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Antibiotics
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Current Technique for Antibiotic Susceptibility Test: Advantages and Limitations; Need...
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Current Technique for Antibiotic Susceptibility Test: Advantages and Limitations; Need for Next-Generation Test

A special issue of Antibiotics (ISSN 2079-6382).

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 64577

Special Issue Editor

Dr. Eleonora Nicolai

E-Mail Website
Guest Editor
Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
Interests: fluorescence; rapid AST (antibiotic susceptibility testing); microbiology diagnostic; FCS (fluorescence correlation spectroscopy); biophysics; fast bacteriuria screening
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Rapid diagnostics plays a pivotal role in the treatment of bacterial infection.

Overuse or misuse of antibiotics recommended by physicians/self-medication at the time of infection has meant that drug-resistant pathogens have become a major healthcare issue, with millions of reported cases every year.

A recent report on the casualties related to antibiotic resistance by the World Health Organization (WHO) depicted an alarming 700,000 lives per year currently and predicts a disturbing 10 million/year by 2050, ensuring that antibiotic resistance will be the most prevalent cause of death. Adding to this, WHO also forewarns the severity of antibiotic resistance, stating that “it threatens the achievements of modern medicine, a post-antibiotic era—in which common infections and minor injuries can kill—is a very real possibility for the 21st century”.

For the timely treatment of patients, a rapid antimicrobial susceptibility test (AST) is urgently needed. Rapid, sensitive detection of pathogenic bacteria could be a key to initiating timely treatment with proper antibiotics, preventing disease spread, and identifying infection sources in hospitals, homes, and other field settings. Advanced diagnostics would allow clinicians to more quickly determine the most effective treatment, reduce the nonspecific use of broad-spectrum antimicrobials, and facilitate enrollment in new antibiotic treatments.

Although bacterial culture is the clinical gold standard, it has drawbacks, including long process times (up to several days), personnel cost, and the need for specialized equipment and species-specific protocols. Technical challenges, however, still remain in translating new tests into routine clinical workflows. System operation must be simple, with no need for trained operators and assay costs lower than those for conventional screening.

A rise in antibiotic resistance is a certainty; therefore, we must develop technologies that will permit rapid AST (within few hours) and are non-invasive (saliva- or urine-based) or minimally invasive.

Thus, this Special Issue will cover but not be limited to:

  • Current AST techniques;
  • Rapid AST;
  • Automation in diagnostics for AST;
  • Diagnostics need to limit antibiotic resistance;
  • Non-invasive methods for AST;
  • Low cost and user-friendly techniques applicable to AST.

Dr. Eleonora Nicolai
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Antibiotics is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • rapid AST
  • microbiology diagnostics
  • antibiotic resistance
  • antibiotic activity
  • automated diagnostics

Published Papers (10 papers)

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Editorial

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3 pages, 176 KiB  
Editorial
Editorial for the Special Issue: “Current Technique for Antibiotic Susceptibility Test: Advantages and Limitations; Need for Next-Generation Test”
by Eleonora Nicolai
Antibiotics 2023, 12(4), 750; https://doi.org/10.3390/antibiotics12040750 - 13 Apr 2023
Viewed by 1057
Abstract
The overuse or misuse of antibiotics, either when recommended by physicians or administered through self-medication at the time of infection, has caused drug-resistant pathogens to become a major healthcare issue, with millions of reported cases every year [...] Full article
(This article belongs to the Special Issue Current Technique for Antibiotic Susceptibility Test: Advantages and Limitations; Need for Next-Generation Test)

Research

Jump to: Editorial, Review, Other

11 pages, 1297 KiB  
Article
Trends in Antibiotic Resistance of Nosocomial and Community-Acquired Infections in Italy
by Paola Cerini, Francesca Rita Meduri, Flaminia Tomassetti, Isabella Polidori, Marta Brugneti, Eleonora Nicolai, Sergio Bernardini, Massimo Pieri and Francesco Broccolo
Antibiotics 2023, 12(4), 651; https://doi.org/10.3390/antibiotics12040651 - 24 Mar 2023
Cited by 8 | Viewed by 3064
Abstract
The World Health Organization has recently identified three categories of pathogens, namely: critical, high, and medium priority, according to the need for new antibiotics. Critical priority pathogens include carbapenem-resistant microorganism (CPO) such as A. baumannii and P. aeruginosa, K. pneumoniae, and [...] Read more.
The World Health Organization has recently identified three categories of pathogens, namely: critical, high, and medium priority, according to the need for new antibiotics. Critical priority pathogens include carbapenem-resistant microorganism (CPO) such as A. baumannii and P. aeruginosa, K. pneumoniae, and Enterobacter spp., whereas vancomycin-resistant E. faecium (VRE), methicillin and vancomycin-resistant S. aureus (MRSA) are in the high priority list. We compared the trend of antimicrobial resistants (AMRs) in clinical isolates, divided by year and bacteria spp., of samples obtained from nosocomial and community patients. Patient records were collected, including age, sex, site of infection, isolated organisms, and drug susceptibility patterns. From 2019 to 2022, a total of 113,635 bacterial isolates were tested, of which 11,901 resulted in antimicrobial resistants. An increase in the prevalence of several antibiotics resistant bacteria was observed. Specifically, the percentage of CPO cases increased from 2.62% to 4.56%, the percentage of MRSA increased from 1.84% to 2.81%, and the percentage of VRE increased from 0.58% to 2.21%. AMRs trend resulted in increases in CPO and MRSA for both community and nosocomial. Our work aims to highlight the necessity of preventive and control measures to be adopted in order to reduce the spread of multidrug-resistant pathogens. Full article
(This article belongs to the Special Issue Current Technique for Antibiotic Susceptibility Test: Advantages and Limitations; Need for Next-Generation Test)
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14 pages, 1587 KiB  
Article
Cumulative Antibiogram: A Rapid Method to Hinder Transmission of Resistant Bacteria to Oral Cavity of Newborn Babies
by Mădălina Adriana Malița, Loredana Sabina Cornelia Manolescu, Cristina Florentina Pîrvu, Radu Catalin Costea, Elena Cristina Marcov, Mihai Burlibasa, Daniela Aurelia Pîrvu, Liliana Burlibașa, Mihaela Corina Radu, Irina Prasacu and Viorel Ștefan Perieanu
Antibiotics 2023, 12(1), 80; https://doi.org/10.3390/antibiotics12010080 - 2 Jan 2023
Cited by 3 | Viewed by 2160
Abstract
Background: A rapid bacterial diagnostic is needed more and more in the treatment of patients, because of the emergence of antibiotic resistance. The cumulative antibiogram, an annual report that monitors antimicrobial resistance trends in health care facilities, may provide a profile of empirical [...] Read more.
Background: A rapid bacterial diagnostic is needed more and more in the treatment of patients, because of the emergence of antibiotic resistance. The cumulative antibiogram, an annual report that monitors antimicrobial resistance trends in health care facilities, may provide a profile of empirical therapy useful in diverse emergency situations, such as transmission of resistant bacteria to oral cavity of newborn babies. We aimed to draw a profile of antibiotic resistance encountered. Methods: We assessed the antibiotic resistance (ABR) profile in childbearing women and newborn babies in Ploiesti Obstetrics and Gynecology Hospital by the disk diffusion method characterizing the multidrug-resistant organisms after isolation and identification by phenotypic tests. Extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-E), Carbapenem-resistant Enterobacterales (CRE), vancomycin-resistant Enterococci (VRE), methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin resistant Group B Streptococcus (VR-GBS) were detected. Results: The prevalence of antibiotic resistance was 11.32% (53/468), while the prevalence of the ESBL-E, MRSA, VRE and VR-GBS strains was 8.34% (39/468). Within the bacteria isolated from fifty-three childbearing women, the prevalence of ESBL-E, MRSA, VRE and VR-GBS was 22.64% (12/53), 32.08% (17/53), 11.32% (6/53) and 7.55% (4/53). In the whole studied group, the prevalence was 2.56% (12/468), 3.63% (17/468), 1.28% (6/468) and 0.86% (4/468). Resistant bacteria were detected at birth in the oral cavity of the newborn babies in all cases. Maternal and neonatal isolates shared similar characteristics. Conclusions: Cumulative antibiogram is useful in case of empiric treatment needed in diverse emergencies, such as transmission of resistant bacteria to oral cavity of newborn babies. Full article
(This article belongs to the Special Issue Current Technique for Antibiotic Susceptibility Test: Advantages and Limitations; Need for Next-Generation Test)
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12 pages, 263 KiB  
Article
Relationship between Phenotypic and Genotypic Resistance of Subgingival Biofilm Samples in Patients with Periodontitis
by Moritz Sparbrod, Yann Gager, Anne-Katrin Koehler, Holger Jentsch and Catalina-Suzana Stingu
Antibiotics 2023, 12(1), 68; https://doi.org/10.3390/antibiotics12010068 - 30 Dec 2022
Cited by 4 | Viewed by 1747
Abstract
The phenotypic expression of antibiotic resistance genes (ARGs) can hamper the use of antibiotics as adjuncts to subgingival instrumentation in the treatment of periodontitis patients. The aim of the study was to analyze the relationship between the phenotypic and genotypic resistance against ampicillin-sulbactam, [...] Read more.
The phenotypic expression of antibiotic resistance genes (ARGs) can hamper the use of antibiotics as adjuncts to subgingival instrumentation in the treatment of periodontitis patients. The aim of the study was to analyze the relationship between the phenotypic and genotypic resistance against ampicillin-sulbactam, clindamycin, doxycycline and metronidazole of subgingival biofilm samples from 19 periodontitis patients. Samples were analyzed with shotgun sequencing and cultivated anaerobically for 7 days on microbiological culture media incorporating antibiotics. All growing isolates were identified to the species level using MALDI-TOF-MS and sequence analysis of the 16S ribosomal RNA (rRNA) gene. Phenotypic resistance was determined using EUCAST-breakpoints. The genetic profile of eight patients matched completely with phenotypical resistance to the tested antibiotics. The positive predictive values varied from 1.00 for clindamycin to 0.57 for doxycycline and 0.25 for ampicillin-sulbactam. No sample contained the nimI gene. It can be concluded that antibiotic resistance may be polygenetic and genes may be silent. Every biofilm sample harboring erm genes was phenotypic resistant. The absence of cfx and tet genes correlated to 100%, respectively, to 75%, with the absence of phenotypic resistance. The absence of nimI genes leads to the assumption that constitutive resistance among several species could explain the resistance to metronidazole. Full article
(This article belongs to the Special Issue Current Technique for Antibiotic Susceptibility Test: Advantages and Limitations; Need for Next-Generation Test)
16 pages, 269 KiB  
Article
Antimicrobial Susceptibility Profile of Rare Anaerobic Bacteria
by Lena Josephine Wolf and Catalina-Suzana Stingu
Antibiotics 2023, 12(1), 63; https://doi.org/10.3390/antibiotics12010063 - 29 Dec 2022
Cited by 6 | Viewed by 2807
Abstract
Anaerobes play an important role in clinically relevant infections and resistance is increasing worldwide. We tested 120 rare anaerobic isolates belonging to 16 genera for antimicrobial resistance using the agar dilution method and compared those results to the time-saving E-test method. The susceptibility [...] Read more.
Anaerobes play an important role in clinically relevant infections and resistance is increasing worldwide. We tested 120 rare anaerobic isolates belonging to 16 genera for antimicrobial resistance using the agar dilution method and compared those results to the time-saving E-test method. The susceptibility data for 12 antimicrobial substances (benzylpenicillin, ampicillin/sulbactam, piperacillin/tazobactam, imipenem, meropenem, cefoxitin, metronidazole, moxifloxacin, clindamycin, doxycycline, tigecycline, eravacycline) were collected. Susceptibility testing showed low resistance to β-lactam/β-lactamase inhibitor combinations and no resistance to carbapenems and tigecycline. We observed moderate to high rates of resistance to moxifloxacin and clindamycin which differed depending on the methodology used. The essential and categorical agreement was over 90% for ampicillin/sulbactam, meropenem, moxifloxacin, and tigecycline. For metronidazole and clindamycin, the essential agreement was below 90% but the categorical agreement was near or above 90%. Penicillin presented with the lowest categorical agreement of 86.7% and a very high very major error rate of 13.3%. The resistance rates reported in this study are concerning and show the importance of routine susceptibility testing. Further investigations are necessary to determine the reason for high error rates and how to improve susceptibility testing of fastidious anaerobes. Full article
(This article belongs to the Special Issue Current Technique for Antibiotic Susceptibility Test: Advantages and Limitations; Need for Next-Generation Test)
10 pages, 1872 KiB  
Article
Conventional and Real-Time PCR Targeting blaOXA Genes as Reliable Methods for a Rapid Detection of Carbapenem-Resistant Acinetobacter baumannii Clinical Strains
by Dagmara Depka, Agnieszka Mikucka, Tomasz Bogiel, Mateusz Rzepka, Patryk Zawadka and Eugenia Gospodarek-Komkowska
Antibiotics 2022, 11(4), 455; https://doi.org/10.3390/antibiotics11040455 - 28 Mar 2022
Cited by 4 | Viewed by 2795
Abstract
Multidrug-resistant Acinetobacter baumannii, particularly those producing carbapenemases, are spread worldwide. A reliable detection of carbapenemases is essential to choose the appropriate antimicrobial therapy and, consequently, prevent the dissemination of carbapenem-resistant strains. The aim of this study is to examine the molecular basis [...] Read more.
Multidrug-resistant Acinetobacter baumannii, particularly those producing carbapenemases, are spread worldwide. A reliable detection of carbapenemases is essential to choose the appropriate antimicrobial therapy and, consequently, prevent the dissemination of carbapenem-resistant strains. The aim of this study is to examine the molecular basis of the carbapenem resistance mechanism and estimation of conventional PCR and real-time PCR usefulness for the detection of oxacillinases when compared to phenotypic carbapenemases detection. The following methods were evaluated: the CarbAcineto NP test, Carbapenem Inactivation Method, CPO panels of semiautomated antimicrobial susceptibility testing method on the BD Phoenix™ M50 system, conventional Polymerase Chain Reaction and real-time PCR. The eazyplex® SuperBug complete A assay was used as the reference method. Among the tested strains, 39 (67.2%) carried the blaOXA-40 gene, while the blaOXA-23 gene was noted amongst 19 (32.8%) isolates. The diagnostic sensitivities of the studied assays were as follows: CarbAcineto NP—65.5%; CIM—100%; CPO—100%; conventional PCR—100%; real-time PCR—100%. Full article
(This article belongs to the Special Issue Current Technique for Antibiotic Susceptibility Test: Advantages and Limitations; Need for Next-Generation Test)
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11 pages, 1482 KiB  
Article
Bacterial Infection Diagnosis and Antibiotic Prescription in 3 h as an Answer to Antibiotic Resistance: The Case of Urinary Tract Infections
by Eleonora Nicolai, Massimo Pieri, Enrico Gratton, Guido Motolese and Sergio Bernardini
Antibiotics 2021, 10(10), 1168; https://doi.org/10.3390/antibiotics10101168 - 26 Sep 2021
Cited by 6 | Viewed by 1892
Abstract
Current methods for the diagnosis of urinary tract infections with antimicrobial susceptibility testing take 2–3 days and require a clinical laboratory. The lack of a rapid, point-of-care antibiotic susceptibility test (AST) has contributed to the misuse of antibiotics when treating urinary tract infections [...] Read more.
Current methods for the diagnosis of urinary tract infections with antimicrobial susceptibility testing take 2–3 days and require a clinical laboratory. The lack of a rapid, point-of-care antibiotic susceptibility test (AST) has contributed to the misuse of antibiotics when treating urinary tract infections (UTIs) and consequently to the rise of multi-drug-resistant organisms. The current clinical approach has led to reduced treatment options and increased costs of diagnosis and therapy. To address this issue, novel diagnostics are needed for the timely determination of antimicrobial susceptibility. We present a rapid, point-of-care, phenotypic AST device that can report the antibiotic susceptibility/resistance of a uropathogen to a panel of antibiotics in as few as 3 h by utilizing fluorescent-labelling chemistry and a highly sensitive particle-counting instrument. We analysed 744 urine samples from the outpatients and inpatients of two Italian hospitals. The 130 UTI-positive patient urine samples we found were measured using a panel of six common UTI antibiotics plus a growth control. By comparing our results to hospital laboratory urine cultures, we obtained an overall sensitivity = 81%, a specificity = 83%, an SPV (sensitivity predicted value) = 95%, and an RPV (resistance predicted value) = 54%. According to our preliminary data, the sensitivity predicted value for a single antibiotic agent was 95%, thus allowing (in the vast majority of cases) an early (within 3 h) recognition of an effective agent for a single patient. Full article
(This article belongs to the Special Issue Current Technique for Antibiotic Susceptibility Test: Advantages and Limitations; Need for Next-Generation Test)
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13 pages, 1183 KiB  
Article
A Combined Phenotypic-Genotypic Predictive Algorithm for In Vitro Detection of Bicarbonate: β-Lactam Sensitization among Methicillin-Resistant Staphylococcus aureus (MRSA)
by Selvi C. Ersoy, Warren E. Rose, Robin Patel, Richard A. Proctor, Henry F. Chambers, Ewan M. Harrison, Youngju Pak and Arnold S. Bayer
Antibiotics 2021, 10(9), 1089; https://doi.org/10.3390/antibiotics10091089 - 9 Sep 2021
Cited by 8 | Viewed by 2566
Abstract
Antimicrobial susceptibility testing (AST) is routinely used to establish predictive antibiotic resistance metrics to guide the treatment of bacterial pathogens. Recently, a novel phenotype termed “bicarbonate (NaHCO3)-responsiveness” was identified in a relatively high frequency of clinical MRSA strains, wherein isolates demonstrate [...] Read more.
Antimicrobial susceptibility testing (AST) is routinely used to establish predictive antibiotic resistance metrics to guide the treatment of bacterial pathogens. Recently, a novel phenotype termed “bicarbonate (NaHCO3)-responsiveness” was identified in a relatively high frequency of clinical MRSA strains, wherein isolates demonstrate in vitro “susceptibility” to standard β-lactams (oxacillin [OXA]; cefazolin [CFZ]) in the presence of NaHCO3, and in vivo susceptibility to these β-lactams in experimental endocarditis models. We investigated whether a targeted phenotypic-genotypic screening of MRSA could rule in or rule out NaHCO3 susceptibility upfront. We studied 30 well-characterized clinical MRSA bloodstream isolates, including 15 MIC-susceptible to CFZ and OXA in NaHCO3-supplemented Mueller–Hinton Broth (MHB); and 15 MIC-resistant to both β-lactams in this media. Using a two-tiered strategy, isolates were first screened by standard disk diffusion for susceptibility to a combination of amoxicillin-clavulanate [AMC]. Isolates then underwent genomic sequence typing: MLST (clonal complex [CC]); agr; SCCmec; and mecA promoter and coding region. The combination of AMC disk susceptibility testing plus mecA and spa genotyping was able to predict MRSA strains that were more or less likely to be NaHCO3-responsive in vitro, with a high degree of sensitivity and specificity. Validation of this screening algorithm was performed in six strains from the overall cohort using an ex vivo model of endocarditis. This ex vivo model recapitulated the in vitro predictions of NaHCO3-responsiveness vs. nonresponsiveness above in five of the six strains. Full article
(This article belongs to the Special Issue Current Technique for Antibiotic Susceptibility Test: Advantages and Limitations; Need for Next-Generation Test)
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Review

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26 pages, 1707 KiB  
Review
Antimicrobial Susceptibility Testing: A Comprehensive Review of Currently Used Methods
by Ina Gajic, Jovana Kabic, Dusan Kekic, Milos Jovicevic, Marina Milenkovic, Dragana Mitic Culafic, Anika Trudic, Lazar Ranin and Natasa Opavski
Antibiotics 2022, 11(4), 427; https://doi.org/10.3390/antibiotics11040427 - 23 Mar 2022
Cited by 106 | Viewed by 41955
Abstract
Antimicrobial resistance (AMR) has emerged as a major threat to public health globally. Accurate and rapid detection of resistance to antimicrobial drugs, and subsequent appropriate antimicrobial treatment, combined with antimicrobial stewardship, are essential for controlling the emergence and spread of AMR. This article [...] Read more.
Antimicrobial resistance (AMR) has emerged as a major threat to public health globally. Accurate and rapid detection of resistance to antimicrobial drugs, and subsequent appropriate antimicrobial treatment, combined with antimicrobial stewardship, are essential for controlling the emergence and spread of AMR. This article reviews common antimicrobial susceptibility testing (AST) methods and relevant issues concerning the advantages and disadvantages of each method. Although accurate, classic technologies used in clinical microbiology to profile antimicrobial susceptibility are time-consuming and relatively expensive. As a result, physicians often prescribe empirical antimicrobial therapies and broad-spectrum antibiotics. Although recently developed AST systems have shown advantages over traditional methods in terms of testing speed and the potential for providing a deeper insight into resistance mechanisms, extensive validation is required to translate these methodologies to clinical practice. With a continuous increase in antimicrobial resistance, additional efforts are needed to develop innovative, rapid, accurate, and portable diagnostic tools for AST. The wide implementation of novel devices would enable the identification of the optimal treatment approaches and the surveillance of antibiotic resistance in health, agriculture, and the environment, allowing monitoring and better tackling the emergence of AMR. Full article
(This article belongs to the Special Issue Current Technique for Antibiotic Susceptibility Test: Advantages and Limitations; Need for Next-Generation Test)
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Other

13 pages, 2235 KiB  
Perspective
Anti-Infective Treatment and Resistance Is Rarely Problematic with Eye Infections
by Regis P. Kowalski, Shannon V. Nayyar, Eric G. Romanowski and Vishal Jhanji
Antibiotics 2022, 11(2), 204; https://doi.org/10.3390/antibiotics11020204 - 6 Feb 2022
Cited by 5 | Viewed by 2660
Abstract
The treatment of eye infections is very different than treating other body infections that require systemic anti-infectives. Endophthalmitis, keratitis, conjunctivitis, and other ocular infections are treated with direct injection and with topical drops directly to the infection site. There are no anti-infective susceptibility [...] Read more.
The treatment of eye infections is very different than treating other body infections that require systemic anti-infectives. Endophthalmitis, keratitis, conjunctivitis, and other ocular infections are treated with direct injection and with topical drops directly to the infection site. There are no anti-infective susceptibility standards to interpret treatment success, but the systemic standards can be used to guide ocular therapy if the concentration of anti-infective in the ocular tissue is assumed to be higher than the concentration in the blood serum. This Perspective describes: (1) eye infections, (2) diagnostics of eye infections, (3) anti-infective treatment of eye infections, (4) anti-infective resistance of ocular pathogens, and (5) alternative anti-infective delivery and therapy. The data, based on years of clinical and laboratory research, support the premise that ocular infections are less problematic if etiologic agents are laboratory-diagnosed and if prompt, potent, anti-infective therapy is applied. Anti-infective susceptibility should be monitored to assure continued therapeutic success and the possibility of new-found resistance. New delivery systems and therapies may be helpful to better treat future ocular infections. Full article
(This article belongs to the Special Issue Current Technique for Antibiotic Susceptibility Test: Advantages and Limitations; Need for Next-Generation Test)
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