginosa and their relationship to biofilm formation. Each of the four TCS systems produces its own autoinducer (C12-HSL, PQS, IqsR, or C4-HSL) that acts on the corresponding receptor (LasR, PqsR, IqsR, or RhlR). The receptors, in turn, elicit phosphorelay cascades resulting in altered expression of a large number of genes. In addition, there is crosstalk between these TCSs. LasR affects PqsR, IqsR, and RhlR. There is also mutual communication between PqsR and RhlR. LasR is involved in biofilm development and maturation. PqsR is involved in early biofilm formation and the release of extracellular DNA. RhlR is involved in the maintenance of biofilm channels and the detachment of biofilm-embedded cells. IqsR promotes biofilm formation by acting on PqsR and RhlR.
Figure 8. Crosstalk of the four QS systems Las, Rhl, Pqs, and Iqs in Pseudomonas aeruginosa and their relationship to biofilm formation. Each of the four TCS systems produces its own autoinducer (C12-HSL, PQS, IqsR, or C4-HSL) that acts on the corresponding receptor (LasR, PqsR, IqsR, or RhlR). The receptors, in turn, elicit phosphorelay cascades resulting in altered expression of a large number of genes. In addition, there is crosstalk between these TCSs. LasR affects PqsR, IqsR, and RhlR. There is also mutual communication between PqsR and RhlR. LasR is involved in biofilm development and maturation. PqsR is involved in early biofilm formation and the release of extracellular DNA. RhlR is involved in the maintenance of biofilm channels and the detachment of biofilm-embedded cells. IqsR promotes biofilm formation by acting on PqsR and RhlR.
Microorganisms 10 01239 g008
Figure 9. The Agr QS system of Staphylococcus aureus. The arg operon consists of the 4 genes: agrB, agrD, agrC, and agrA. AgrD encodes for a precursor of the autoinducer peptide AIP that is processed and transported through the cell membrane by AgrB. The mature AIP interacts with its receptor AgrC eliciting a phosphorelay, resulting in the phosphorylation and activation of the response regulator AgrA that affects the expression of multiple genes including the genes of the agr operon by binding to the P2 promoter, and the RNAIII regulatory RNA by binding to the P3 promoter. RNAIII affects the expression of a large number of genes, thereby promoting the virulence of Staphylococcus aureus. A small part of the RNAIII transcript encodes for the δ-toxin (delta-hemolysin; hld). Additionally, AgrA activates the TCSs ArlRS and SaePQRS, as well as upregulating the expression of the virulence factors phenol-soluble modulins (PSMs) alpha and beta. As shown in Figure 1B, ArlRS modulates the expression of the NorA efflux channel responsible for fluoroquinolone resistance and regulates virulence factors through the induction of MgrA. The SaePQRS TCS regulates the expression of various virulence factors.
Figure 9. The Agr QS system of Staphylococcus aureus. The arg operon consists of the 4 genes: agrB, agrD, agrC, and agrA. AgrD encodes for a precursor of the autoinducer peptide AIP that is processed and transported through the cell membrane by AgrB. The mature AIP interacts with its receptor AgrC eliciting a phosphorelay, resulting in the phosphorylation and activation of the response regulator AgrA that affects the expression of multiple genes including the genes of the agr operon by binding to the P2 promoter, and the RNAIII regulatory RNA by binding to the P3 promoter. RNAIII affects the expression of a large number of genes, thereby promoting the virulence of Staphylococcus aureus. A small part of the RNAIII transcript encodes for the δ-toxin (delta-hemolysin; hld). Additionally, AgrA activates the TCSs ArlRS and SaePQRS, as well as upregulating the expression of the virulence factors phenol-soluble modulins (PSMs) alpha and beta. As shown in Figure 1B, ArlRS modulates the expression of the NorA efflux channel responsible for fluoroquinolone resistance and regulates virulence factors through the induction of MgrA. The SaePQRS TCS regulates the expression of various virulence factors.
Microorganisms 10 01239 g009
Figure 10. The Cpx envelope stress-response system. The CpxAR TCS is activated by various stress stimuli including protein misfolding, certain antibiotics, inner membrane disruption, alkaline pH, starvation, high osmolarity, and adherence to an abiotic surface. The activation of CpxAR leads to large alterations in gene expression in an attempt to protect the bacteria from the environmental stressor. Among others, it induces the expression of genes assisting in removing misfolded proteins and genes involved in biofilm formation. Additionally, CpxAR increases the expression of various genes (e.g., efflux pumps, porins, amidases, and the ldtD transpeptidase) that confer multidrug resistance and copper tolerance.
Figure 10. The Cpx envelope stress-response system. The CpxAR TCS is activated by various stress stimuli including protein misfolding, certain antibiotics, inner membrane disruption, alkaline pH, starvation, high osmolarity, and adherence to an abiotic surface. The activation of CpxAR leads to large alterations in gene expression in an attempt to protect the bacteria from the environmental stressor. Among others, it induces the expression of genes assisting in removing misfolded proteins and genes involved in biofilm formation. Additionally, CpxAR increases the expression of various genes (e.g., efflux pumps, porins, amidases, and the ldtD transpeptidase) that confer multidrug resistance and copper tolerance.
Microorganisms 10 01239 g010
Figure 11. The role of c-di-GMP in biofilm formation and antibiotic resistance. The secondary metabolite c-di-GMP is a central mediator of biofilm formation in Gram-negative bacteria. It modulates the expression of various genes (e.g., fimX, alg44, pelD, fleQ) involved in the production of pili, flagella, alginate, and exopolysaccharides (Pel and Psl) that contribute to the development of the biofilm. Moreover, it induces the transcriptional responser BrlR that regulates the expression of efflux pumps involved in antibiotic resistance. The activity of BrlR is affected by SagS, which is involved in the molecular switch from a planktonic to a biofilm lifestyle (see Figure 12 below). The c-di-GMP level is affected by various factors including cell adhesion and cell envelope stress. Its synthesis is mediated by diguanylate cyclases (DGCs) and degraded by c-di-GMP phosphodiesterases (PDEs).
Figure 11. The role of c-di-GMP in biofilm formation and antibiotic resistance. The secondary metabolite c-di-GMP is a central mediator of biofilm formation in Gram-negative bacteria. It modulates the expression of various genes (e.g., fimX, alg44, pelD, fleQ) involved in the production of pili, flagella, alginate, and exopolysaccharides (Pel and Psl) that contribute to the development of the biofilm. Moreover, it induces the transcriptional responser BrlR that regulates the expression of efflux pumps involved in antibiotic resistance. The activity of BrlR is affected by SagS, which is involved in the molecular switch from a planktonic to a biofilm lifestyle (see Figure 12 below). The c-di-GMP level is affected by various factors including cell adhesion and cell envelope stress. Its synthesis is mediated by diguanylate cyclases (DGCs) and degraded by c-di-GMP phosphodiesterases (PDEs).
Microorganisms 10 01239 g011
Figure 12. (A). Regulation of RsmY/RsmZ small RNAs by the GacSA TCS and c-di-GMP in Pseudomonas aeruginosa and the impact on biofilm formation. RsmY and RsmZ are small regulatory RNAs involved in the regulation of biofilm formation. Their expression is regulated by the TCS GacSA, whose activity is, in turn, regulated by the LadS, RetS, and P1611 kinases. RsmY and RsmZ sequester the translational repressor RsmA, thereby relieving its inhibitory action on c-di-GMP production and biofilm formation. Since RsmA increases motility through the type III secretion system (T3SS), an increase in the RsmY and RsmZ levels would result in reduced motility. (B). Additional TCS components regulating biofilm formation. In the planktonic state, SagS is phosphorylated and prevents the activity of BfiSR. Dephosphorylation of SagS leads to phosphorylation of BfiSR resulting in the switch from a reversible attachment to an irreversible attachment. This is followed by phosphorylation of BfmSR, which initiates biofilm maturation, and phosphorylation of MifSR, which is required for full biofilm maturation.
Figure 12. (A). Regulation of RsmY/RsmZ small RNAs by the GacSA TCS and c-di-GMP in Pseudomonas aeruginosa and the impact on biofilm formation. RsmY and RsmZ are small regulatory RNAs involved in the regulation of biofilm formation. Their expression is regulated by the TCS GacSA, whose activity is, in turn, regulated by the LadS, RetS, and P1611 kinases. RsmY and RsmZ sequester the translational repressor RsmA, thereby relieving its inhibitory action on c-di-GMP production and biofilm formation. Since RsmA increases motility through the type III secretion system (T3SS), an increase in the RsmY and RsmZ levels would result in reduced motility. (B). Additional TCS components regulating biofilm formation. In the planktonic state, SagS is phosphorylated and prevents the activity of BfiSR. Dephosphorylation of SagS leads to phosphorylation of BfiSR resulting in the switch from a reversible attachment to an irreversible attachment. This is followed by phosphorylation of BfmSR, which initiates biofilm maturation, and phosphorylation of MifSR, which is required for full biofilm maturation.
Microorganisms 10 01239 g012
Table 2. Examples of two-component systems (TCSs) involved in antibiotic resistance.
Table 2. Examples of two-component systems (TCSs) involved in antibiotic resistance.
TCS Involved
in Antibiotic
Resistance
FunctionBacterial SpeciesReferences
AdeRS
-
AdeRS induces the expression of adeABC multidrug efflux pump that confers resistance to various antibiotics including tigecycline, aminoglycosides, chlorhexidine, and pentamidine.
-
Inactivation of AdeS leads to aminoglycoside sensitivity.
-
Mutation of AdeR leads to constitutive expression of the adeABC efflux pump and antibiotic resistance.
Acinetobacter baumannii[226,389,390,391,392]
AirSR (YhcSR)
-
An airSR mutant showed reduced autolysis rates and higher susceptibility to vancomycin.
-
Mutation in airR caused increased resistance to hydrogen peroxide, vancomycin, norfloxacin, and ciprofloxacin under anaerobic conditions.
-
AirSR regulates the nitrate respiratory pathway.
-
AirSR senses oxygen tension and regulates redox signaling.
-
AirSR regulates the expression of genes that function in cell wall metabolism (cap, pbp1, and ddl) and autolysis (lytM).
Staphylococcus aureus[393,394]
AmgRS
-
AmgRS is a membrane stress-responsive TCS that causes intrinsic tobramycin resistance and increases virulence.
-
AmgRS is activated by aminoglycosides such as paromomycin.
-
AmgRS induces the expression of various genes that contribute to aminoglycoside resistance including the mexXY and mexAB-oprM efflux pumps; a modulator of FtsH protease (YccA); a membrane protease (HtpX); and the membrane protein PA5528.
-
AmgRS is activated by zinc ions and protects the bacteria from zinc-mediated membrane damage.
Pseudomonas aeruginosa[52,197,395,396,397]
ApsRS
-
ApsRS confers resistance to antimicrobial peptides by inducing the expression of the dlt operon that adds D-alanine to teichoic acid in the cell wall, and mprF (fmtC) that adds lysine to phosphatidylglycerol in cell membranes.
Staphylococcus aureus[381,382,383]
ArlRS
-
ArlRS modulates norA gene expression.
-
arlS mutation leads to increased norA expression, with consequent resistance to fluoroquinolones.
-
Deletion of arlRS in MRSA USA300 strain resulted in increased susceptibility to oxacillin, which was attributed to a downregulation of spx, a global regulator that impacts stress tolerance. Overexpression of spx restored oxacillin resistance in the ΔarlRS mutant.
-
ArlRS affects autolysis, biofilm formation, capsule synthesis, and virulence.
-
ArlRS activates the expression of the global regulator MgrA.
Staphylococcus aureus[182,398,399,400]
BaeSR
-
BaeSR functions as a stress responder under high osmotic conditions.
-
BaeR confers resistance to novobiocin and deoxycholate by upregulating the expression of the yegMNOB (mdtABCD)–baeSR operon by binding to the yegM promoter in Escherichia coli. The MdtB/MdtC efflux pump confers resistance to bile salts in Escherichia coli. The YegO and YegN RND transporters, but not the YegB MFS transporter, confer antibiotic resistance to novobiocin.
-
Overexpression of baeR conferred resistance to carbenicillin, aztreonam, and carumonam in Escherichia coli.
-
In Salmonella typhimurium, ciprofloxacin induces mdtA expression via activation of BaeRS. MdtA pumps out novobiocin and deoxycholate.
-
BaeR regulates tigecycline susceptibility in Acinetobacter baumannii through positively regulating the efflux pump genes adeA, adeB, adeIJK, and macAB-tolC.
Escherichia coli,
Salmonella typhimurium,
Acinetobacter baumannii
[401,402,403,404,405,406]
BasSR
-
BasSR regulates susceptibility to polymyxin, deoxycholic acid, sodium dodecyl sulfate, fluoroquinolones, tetracyclines, erythromycin, clindamycin, and lincomycin.
-
BasSR regulates the expression of the multidrug efflux pump EmrD.
Escherichia coli[407]
BqsRS
-
BqsRS induces the expression of arnBCADTEF, which confers resistance to polymyxins and other antimicrobial peptides.
-
BqsRS senses extracellular Fe2+ ions.
Pseudomonas aeruginosa[408]
BraRS
-
BraRS induces resistance to bacitracin and nisin by upregulating the ABC transporters braAB, braDE, and vraDE.
-
Low concentrations of bacitracin and nisin induce BraRS-dependent transcription of braDE and vraDE. BraDE is involved in bacitracin sensing and signaling through BraRS. VraDE acts as a detoxification module.
Staphylococcus aureus[409,410]
ChtRS
-
ChtRS contributes to chlorhexidine and bacitracin tolerance.
Enterococcus faecium[411]
CiaRH
-
CiaRH is a TCS induced by cell wall stress caused by cycloserine, bacitracin, and vancomycin.
-
CiaRH is required for survival under various lysis-inducing conditions and confers resistance to cell wall inhibitors including β-lactams, cycloserine, bacitracin, and vancomycin.
-
CiaRH promotes intracellular survival within neutrophils and macrophages and protects against antimicrobial peptides and reactive oxygen species.
Streptococcus pneumoniae[412,413,414]
ColRS
-
ColRS regulates the expression of a pEtN transferase that modifies LPS by transferring phosphoethanolamine to lipid A, thus resulting in polymyxin resistance.
-
ColRS is activated by zinc ions.
Pseudomonas aeruginosa[415]
CopRS
-
In the presence of copper or zinc ions, CopR represses the oprD porin, resulting in carbapenem resistance.
Pseudomonas aeruginosa[416,417]
CprRS
-
CprRS induces the expression of arnBCADTEF, which adds arabinosamine to LPS, thereby causing resistance to antimicrobial peptides.
Pseudomonas aeruginosa[418,419]
CpxAR
-
CpxAR is a membrane stress-response TCS that is associated with the resistance to several cell-envelope-targeting drugs.
-
CpxAR induces the expression of the KpnEF efflux pump.
-
CpxAR induces the expression of N-acetylmuramoyl-L-alanine amidases amiA and amiC, which confer drug resistance to protamine.
-
CpxAR activates the expression of the marRAB operon that facilitates multidrug resistance by enhancing the expression of TolC tripartite multidrug transporters.
-
CpxAR regulates the expression of the porins ompC and ompF.
-
It contributes to Cu tolerance.
-
CpxAR is induced by antimicrobial peptides including polymyxin B, melittin, and LL-37, as well as copper ions.
-
CpxAR responds to periplasmic stress including misfolded proteins, inner membrane disruption, alkaline pH, starvation, and high osmolarity.
Escherichia coli,
Klebsiella pneumoniae, Salmonella typhimurium and other Gram-negative bacteria
[420,421,422,423,424,425]
CreBC
-
CreBC is a TCS activated by low concentrations of the β-lactam cefoxitin that inhibits PBP4, resulting in resistance to β-lactam due to induction of the AmpC cephalosporinase.
Pseudomonas aeruginosa[426]
CroRS
-
CroRS drives resistance to ampicillin and cephalosporins, among others, by upregulating PBP5 with low affinity to β-lactams.
-
The IreK kinase positively affects CroR-dependent gene expression through threonine phosphorylation of CroS, resulting in antibiotic resistance.
-
CroRS is activated by antibiotic-induced cell wall damage.
Enterococcus faecium[427,428,429,430]
CzcRS
-
Activation of CzcRS by zinc, cadmium, and cobalt ions leads to the expression of the CzcCBA efflux pump which expels these ions.
-
CzcR confers carbapenem resistance by repressing the expression of oprD porin, which is required for the uptake of these antibiotics.
Pseudomonas aeruginosa[416,431,432,433]
EvgAS
-
EvgAS confers resistance to bile salts by upregulating the emrKY and yhiUV efflux pump genes.
Escherichia coli[434,435,436,437,438]
GraRS (ApsRS)
-
GraRS regulates the expression of the ABC transporter genes vraFG, which confer resistance to vancomycin; the lysyl-phosphatidylglycerol synthase mprF, which adds positively charged lysine residues to phosphatidylglycerol; and dltABCD, which contributes to the net positive surface charge by covalently attaching D-alanine to the cell wall teichoic acids.
-
Besides vancomycin, GraRS confers resistance to cationic antimicrobial peptides such as cathelicidin LL-37, nisin A, and class I bacteriocins, which is supposedly due to its induction of the dlt operon involved in D-alanylation of teichoic acid.
-
GraRS is induced by polymyxin B and the host defense tPMP-1 (Thrombin-induced platelet microbicidal proteins) and the synthetic RP-1.
-
ΔgraRS MRSA strains showed increased susceptibility to ampicillin, oxacillin, vancomycin, gentamicin, antimicrobial peptides, and neutrophil defense mechanisms.
Staphylococcus aureus[410,439,440,441,442,443]
LiaFSR
-
LiaFSR confers resistance to bile salts, daptomycin, and telavancin.
Enterococcus faecium,
Enterococcus faecalis
[210,444]
LrgAB
-
LrgAB has an inhibitory effect on murein hydrolase activity.
-
A lrgAB mutant showed increased extracellular murein hydrolase activity compared to that of the wild-type strain.
-
LrgAB promotes antibiotic tolerance to penicillin.
-
LrgAB is regulated by the LytSR TCS.
Staphylococcus aureus[289]
LytSR
-
LytSR is a sensor of altered membrane potential that confers resistance to antimicrobial peptides.
-
LytSR affects the murein hydrolase activities by upregulating lrgA and lrgB. LrgA is an antiholin-like protein that inhibits autolysis.
-
lytSR mutants are more sensitive to cationic antimicrobial peptides.
Staphylococcus aureus[445,446]
NsaRS
-
NsaRS confers resistance to the lantibiotic nisin.
-
NsaRS induces the expression of the ABC transporters braDE and vraDE. BraDE senses nisin and physically interacts with NsaSR. VraDE is important for the detoxification of nisin.
-
NsaRS is activated by various cell wall damaging antibiotics including phosphomycin, β-lactams, nisin, and gramicidin.
Staphylococcus aureus[447,448]
ParRS
-
ParRS upregulates the expression of the mexXY multidrug efflux operon.
-
ParRS represses the expression of the carbapenem-selective porin oprD.
-
ParRS induces the expression of arnBCADTEF in response to indolicidin and polymyxin, resulting in resistance to polymyxins and other antimicrobial peptides.
Pseudomonas aeruginosa[66,189,419,449,450]
PhoBR
-
PhoBR increases the expression of the kpnO porin, which affects the susceptibility to tetracycline, nalidixic acid, tobramycin, streptomycin, and spectinomycin.
-
Both phoB mutant and ΔkpnO mutant show decreased susceptibility to antibiotics.
-
The ΔkpnO mutant showed reduced virulence.
Klebsiella pneumoniae[451]
PhoPQ and PmrAB
-
Both PhoPQ and PmrAB induce the expression of arnBCADTEF in response to low Mg2+ concentration, resulting in resistance to cationic antimicrobial peptides, polymyxins, and aminoglycosides.
-
PhoPQ regulates the enzyme pagP, which catalyzes the transfer of palmitate from outer membrane phospholipids to lipid A, thus conferring resistance to some antimicrobial peptides.
-
The PhoPQ signaling cascade is induced under conditions of low extracellular Mg2+ conditions, resulting in the induction of the pmrB/pmrA TCS, which confers polymyxin resistance, and the small outer membrane protein oprH, which facilitates the uptake of divalent cations.
-
PhoPQ is activated by sub-MIC concentrations of polymyxin in Salmonella enterica.
-
In Salmonella enterica, PhoP can activate pmrAB.
-
PmrAB is activated by Fe3+ and low pH.
-
In Klebsiella pneumoniae, PhoP activates PmrD that in turn binds to and activates PmrA responsible for polymyxin B resistance.
Pseudomonas aeruginosa,
Salmonella enterica,
Klebsiella pneumoniae,
Acinetobacter baumannii
[91,419,452,453,454,455,456,457,458,459,460]
QseBC
-
QseBC increases the transcription of efflux pump-associated genes marA, acrA, acrB, acrD, emrD, and mdtH.
Escherichia coli[249]
TarRS
-
TarRS confer multidrug resistance through interaction with the chaperonin GroEL.
-
A Δtartas strain shows high susceptibility to kanamycin, gentamycin, tetracycline, and imipenem.
-
The regulator FleQ indirectly activates tarR-tarS transcription.
-
c-di-GMP antagonizes FleQ activation and thus inhibits tarR-tarS transcription.
-
The sigma factor FliA directly activates tarR-tarS transcription.
Pseudomonas aeruginosa[461]
VanRS
-
Binding of vancomycin and teicoplanin to VanS induced a long-lived phosphorylation state of VanS, resulting in the phosphorylation of VanR, and the consequent regulation of vanA responsible for vancomycin resistance.
Enterococcus faecium[462]
VraTSR
-
VraTSR is a three-component system that senses and responds to cell wall stress.
-
VraTSR regulates genes associated with cell wall synthesis including the transpeptidase pbp2, the transglycosylase sgtB, and the UDP-N-acetylglucosamine enolpyruvyl transferase murZ.
-
VraTSR confers resistance to cell wall antibiotics including methicillin, vancomycin, cycloserine, teicoplanin, bacitracin, and daptomycin.
-
Inhibition of VraTSR by small molecules sensitized MRSA to oxacillin.
Staphylococcus aureus[463,464,465,466,467]
WalKR (YycFG, VicRK, MicAB)
-
WalKR is involved in the regulation of cell wall synthesis and cell division through the regulation of autolysin production such as lytM, atlA, sle1, ssaA, and sceD.
-
Single nucleotide substitutions within either walK or walR led to resistance to vancomycin and daptomycin.
Staphylococcus aureus[468,469,470]
Table 4. Examples of QS inhibitors/QS quenchers.
Table 4. Examples of QS inhibitors/QS quenchers.
CompoundEffects on BacteriaReferences
Ajoene
-
Ajoene represses quorum sensing, virulence, and biofilm formation by reducing the sRNAs RsmY and RsmZ in Pseudomonas aeruginosa and reduces the regulatory RNAIII in Staphylococcus aureus.
-
Ajoene acts synergistically with tobramycin to kill Pseudomonas aeruginosa in biofilms.
[823,824]
Allicin
-
Allicin inhibits the production of Pseudomonas aeruginosa virulence-associated factors, such as elastase, pyocyanin, pyoverdine, and rhamnolipids, by inhibiting the Rhl and Pqs QS systems.
[825]
Baicalin (5,6,7-
trihydroxyflavone) and 3,5,7-
Trihydroxyflavone
-
Baicalin is an AHL-based QS inhibitor.
-
Sub-MIC concentrations of baicalin inhibit Pseudomonas aeruginosa biofilm formation, reduce virulence phenotypes (e.g., LasA protease, LasB elastase, pyocyanin, and rhamnolipid) regulated by QS, reduce the expression of QS regulatory genes (lasI/lasR, rhlI/rhlR, pqsR/pqsA) and enhance the antibacterial effects of amikacin, tobramycin, and ceftazidime.
-
Baicalin reduces the expression of the Type III secretion system (T3SS) in Pseudomonas aeruginosa by a process depending on PqsR.
-
In a fruit fly infection model and a rat pulmonary infection model of Pseudomonas aeruginosa, baicalin reduced inflammatory responses and enhanced bacterial clearance.
-
In avian pathogenic Escherichia coli (APEC), baicalin inhibited AI-2 secretion, biofilm formation, and the expression of virulence genes such as lsrB, lsrK, luxS, pfs, csgA, csgB, and rpoS.
-
3,5,7-Trihydroxyflavone interferes with the LasR TCS and prevents biofilm formation of Pseudomonas aeruginosa.
-
Baicalin acts in synergy with linezolid against MRSA biofilms.
[531,826,827,828,829,830]
Berberine
-
Berberine inhibits QS and biofilm formation of Escherichia coli and downregulates the QS-related genes: luxS, pfS, sdiA, hflX, motA, and fliA.
-
Berberine prevents Salmonella Typhimurium biofilm formation by preventing type I fimbria formation.
[831,832]
Betulin and
betulinic acid
-
Betulin and betulinic acid attenuate the production of QS-regulated virulence factors and biofilm formation in Pseudomonas aeruginosa.
-
Betulin and betulinic acid interfere with the initial stages of biofilm development by decreasing the exopolysaccharide production and cell-surface hydrophobicity.
-
Betulin and betulinic acid act as competitive inhibitors of the QS regulators LasR and RhlR.
[833]
meta-
Bromothiolactone
-
meta-Bromothiolactone inhibits LasR and RhlR via competition with the natural autoinducers for occupancy of the ligand binding sites.
-
It inhibits both the production of the virulence factor pyocyanin and biofilm formation.
-
It protects Caenorhabditis elegans and human lung epithelial cells from killing by Pseudomonas aeruginosa.
[834]
Cajaninstilbene
acid analogs
-
Cajaninstilbene acid analogs have potent anti-biofilm activity against Pseudomonas aeruginosa through suppression of lasB and pqsA and their corresponding virulence factors.
[835]
Cannabigerol (CBG) and
Cannabidiol (CBD)
-
CBG reduces the QS-regulated bioluminescence and biofilm formation of Vibrio harveyi without affecting the planktonic bacterial growth.
-
CBG reduces the motility of Vibrio harveyi in a dose-dependent manner.
-
CBG increases LuxO expression and activity, with a concomitant 80% downregulation of the LuxR gene in Vibrio harveyi.
-
CBG has antibacterial and anti-biofilm activities against Streptococcus mutans, MSSA, and MRSA.
-
CBD has antibacterial and anti-biofilm activities against MSSA and MRSA.
[803,804,805,836,837,838,839]
Carvacrol
-
Carvacrol inhibits acyl-homoserine lactone synthesis by inhibiting LasI of Pseudomonas aeruginosa.
-
It reduces the expression of cviI encoding the N-acyl-L-homoserine lactone synthase and the production of violacein in Chromobacterium violaceum.
-
Carvacrol inhibits biofilm formation of Chromobacterium violaceum, Pseudomonas aeruginosa, Salmonella enterica subsp. typhimurium, and Staphylococcus aureus.
-
Carvacrol targets SarA and CrtM of MRSA, resulting in reduced biofilm formation and staphyloxanthin synthesis.
-
Carvacrol synergizes with the efflux pump inhibitor phenylalanine-arginine β-naphthylamide (PAβN) to kill MexAB-OprM-overexpressing Pseudomonas aeruginosa.
[819,840,841,842]
Cinnamic acid
-
Cinnamic acid inhibits the production of QS-dependent virulence factors and biofilm formation in Pseudomonas aeruginosa.
-
In silico analysis suggests that cinnamic acid acts as a competitive inhibitor for the natural ligands to LasR and RhiR.
-
The cinnamic acid analog 4-methoxybenzalacetone showed stronger anti-QS activities than cinnamic acid and suppressed the production of pyocyanin and rhamnolipids, as well as the swarming motility of Pseudomonas aeruginosa.
[843,844]
Cinnamaldehyde
-
Cinnamaldehyde inhibits the activity of LasB, RhlA, and PqsA and reduces the intracellular level of c-di-GMP in Pseudomonas aeruginosa.
-
It inhibits biofilm formation of Pseudomonas aeruginosa and disperses preformed biofilms.
-
Cinnamaldehyde has a synergistic effect with colistin, but not with carbenicillin, tobramycin, or erythromycin, on Pseudomonas aeruginosa.
-
It prevents biofilm formation and epithelial attachment of uropathogenic Escherichia coli (UPEC).
-
Cinnamaldehyde could detach and kill MRSA and Staphylococcus epidermidis in pre-existing biofilms.
-
Cinnamaldehyde suppresses the Fsr QS pathway and inhibits biofilm formation and EPS production by Enterococcus faecalis.
[845,846,847,848,849,850,851]
Clofoctol
-
Clofoctol is an approved antimicrobial compound that inhibits the PQS quorum sensing system of Pseudomonas aeruginosa.
-
Clofoctol inhibits the expression of PQS-controlled virulence traits, such as pyocyanin production, swarming motility, biofilm formation, and expression of genes involved in siderophore production.
[852]
Clotrimazole
and miconazole
-
Clotrimazole and miconazole are antifungal drugs that have been shown to inhibit the PQS quorum sensing system of Pseudomonas aeruginosa.
[852]
Curcumin
-
Curcumin reduces the expression of the LasR and RhlR QS regulators in Pseudomonas aeruginosa, inhibits biofilm formation, and acts in synergism with azithromycin, gentamicin, ceftazidime, and ciprofloxacin.
-
Curcumin inhibits the response regulator BfmR in Acinetobacter baumannii resulting in reduced biofilm formation and virulence.
-
It inhibits pellicle formation and surface motility of Acinetobacter baumannii.
-
Curcumin inhibits Sortase A of Streptococcus mutans.
-
Bisdemethoxycurcumin sensitizes MRSA to gentamicin, and to a lesser extent to methicillin and oxacillin.
[853,854,855,856,857,858,859]
Domperidone
-
Domperidone has anti-virulence and anti-biofilm activities against Staphylococcus aureus.
-
It reduces the expression levels of crtM, sigB, sarA, agrA, hla, fnbA, and icaA genes.
-
It is a clinically approved drug that acts as a dopamine antagonist in the treatment of nausea and vomiting.
[860]
Falcarindol
-
Falcarindol is a major constituent of Notopterygium incisum.
-
It inhibits biofilm formation by repressing QS-related genes (lasB, phzH, rhlA, lasI, rhlI, pqsA, and rhlR) in Pseudomonas aeruginosa.
[861]
Flavonoids
-
Flavonoids inhibit QS by preventing LasR/RhlR DNA binding in Pseudomonas aeruginosa.
-
The flavonoid catechin interferes with the RhlR TCS and reduces virulence factors such as pyocyanin and elastase, and prevents biofilm formation in Pseudomonas aeruginosa.
-
The flavanones naringenin, eriodictyol, and taxifolin reduce the production of pyocyanin and elastase in Pseudomonas aeruginosa.
-
Naringenin prevents the production of autoinducers driven by LasI and RhlI in Pseudomonas aeruginosa.
-
Naringenin, kaempferol, quercetin, and apigenin suppressed biofilm formation in Vibrio harveyi and Escherichia coli.
[862,863,864,865]
4-Fluoro-
5-hydroxypentane-2,3-dione (F-DPD)
-
4-Fluoro-5-hydroxypentane-2,3-dione is a fluoro-DPD analog that disrupts autoinducer-2-dependent quorum sensing in Vibrio harveyi.
[866]
Gingerol
-
Gingerol interferes with the LasR, PhzR, and RhlR TCSs resulting in an impact on the production of EPS, biofilm, pyocyanin, and rhamnolipids of Pseudomonas aeruginosa.
-
Gingerol increased the susceptibility of the bacteria to ciprofloxacin.
[867,868]
Halogenated furanones
-
The quorum-sensing disrupter (5Z)-4-bromo-5-(bromomethylene)-3-butyl-2(5H)-furanone inhibits the swarming motility and biofilm formation of Escherichia coli through inhibition of autoinducer-2 signaling.
-
Furanone C-30 is a brominated derivative of furanone that acts as a quorum sensing inhibitor and together with tobramycin or colistin it reduces Pseudomonas aeruginosa biofilm biomass.
-
Halogenated furanones blocks cell signaling and quorum sensing in Pseudomonas aeruginosa biofilms thus affecting the architecture of the biofilm and enhancing the process of bacterial detachment.
[869,870,871,872,873,874]
Halogenated
thiophenones
-
Halogenated thiophenones are anti-QS compounds with anti-biofilm activities against Vibrio species and Staphylococcus epidermidis.
[875,876,877]
Hamamelitannin
-
Hamamelitannin is a QS inhibitor that increases the susceptibility of biofilm-associated Staphylococcus aureus to vancomycin and clindamycin.
[531]
4-
Hydroxybenzylidene indolinone
-
4-Hydroxybenzylidene indolinone downregulates the Agr quorum sensing system in Staphylococcus aureus, upregulates the sceD peptidoglycan hydrolase, and sensitizes the bacteria to β-lactam antibiotics and vancomycin.
-
It inhibits c-di-AMP synthase.
[878,879]
Luteolin
-
Luteolin inhibits biofilm formation and production of virulence factors by Pseudomonas aeruginosa through interaction with LasR.
[880]
Methyl anthranilate
-
Methyl anthranilate attenuates QS-related virulence production and biofilm formation of Pseudomonas aeruginosa.
-
One mechanism could be by disrupting autoinducer PQS biosynthesis.
[881,882]
2-[(Methylamino)
methyl]phenol
-
It targets the quorum regulator SarA in Staphylococcus aureus and inhibits biofilm and downregulates virulence genes such as fnbA, hla, and hld.
[883]
MHY1383 and MHY1387
-
MHY1383 and MHY1387 show anti-QS and anti-virulence activity towards Pseudomonas aeruginosa at a low concentration of 100 pM.
-
They reduce protease production.
-
They show anti-biofilm activity toward Pseudomonas aeruginosa at the low concentration of 1–10 pM by reducing intracellular c-di-GMP levels.
[884]
MomL
-
MomL is an N-acyl homoserine lactonase from Muricauda olearia that degrades AHL autoinducers.
-
MomL attenuated the virulence of Pseudomonas aeruginosa in a Caenorhabditis elegans infection model.
-
A recombinant MomL produced in Bacillus brevis reduced the secretion of pathogenic factors and dampened the pathogenicity of Pseudomonas aeruginosa.
[885,886]
Mosloflavone
-
Mosloflavone from the herb Mosla soochouensis Matsuda inhibits QS-regulated virulence and biofilm formation of Pseudomonas aeruginosa by downregulating the expression of lasI, lasR, rhlI, chiC, phzM, exoS, algD, pelA, and pyocyanin production.
-
It binds to the QS regulatory proteins LasR and RhlR by competitively inhibiting the binding of the natural autoinducers.
[887]
Niclosamide
-
Niclosamide is an anthelmintic drug that inhibits the QS in Pseudomonas aeruginosa and prevents the production of autoinducers, resulting in the suppression of motility, biofilm formation, and the production of virulence factors such as elastase, pyocyanin, and rhamnolipids.
[888]
Nitrofurazone and erythromycin estolate
-
The two antibiotics nitrofurazone and erythromycin estolate reduce the expression of PqsE-dependent virulence traits and biofilm formation by Pseudomonas aeruginosa.
[889]
Oritavancin
-
Oritavancin inhibits the ATPase activity of the histidine kinase ArlS and increases the sensitivity of MRSA to oxacillin both in the planktonic and biofilm state.
[399]
An Oxoquinazolin derivate
-
It inhibits PqsR and reduces the level of pyocyanin, and the autoinducers HHQ and PQS in Pseudomonas aeruginosa.
-
It potentiates the antimicrobial effect of ciprofloxacin.
[890]
Paeonol
-
Paeonol exhibits anti-biofilm activity and interferes with the AHL-mediated QS system in Pseudomonas aeruginosa.
-
It downregulates the transcription level of the QS-related genes lasI/R, rhlI/R, pqs/mvfR, as well as the virulence factors lasA, lasB, rhlA, rhlC, phzA, phzM, phzH, and phzS.
[891]
Palmitoyl-
DL-carnitine
-
Palmitoyl-DL-carnitine impairs Pseudomonas aeruginosa and Escherichia coli biofilm formation.
-
It inhibits the Las QS system and prevents the biofilm-promoting effects of subminimal inhibitory concentrations of aminoglycosides.
[892]
Parthenolide
-
Parthenolide has anti-biofilm and anti-QS activities against Pseudomonas aeruginosa.
-
It downregulates lasI/lasR and rhlI/rhlR as well as reduces EPS production.
[893]
Phenyl lactic acid
-
Phenyl lactic acid attenuates virulence and pathogenicity of Pseudomonas aeruginosa and Staphylococcus aureus.
-
It decreases the adherence of the bacteria to biotic and abiotic surfaces.
-
It increases the sensitivity of Pseudomonas aeruginosa to antibiotics.
[894]
N-(2-Pyrimidyl)
butanamide
-
N-(2-Pyrimidyl)butanamide inhibits the Las and Rhl TCSs of Pseudomonas aeruginosa, reduces biofilm formation, and sensitizes the bacteria to ciprofloxacin, tobramycin, and colistin.
[895]
Quinazolinone
analogs
-
Quinazolinone analogs are antagonists of the PqsR QS receptor of Pseudomonas aeruginosa.
-
They attenuate pyocyanin production.
[351,896]
Quercetin
-
Quercetin interferes with the LasR, PhzR, and RhlR TCSs of Pseudomonas aeruginosa.
-
A synergistic effect was observed between quercetin and amoxicillin against Staphylococcus epidermidis and Staphylococcus aureus.
-
Quercetin in combination with tetracycline was bactericidal for Escherichia coli.
[862,867,897,898,899,900]
Resveratrol(3,5,4′-
trihydroxystilbene)
-
Resveratrol inhibits the expression of the QS-related lasI and rhlI in Pseudomonas aeruginosa.
-
Resveratrol enhances the antibacterial effects of aminoglycosides on Pseudomonas aeruginosa biofilms.
-
It is proposed that the antioxidant property of resveratrol inhibits the QS system by relieving oxidative stress.
-
Resveratrol inhibits biofilm formation in MRSA by interfering with genes related to QS and capsular polysaccharides.
-
It inhibits the hemolytic activity of Staphylococcus aureus.
[901,902,903,904]
Rifampicin
-
Rifampicin was found to target the AmgRS envelope stress responsive TCS that is responsible for the upregulation of the mexXY efflux pump.
-
Rifampicin could potentiate the activity of aminoglycosides against various clinical isolates of Pseudomonas aeruginosa.
[905,906]
Sesamin and
Sesamolin lignans
-
Sesamin and Sesamolin lignans inhibit the LasR TCS of Pseudomonas aeruginosa and prevent biofilm formation by reducing the production of alginate, exopolysaccharides, and rhamnolipids.
-
The two lignans rescued pre-infected worms of Caenorhabditis elegans and reduced the colonization of bacteria inside the intestine.
[818]
Sinefungin
-
Sinefungin is a nucleoside analog of S-adenosylmethionine that prevents biofilm formation by Streptococcus epidermidis.
-
It reduces the expression of LuxS and inhibits the production of autoinducer-2.
[907]
Staquorsin
-
Staquorsin is an AgrA inhibitor that impairs QS and virulence in Staphylococcus aureus.
[908]
Tryptanthrin
-
Tryptanthrin has anti-biofilm activity against Vibrio cholerae by targeting LuxO.
-
It has a synergistic effect with ciprofloxacin.
[909]
Tryptophan-containing
antibacterial peptides
-
Tryptophan-containing peptides downregulate the gene expression of both the las and rhl TCSs in Pseudomonas aeruginosa.
-
Inhibition of biofilm formation by these peptides was associated with reduced expression of pelA, algD, and pslA in Pseudomonas aeruginosa.
-
Tryptophan-containing peptides showed a synergistic effect with ceftazidime and piperacillin. This was related to reduced expression of the efflux pump genes oprM, mexX, and mexA in Pseudomonas aeruginosa.
-
These peptides increased the susceptibility of multidrug-resistant Staphylococcus epidermidis to erythromycin and β-lactam antibiotics.
[820,910]
Unsaturated
fatty acids
-
The mono-unsaturated fatty acids palmitoleic and myristoleic acids decrease biofilm formation and motility of Acinetobacter baumannii. These fatty acids decrease the expression of the regulator abaR of the AbaIR TCS and consequently reduce the production of the AHL autoinducer.
-
Linoleic acid induces biofilm dispersion of Pseudomonas aeruginosa by stimulating the phosphodiesterase activity thereby reducing the intracellular cyclic diguanylate concentration.
-
Linoleic acid inhibits biofilm formation and synergizes with gentamicin to kill Staphylococcus aureus.
-
Palmitoleate inhibits the growth of Staphylococcus aureus.
-
cis-2-Decenoic acid is a diffusible signal factor of Pseudomonas aeruginosa that at 2.5 nM causes biofilm dispersion. It also causes dispersion of several other bacterial biofilms including Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Streptococcus pyogenes, and Staphylococcus aureus.
-
The omega fatty acids cis-4,7,10,13,16,19-docosahexaenoic acid (DHA) and cis-5,8,11,14,17-eicosapentaenoic acid (EPA) inhibit Staphylococcus aureus biofilm formation and decreases hemolysis.
-
Caprylic acid prevents and eradicates Klebsiella pneumoniae biofilm.
-
The polyunsaturated arachidonic acid increases the susceptibility of MSSA, MRSA, and Staphylococcus aureus small colony variants to aminoglycosides.
-
Arachidonic acid increases the membrane fluidity of Staphylococcus aureus.
-
Arachidonic acid and docosahexaenoic acid increase the membrane permeability of Escherichia coli and make the bacteria less susceptible to colistin.
[911,912,913,914,915,916,917,918,919,920,921]
Zingerone
-
Zingerone interferes with the LasR, PhzR, PqsR, TraR, and RhlR TCSs of Pseudomonas aeruginosa resulting in attenuation of virulence and inhibition of biofilm formation.
-
Zingerone increases the susceptibility of Pseudomonas aeruginosa to ciprofloxacin.
[867,922,923]
Walkmycin B
-
Walkmycin B, which is produced by Streptomyces species, inhibits the histidine kinase activity of WalK in Staphylococcus aureus leading to bacterial growth inhibition.
[924]
Table 5. Examples of biofilm inhibitors.
Table 5. Examples of biofilm inhibitors.
CompoundEffects on BacteriaReferences
Astilbin
-
Astilbin is a plant-derived flavanone compound that inhibits SrtA and prevents biofilm formation by Streptococcus mutans.
[945]
Trans-Chalcone
-
Trans-chalcone is a natural plant product that inhibits SrtA and prevents biofilm formation by Streptococcus mutans.
[944]
Chitosan
-
The anti-biofilm activity of chitosan has been attributed to its polycationic nature that binds to negatively charged biofilm constituents such as EPS, eDNA, proteins, and lipids. This leads to changes in membrane permeability and biofilm dispersion.
-
It also affects biological processes through the chelation of essential metal ions.
-
Chitosan has been used as a carrier for various antimicrobial and anti-biofilm drugs for synergistic action against biofilms.
-
Conjugation of streptomycin with chitosan efficiently damaged established biofilms of Pseudomonas aeruginosa and Listeria monocytogenes.
[950,951,952]
Clemastine
-
Clemastine inhibits biofilm formation of Staphylococcus aureus and enhances the antibacterial activity of oxacillin.
-
Clemastine inhibits the release of eDNA during biofilm formation and decreases hemolytic activity.
-
Clemastine reduces the transcription of biofilm formation-related genes (fnbB, icaA, and icaB) and virulence genes (hlg, hld, lukde, lukpvl, beta-PSM, delta-PSM, and cap5A).
-
One of its targets is the cyclic di-AMP phosphodiesterase GdpP.
[953]
Compound 62520
(5-fluoro-1-((1R,3S)-
3-(hyroxymethyl)-
1,3-dihydroisobenzofuran-
1-yl)pyrimidine-
2,4-(1H,3H)-dione)
-
Compound 62520 inhibits ompA expression and biofilm formation in Acinetobacter baumannii.
[122]
DMNP—A diterpene analog
-
4-(4,7-Dimethyl-1,2,3,4-tetrahydronaphthalene-1-yl)pentanoic acid (DMNP) suppresses persistence and eradicates biofilms of Mycobacterium smegmatis by inhibiting Rel (p)ppGpp synthetases.
[954]
Epigallocatechin-
3-gallate (EGCG)
-
EGCG inhibits biofilm formation and virulence of Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus mutans.
-
EGCG prevents curli production by suppressing the expression of curli-related proteins and the sigma factor RpoS in Escherichia coli.
-
EGCG promotes RpoS degradation by the ATP-dependent protease ClpXP in combination with its adaptor RssB.
-
EGCG is an antioxidant.
[955,956,957]
Eugenol/carvacrol
-
The combined treatment of eugenol and carvacrol eradicates pre-established biofilms of MSSA and MRSA.
[958]
Gallium nitrate
-
Gallium nitrate leads to nutritional iron starvation and sensitizes MRSA biofilms to vancomycin.
-
Gallium nitrate inhibits biofilm formation of Pseudomonas aeruginosa by disrupting bacterial iron homeostasis. Together with sub-MIC concentrations of tetracycline, gallium nitrate inhibits pyoverdine and suppresses bacterial growth.
[959,960,961,962,963]
5-Episinuleptolide
-
5-Episinuleptolide inhibits biofilm formation of Acinetobacter baumannii, and decreases the expression of genes from the pgaABCD operon, which encodes the extracellular polysaccharide poly-β-(1,6)-N-acetylglucosamine (PNAG).
-
5-Episinuleptolide increases the sensitivity of Acinetobacter baumannii to levofloxacin.
[964]
Flavonoids
-
Various glycone (myricitrin, hesperidin, and phloridzin) and aglycone flavonoids (myricetin, hesperetin, and phloretin) inhibit Staphylococcus aureus biofilm formation, without affecting their growth.
[156]
5-Hydroxymethylfurfural
-
5-Hydroxymethylfurfural inhibits biofilm formation of Acinetobacter baumannii.
-
It inhibits EPS production and downregulates the expression of bfmR, csuA/B, ompA, and katE virulence genes.
[965]
Kaempferol
-
Kaempferol inhibits biofilm formation of Staphylococcus aureus by inhibiting SrtA and reducing the expression of adhesion-related genes. Kaempferol had no effect on planktonic growth.
-
Kaempferol in combination with azithromycin suppressed biofilm formation and growth of azithromycin-resistant Staphylococcus aureus.
[966,967]
α-Mangostin
-
α-Mangostin inhibits biofilm formation of Acinetobacter baumannii.
-
It downregulates the expression of bfmR, pgaA, pgaC, csuA/B, ompA, and katE virulence genes.
[968]
Meloxicam
-
Meloxicam inhibits biofilm formation of Pseudomonas aeruginosa and enhances the antimicrobial activity of tetracycline, gentamicin, tobramycin, ciprofloxacin, ceftriaxone, ofloxacin, norfloxacin, and ceftazidime.
-
Docking studies suggest that meloxicam can bind to the active site of the QS proteins LasR and PqsE.
[969,970]
ML346
-
ML346 is a compound with a barbituric acid and cinnamaldehyde scaffold that functions as an irreversible inhibitor of Staphylococcus aureus SrtA and Streptococcus pyogenes SrtA.
-
It reduces the virulence phenotype of Staphylococcus aureus.
[971]
Myrtenol
-
Myrtenol attenuates MRSA biofilm and virulence by suppressing sarA expression.
-
It inhibits the synthesis of slime, lipase, α-hemolysin, staphyloxanthin, and autolysin by MRSA.
-
Myrtenol sensitizes MRSA to hydrogen peroxide.
-
It prevents biofilm formation and suppresses the expression of the biofilm-associated genes bmfR, csuA/B, bap, ompA, pgaA, pgaC, and katE in Acinetobacter baumannii.
-
It increases the susceptibility of Acinetobacter baumannii to amikacin, ciprofloxacin, gentamicin, and trimethoprim.
[972,973]
Orientin
-
Orientin is a natural compound found in several plants that inhibits SrtA and prevents the binding of Staphylococcus aureus to fibrinogen and diminishes biofilm formation and virulence.
[974]
1,2,4-
Oxadiazole derivatives
-
1,2,4-Oxadiazole derivatives belonging to the topsentin family inhibit Sortase A transpeptidase activity resulting in biofilm inhibition of Staphylococcus aureus and Pseudomonas aeruginosa.
[943]
Pyrimidinedione
-
Pyrimidinedione is a DNA adenine methyltransferase (Dam) inhibitor that inhibits biofilm formation by Streptococcus pneumoniae.
[975]
Pyrogallol
-
Pyrogallol inhibits biofilm formation of Acinetobacter baumannii.
-
It downregulates the expression of pgaA, pgaC, csuA/B, ompA, and katE virulence genes.
[976]
Quercetin and
tannic acid
-
Quercetin and tannic acid inhibit biofilm formation and hemolytic activity of Staphylococcus aureus.
[977,978,979,980]
Taxifolin
-
Taxifolin is a flavonoid plant compound that inhibits SrtA in MRSA and prevents their virulence, biofilm formation, and binding to lung epithelial tissue.
[949]
Thiazolidinediones (e.g., ciglitazone, TZD-C8, and thiazolidinedione-8)
-
Ciglitazone, a glucose-lowering drug, reduced the bacterial load of Streptococcus pneumoniae in the lungs of mice in an infection model.
-
TZD-C8 inhibits biofilm formation of Pseudomonas aeruginosa by inhibiting the autoinducer synthase LasI and downregulating the genes of the pqsABCDE and arcDABC operons.
-
Thiazolidinedione-8 inhibits the biofilm formation of Candida albicans.
-
Thiazolidinediones blocked AI-2 QS in Vibrio harveyi by decreasing the DNA-binding ability of LuxR.
[981,982,983,984]
Ursolic acid
and Asiatic acid
-
Ursolic acid and asiatic acid are pentacyclic triterpenes that inhibit biofilm formation by Escherichia coli and Pseudomonas aeruginosa without affecting the QS.
-
Ursolic acid prevents biofilm formation of MRSA by reducing amino acid metabolism and adhesins expression.
[903,985,986]
Virstatin (4-
[N-(1,8-naphthalimide)]-
n-butyric acid)
-
Virstatin prevents pili biosynthesis in Acinetobacter baumannii.
-
It targets the AnoR regulator in Acinetobacter nosocomialis that is involved in the synthesis of the autoinducer N-(3-hydroxy-dodecanoyl)-L-homoserine lactone.
-
It inhibits the transcriptional regulator ToxT in Vibrio cholerae, thereby preventing the expression of cholera toxin encoding by ctx genes and the co-expressed pili type IV.
-
Virstatin protected infant mice from intestinal colonization by Vibrio cholerae.
[987,988,989]
Zerumbone
-
Zerumbone inhibits biofilm formation and disrupts established Acinetobacter baumannii biofilms.
-
It downregulates the expression of adeA, adeB, adeC, and bap.
[990]
Table 6. Examples of efflux pump inhibitors (EPIs) 1.
Table 6. Examples of efflux pump inhibitors (EPIs) 1.
CompoundEffects on BacteriaReferences
Alkylaminoquinolines
-
Alkylaminoquinolines inhibit the AcrAB-TolC efflux pump of Enterobacter aerogenes, resulting in increased intracellular levels of norfloxacin, tetracycline, and chloramphenicol.
-
They reduce the MIC of these antibiotics.
[999]
2-(2-Aminophenyl)
indole
-
2-(2-Aminophenyl) indole inhibits NorA in Staphylococcus aureus and potentiates the activity of fluoroquinolones.
[1000]
6-(Aryl)alkoxypyridine-
3-boronic acid derivatives
-
They inhibit NorA in Staphylococcus aureus and potentiate the activity of fluoroquinolones.
[1001]
Arylpiperazines such as 1-(1-naphthylmethyl)-piperazine (NMP)
-
Arylpiperazines inhibit the AcrAB-TolC efflux pump by binding to AcrB.
[810]
Berberine
-
Berberine inhibits the MexXY-OprM efflux pump in Pseudomonas aeruginosa.
-
A combination of a berberine derivative with tobramycin increased the sensitivity of Pseudomonas aeruginosa to the antibiotic.
[1002,1003]
Boeravinone B
-
Boeravinone B inhibits NorA efflux pump in Staphylococcus aureus, increases the sensitivity to ciprofloxacin, and prevents biofilm formation and bacterial invasiveness.
[786]
Boronic acid
-
Boronic acid inhibits NorA in Staphylococcus aureus and increases the sensitivity to ciprofloxacin.
[1001]
Capsaicin
-
Capsaicin inhibits NorA in Staphylococcus aureus and increases the sensitivity to ciprofloxacin.
-
It reduces the invasiveness of Staphylococcus aureus.
[1004]
Carvacrol
-
Carvacrol inhibits NorA in Staphylococcus aureus and sensitizes the bacteria to norfloxacin.
[1005]
Conessine
-
Conessine inhibits the MexAB-OprM efflux pump and likely other efflux pumps too in Pseudomonas aeruginosa.
-
It sensitizes the bacteria to various antibiotics including cefotaxime, erythromycin, levofloxacin, and tetracycline.
-
Combined treatment of conessine and levofloxacin reduced Galleria mellonella larval burden of Pseudomonas aeruginosa.
[1006,1007]
D13-9001(A 4-oxo-
4H-pyrido [1,2-a]
pyrimidine derivative)
-
D13-9001 inhibits the AcrAB-TolC of Escherichia coli by binding to AcrB.
-
It inhibits the MexAB-OprM of Pseudomonas aeruginosa and sensitizes the bacteria to aztreonam.
[810,1008]
Doxorubicin
-
Doxorubicin inhibits the AcrAB-TolC efflux pump by binding to AcrB.
[810]
Endocannabinoids
-
Anandamide inhibits drug efflux in MRSA and MDRSA by altering the membrane properties and dispatching the protein motive force.
-
Anandamide and its analog arachidonoyl L-serine (AraS) sensitize MRSA and MDRSA to various antibiotics including methicillin, ampicillin, tetracycline, gentamicin, and norfloxacin.
-
Anandamide and AraS inhibit biofilm formation of MSSA, MRSA, and MDRSA.
[789,1009,1010]
Eugenol derivatives
-
Eugenol derivatives inhibit NorA in Staphylococcus aureus and sensitize the bacteria to norfloxacin.
[1011]
IITR08027
-
IITR08027 inhibits the AbeM efflux pump of Acinetobacter baumannii by inducing membrane depolarization and increases the sensitivity to fluoroquinolones and chlorhexidine.
[995]
Isoliquiritigenin derivates (e.g., IMRG4)
-
Isoliquiritigenin derivates inhibit NorA in Staphylococcus aureus and potentiate the activity of fluoroquinolones.
[1012]
Ketoconazole
-
Ketoconazole inhibits NorA in Staphylococcus aureus, potentiates the activity of fluoroquinolones, and inhibits biofilm formation.
[787]
MBX2319
(A pyranopyridine)
-
MBX2319 inhibits the AcrAB-TolC by binding to AcrB.
-
It increases the susceptibility of Enterobacteriaceae to ciprofloxacin, levofloxacin, and piperacillin.
[810,1013]
Meropenem
-
Meropenem is a carbapenem antibiotic that inhibits the MexXY-OprM efflux pump of Pseudomonas aeruginosa.
-
Meropenem sensitizes Pseudomonas aeruginosa to various aminoglycosides including paromomycin.
[1014]
Metformin
-
Metformin increases the sensitivity of Staphylococcus aureus to various antibiotics including levofloxacin, linezolid, ampicillin-sulbactam, vancomycin, and doxycycline.
[1015]
Minocycline
-
Minocycline inhibits the AcrAB-TolC efflux pump by binding to AcrB.
[810]
1-(1-Naphthylmethyl)
piperazine
-
The EPI 1-(1-Naphthylmethyl)piperazine sensitizes Escherichia coli and Klebsiella pneumoniae to tetracycline.
[153]
Nilotinib
-
Nilotinib is a tyrosine kinase inhibitor that inhibits NorA efflux channel in Staphylococcus aureus and sensitizes the bacteria to ciprofloxacin.
-
Nilotinib together with ciprofloxacin reduces both biofilm formation and preformed mature biofilms.
[154]
5-Nitro-2-(3-phenylpropoxy)pyridine
-
5-Nitro-2-(3-phenylpropoxy)pyridine inhibits NorA in Staphylococcus aureus and potentiates the activity of fluoroquinolones.
[1016]
Phenylalanine arginyl β-naphthylamide (PAβN)
-
Phenylalanine arginyl β-naphthylamide sensitizes drug-resistant Acinetobacter baumannii to imipenem.
-
Phenylalanine arginyl β-naphthylamide inhibits the efflux activity of AcrAB-TolC by binding to AcrB in Gram-negative bacteria.
-
Phe-Arg-βNaphtylamide prevents biofilm formation of Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, and Salmonella typhimurium.
[45,153,155,810,1017]
Phenothiazines such as chlorpromazine,
thioridazine and
amitriptyline
-
Phenothiazines inhibit the AcrAB-TolC efflux pump by binding to AcrB.
-
Phenothiazines inhibit NorA in Staphylococcus aureus and potentiates the activity of fluoroquinolones.
-
Chlorpromazine affects the potassium flux across the membrane in Staphylococcus aureus resulting in reduced proton motive force required for drug efflux.
-
Thioridazine and chlorpromazine prevent biofilm formation of Escherichia coli, Klebsiella pneumonia, Staphylococcus aureus, Pseudomonas putida, Pseudomonas aeruginosa, and Salmonella typhimurium.
[153,155,774,996,1018,1019,1020]
4-Phenylbenzylidene
derivatives
-
4-Phenylbenzylidene derivatives sensitize MRSA to β-lactams.
-
Molecular docking studies suggest an interaction with the allosteric site of PBP2a.
-
4-Phenylbenzylidene derivatives inhibit AcrAB-TolC efflux pump in Klebsiella aerogenes.
[1021]
Piperazine derivatives
-
Piperazine derivatives inhibit RND efflux pumps such as AcrAB-TolC and AcrEF-TolC and enhance the sensitivity of Escherichia coli to levofloxacin.
[1022]
Piperine analogs
-
Piperine analogs inhibit NorA in Staphylococcus aureus and potentiate the activity of fluoroquinolones.
[1023]
Raloxifene and
pyrvinium
-
Raloxifene and pyrvinium are approved drugs that were found to inhibit NorA in Staphylococcus aureus and sensitize the bacteria to ciprofloxacin.
-
The combination of these efflux pump inhibitors with ciprofloxacin could reduce the burden of preformed biofilms.
-
Raloxifene is a selective estrogen receptor modulator that is used to prevent and treat osteoporosis.
-
Pyrvinium is an anthelmintic drug.
[1024]
Reserpine
-
Reserpine inhibits NorA and TetK of Staphylococcus aureus, thus sensitizing the bacteria to fluoroquinolones.
-
Reserpine inhibits biofilm formation by Staphylococcus aureus and Pseudomonas aeruginosa.
-
Reserpine inhibits virulence factors in Staphylococcus aureus supposedly by interacting with the regulatory proteins AgrA, AtlE, Bap, IcaI, SarA, and SasG.
[1025,1026,1027,1028]
Resveratrol
-
Resveratrol is a phytoalexin found in grapes and other plants.
-
Resveratrol downregulates the adeB efflux pump in Acinetobacter baumannii and increases their sensitivity to chlorhexidine.
-
Resveratrol inhibits the AcrAB-TolC efflux pump of Escherichia coli.
-
Resveratrol inhibits ATP synthase in Staphylococcus aureus and Streptococcus pyogenes.
-
Resveratrol sensitizes Staphylococcus aureus to the antimicrobial peptide human β-defensin hBD4 and polymyxins.
[1029,1030,1031,1032,1033]
Thiazolidinedione
derivatives
-
Thiazolidinedione targets NorA of Staphylococcus aureus, thus sensitizing the bacteria to fluoroquinolones.
-
Thiazolidinedione-8 prevents biofilm formation in a mixed Streptococcus mutans-Candida albicans culture and Candida albicans monoculture.
-
Thiazolidinedione has anti-QS activity against Vibrio harveyi by decreasing the DNA-binding activity of LuxR.
-
(z)-5-Octylidenethiazolidine-2,4-dione prevents biofilm formation and targets the LasI quorum-sensing signal synthase in Pseudomonas aeruginosa.
-
13-5-(2,4-dimethoxyphenyl)thiazolidine-2,4-dione shows a high affinity for PhzS, a key enzyme in the biosynthesis of the virulent factor pyocyanin in Pseudomonas aeruginosa.
[981,982,984,1034,1035,1036]
Thymol
-
Thymol inhibits NorA in Staphylococcus aureus and sensitizes the bacteria to norfloxacin.
[1005]
Totarol
-
Totarol is a phenolic diterpene that sensitizes NorA-overexpressing Staphylococcus aureus to antibiotics by inhibiting the efflux pump.
[1037]
Trimethoprim
-
Trimethoprim inhibits the AcrAB-TolC efflux pump and synergizes with ciprofloxacin in Enterobacteriaceae and Pseudomonas aeruginosa.
[1038]
Verapamil
-
Verapamil inhibits drug efflux and potentiates the antibacterial effect of bedaquiline against Mycobacterium tuberculosis.
-
Verapamil increases the sensitivity of Staphylococcus aureus to various antibiotics including levofloxacin, linezolid, ampicillin-sulbactam, vancomycin, and doxycycline.
[1015,1039]
1 In the studies claiming that the compound inhibits NorA, the research was performed on a Staphylococcus aureus strain (SA-1199B) that overexpresses NorA, but it could be that these compounds also interfere with other efflux pumps.
Table 8. Examples of compounds targeting cell division components.
Table 8. Examples of compounds targeting cell division components.
CompoundEffects on BacteriaReferences
A benzofuroquinolinium derivative
-
It inhibits bacterial cell division by interfering with the GTPase activity of FtsZ, thus preventing its polymerization.
-
It restores the susceptibility of MRSA to β-lactam antibiotics.
[1088]
Berberine
-
It is an isoquinoline alkaloid from Berberis and other plants that inhibits FtsZ.
-
It sensitized multidrug-resistant Acinetobacter baumannii to various antibiotics including tigecycline, sulbactam, meropenem, and ciprofloxacin.
[1089,1090]
Cinnamaldehyde
-
Cinnamaldehyde is a natural compound of cinnamon oils that inhibits FtsZ.
-
It sensitizes MRSA to amikacin, gentamicin, and oxacillin with a dependency on the strain studied.
-
It inhibits biofilm formation.
[1091,1092,1093,1094]
1-Methylquinolinium iodide derivative
-
1-Methylquinolinium iodide derivative inhibits the GTPase activity of FtsZ, thus preventing FtsZ polymerization and cell division.
-
It shows antibacterial activity against MRSA, vancomycin-resistant Enterococcus, and NDM-1 Escherichia coli.
-
It sensitizes MRSA to β-lactams.
[1095]
PC190723
-
PC190723 is a benzamide family analog that inhibits the GTPase activity of FtsZ and sensitizes MRSA to β-lactam antibiotics.
[1083,1096,1097]
Quinuclidine 1
-
Quinuclidine 1 inhibits bacterial cell division by preventing FtsZ protofilament formation and sensitizes MRSA and vancomycin-resistant Enterococcus faecium to β-lactam antibiotics.
[1098]
TXA707
-
TXA707 is an FtsZ inhibitor that sensitizes MRSA to β-lactams.
[1085]
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Share and Cite

MDPI and ACS Style

Sionov, R.V.; Steinberg, D. Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria. Microorganisms 2022, 10, 1239. https://doi.org/10.3390/microorganisms10061239

AMA Style

Sionov RV, Steinberg D. Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria. Microorganisms. 2022; 10(6):1239. https://doi.org/10.3390/microorganisms10061239

Chicago/Turabian Style

Sionov, Ronit Vogt, and Doron Steinberg. 2022. "Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria" Microorganisms 10, no. 6: 1239. https://doi.org/10.3390/microorganisms10061239

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop