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Antibiotic Resistance Genes: Spread and Evolution

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A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Mechanism and Evolution of Antibiotic Resistance".

Deadline for manuscript submissions: closed (31 March 2021) | Viewed by 39701

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Dr. Elena Perrin

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Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
Interests: antibiotic resistance; Burkholderia; efflux pumps; quorum sensing; multipartite genomes
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

An in-depth knowledge of the genes and the mechanisms involved in the development and spread of antibiotic resistance (AR) is fundamental to counteracting this phenomenon.

Some information is already available on the resistome; the collection of all AR genes and their precursors, and the recent developments in -omics technologies have greatly contributed to expand our knowledge on this topic. However, more information is needed in order to more efficiently fight the spread of AR, to prevent its development, and to try to reduce it when it is already present, in order to be able to restore, for example, the activity of existing antibiotics.

This Special Issue invites articles on AR genes and their spread and evolution, including but not limited to the following topics:

The evolution and spread of known mechanisms of AR and the emergence of new mechanisms;
Direct evolution experiments on AR development;
The connections between AR and physiology and cellular metabolism;
The identification of unconventional genes directly or indirectly involved in AR;
Studies on the AR fitness cost.

Dr. Elena Perrin
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

Antibiotic resistance genes
Mobile genetic element
Horizontal gene transfer
Mutation rate
Resistome

Published Papers (11 papers)

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Research

20 pages, 6741 KiB

Open AccessArticle

Molecular Detection of Colistin Resistance mcr-1 Gene in Multidrug-Resistant Escherichia coli Isolated from Chicken

by Md Bashir Uddin, Mohammad Nurul Alam, Mahmudul Hasan, S. M. Bayejed Hossain, Mita Debnath, Ruhena Begum, Mohammed A. Samad, Syeda Farjana Hoque, Md. Shahidur Rahman Chowdhury, Md. Mahfujur Rahman, Md. Mukter Hossain, Mohammad Mahmudul Hassan, Åke Lundkvist, Josef D. Järhult, Mohamed E. El Zowalaty and Syed Sayeem Uddin Ahmed

Antibiotics 2022, 11(1), 97; https://doi.org/10.3390/antibiotics11010097 - 13 Jan 2022

Cited by 8 | Viewed by 3741

Abstract

Zoonotic and antimicrobial-resistant Escherichia coli (hereafter, E. coli) is a global public health threat which can lead to detrimental effects on human health. Here, we aim to investigate the antimicrobial resistance and the presence of mcr-1 gene in E. coli isolated from chicken feces. Ninety-four E. coli isolates were obtained from samples collected from different locations in Bangladesh, and the isolates were identified using conventional microbiological tests. Phenotypic disk diffusion tests using 20 antimicrobial agents were performed according to CLSI-EUCAST guidelines, and minimum inhibitory concentrations (MICs) were determined for a subset of samples. E. coli isolates showed high resistance to colistin (88.30%), ciprofloxacin (77.66%), trimethoprim/sulfamethoxazole (76.60%), tigecycline (75.53%), and enrofloxacin (71.28%). Additionally, the pathotype eaeA gene was confirmed in ten randomly selected E. coli isolates using primer-specific polymerase chain reaction (PCR). The presence of mcr-1 gene was confirmed using PCR and sequencing analysis in six out of ten E. coli isolates. Furthermore, sequencing and phylogenetic analyses revealed a similarity between the catalytic domain of Neisseria meningitidis lipooligosaccharide phosphoethanolamine transferase A (LptA) and MCR proteins, indicating that the six tested isolates were colistin resistant. Finally, the findings of the present study showed that E. coli isolated from chicken harbored mcr-1 gene, and multidrug and colistin resistance. These findings accentuate the need to implement strict measures to limit the imprudent use of antibiotics, particularly colistin, in agriculture and poultry farms. Full article

(This article belongs to the Special Issue Antibiotic Resistance Genes: Spread and Evolution)

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20 pages, 1491 KiB

Open AccessArticle

The Perfect Condition for the Rising of Superbugs: Person-to-Person Contact and Antibiotic Use Are the Key Factors Responsible for the Positive Correlation between Antibiotic Resistance Gene Diversity and Virulence Gene Diversity in Human Metagenomes

by Célia P. F. Domingues, João S. Rebelo, Joël Pothier, Francisca Monteiro, Teresa Nogueira and Francisco Dionisio

Antibiotics 2021, 10(5), 605; https://doi.org/10.3390/antibiotics10050605 - 20 May 2021

Cited by 10 | Viewed by 3649

Abstract

Human metagenomes with a high diversity of virulence genes tend to have a high diversity of antibiotic-resistance genes and vice-versa. To understand this positive correlation, we simulated the transfer of these genes and bacterial pathogens in a community of interacting people that take antibiotics when infected by pathogens. Simulations show that people with higher diversity of virulence and resistance genes took antibiotics long ago, not recently. On the other extreme, we find people with low diversity of both gene types because they took antibiotics recently—while antibiotics select specific resistance genes, they also decrease gene diversity by eliminating bacteria. In general, the diversity of virulence and resistance genes becomes positively correlated whenever the transmission probability between people is higher than the probability of losing resistance genes. The positive correlation holds even under changes of several variables, such as the relative or total diversity of virulence and resistance genes, the contamination probability between individuals, the loss rate of resistance genes, or the social network type. Because the loss rate of resistance genes may be shallow, we conclude that the transmission between people and antibiotic usage are the leading causes for the positive correlation between virulence and antibiotic-resistance genes. Full article

(This article belongs to the Special Issue Antibiotic Resistance Genes: Spread and Evolution)

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14 pages, 2931 KiB

Open AccessArticle

Antimicrobial Resistance Profiles of Human Commensal Neisseria Species

by Maira Goytia, Symone T. Thompson, Skylar V. L. Jordan and Kacey A. King

Antibiotics 2021, 10(5), 538; https://doi.org/10.3390/antibiotics10050538 - 6 May 2021

Cited by 11 | Viewed by 3683

Abstract

Pathogenic Neisseria gonorrhoeae causes the sexually transmitted infection gonorrhea. N. gonorrhoeae has evolved high levels of antimicrobial resistance (AR) leading to therapeutic failures even in dual-therapy treatment with azithromycin and ceftriaxone. AR mechanisms can be acquired by genetic transfer from closely related species, such as naturally competent commensal Neisseria species. At present, little is known about the antimicrobial resistance profiles of commensal Neisseria. Here, we characterized the phenotypic resistance profile of four commensal Neisseria species (N. lactamica, N. cinerea, N. mucosa, and N. elongata) against 10 commonly used antibiotics, and compared their profiles to 4 N. gonorrhoeae strains, using disk diffusion and minimal inhibitory concentration assays. Overall, we observed that 3 of the 4 commensals were more resistant to several antibiotics than pathogenic N. gonorrhoeae strains. Next, we compared publicly available protein sequences of known AR genes, including penicillin-binding-protein 2 (PBP2) from commensals and N. gonorrhoeae strains. We found mutations in PBP2 known to confer resistance in N. gonorrhoeae also present in commensal Neisseria sequences. Our results suggest that commensal Neisseria have unexplored antibiotic resistance gene pools that may be exchanged with pathogenic N. gonorrhoeae, possibly impairing drug development and clinical treatment. Full article

(This article belongs to the Special Issue Antibiotic Resistance Genes: Spread and Evolution)

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13 pages, 1043 KiB

Open AccessArticle

The Bacterial Genomic Context of Highly Trimethoprim-Resistant DfrB Dihydrofolate Reductases Highlights an Emerging Threat to Public Health

by Claudèle Lemay-St-Denis, Sarah-Slim Diwan and Joelle N. Pelletier

Antibiotics 2021, 10(4), 433; https://doi.org/10.3390/antibiotics10040433 - 13 Apr 2021

Cited by 10 | Viewed by 2951

Abstract

Type B dihydrofolate reductase (dfrb) genes were identified following the introduction of trimethoprim in the 1960s. Although they intrinsically confer resistance to trimethoprim (TMP) that is orders of magnitude greater than through other mechanisms, the distribution and prevalence of these short (237 bp) genes is unknown. Indeed, this knowledge has been hampered by systematic biases in search methodologies. Here, we investigate the genomic context of dfrbs to gain information on their current distribution in bacterial genomes. Upon searching publicly available databases, we identified 61 sequences containing dfrbs within an analyzable genomic context. The majority (70%) of those sequences also harbor virulence genes and 97% of the dfrbs are found near a mobile genetic element, representing a potential risk for antibiotic resistance genes. We further identified and confirmed the TMP-resistant phenotype of two new members of the family, dfrb10 and dfrb11. Dfrbs are found both in Betaproteobacteria and Gammaproteobacteria, a majority (59%) being in Pseudomonas aeruginosa. Previously labelled as strictly plasmid-borne, we found 69% of dfrbs in the chromosome of pathogenic bacteria. Our results demonstrate that the intrinsically TMP-resistant dfrbs are a potential emerging threat to public health and justify closer surveillance of these genes. Full article

(This article belongs to the Special Issue Antibiotic Resistance Genes: Spread and Evolution)

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16 pages, 1339 KiB

Open AccessArticle

Prevalence and Characterization of Quinolone-Resistance Determinants in Escherichia coli Isolated from Food-Producing Animals and Animal-Derived Food in the Philippines

by Lawrence Belotindos, Marvin Villanueva, Joel Miguel, Jr., Precious Bwalya, Tetsuya Harada, Ryuji Kawahara, Chie Nakajima, Claro Mingala and Yasuhiko Suzuki

Antibiotics 2021, 10(4), 413; https://doi.org/10.3390/antibiotics10040413 - 9 Apr 2021

Cited by 11 | Viewed by 6386

Abstract

Antimicrobial resistance to quinolones, which constitutes a threat to public health, has been increasing worldwide. In this study, we investigated the prevalence of quinolone-resistant determinants in Escherichia coli not susceptible to quinolones and isolated from food-producing animals and food derived from them, in the Philippines. A total of 791 E. coli strains were isolated in 56.4% of 601 beef, chicken, pork, egg, and milk samples, as well as environmental, cloacal, and rectal swab-collected samples from supermarkets, open markets, abattoirs, and poultry, swine, and buffalo farms. Using the disc diffusion method, it was determined that 78.6% and 55.4% of the isolates were resistant to at least one antimicrobial and multiple drugs, respectively. In 141 isolates not susceptible to quinolones, 115 (81.6%) harbored quinolone-resistant determinants and had mutations predominantly in the quinolone-resistance determining regions (QRDRs) of gyrA and parC. Plasmid-mediated, quinolone resistance (PMQR) and Qnr family (qnrA1, qnrB4, and qnrS1) genes were detected in all isolates. Forty-eight sequence types were identified in isolates harboring mutations in QRDR and/or PMQR genes by multilocus sequence typing analysis. Moreover, 26 isolates harboring mutations in QRDR and/or PMQR genes belonged mostly to phylogroup B1 and Enteroaggregative E. coli. In conclusion, a high prevalence of E. coli was found in food-producing animals and products derived from them, which could potentially spread high-risk clones harboring quinolone-resistance determinants. Full article

(This article belongs to the Special Issue Antibiotic Resistance Genes: Spread and Evolution)

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16 pages, 687 KiB

Open AccessArticle

Trueperella pyogenes Isolates from Livestock and European Bison (Bison bonasus) as a Reservoir of Tetracycline Resistance Determinants

by Ewelina Kwiecień, Ilona Stefańska, Dorota Chrobak-Chmiel, Magdalena Kizerwetter-Świda, Agata Moroz, Wanda Olech, Marina Spinu, Marian Binek and Magdalena Rzewuska

Antibiotics 2021, 10(4), 380; https://doi.org/10.3390/antibiotics10040380 - 3 Apr 2021

Cited by 11 | Viewed by 2742

Abstract

Determinants of tetracycline resistance in Trueperella pyogenes are still poorly known. In this study, resistance to tetracycline was investigated in 114 T. pyogenes isolates from livestock and European bison. Tetracycline minimum inhibitory concentration (MIC) was evaluated by a microdilution method, and tetracycline resistance genes were detected by PCR. To determine variants of tetW and their linkage with mobile elements, sequencing analysis was performed. Among the studied isolates, 43.0% were tetracycline resistant (MIC ≥ 8 µg/mL). The highest MIC₉₀ of tetracycline (32 µg/mL) was noted in bovine and European bison isolates. The most prevalent determinant of tetracycline resistance was tetW (in 40.4% of isolates), while tetA(33) was detected only in 8.8% of isolates. Four variants of tetW (tetW-1, tetW-2, tetW-3, tetW-4) were recognized. The tetW-3 variant was the most frequent and was linked to the ATE-1 transposon. The tetW-2 variant, found in a swine isolate, was not previously reported in T. pyogenes. This is the first report on determinants of tetracycline resistance in T. pyogenes isolates from European bison. These findings highlight that wild animals, including wild ruminants not treated with antimicrobials, can be a reservoir of tetracycline-resistant bacteria carrying resistance determinants, which may be easily spread among pathogenic and environmental microorganisms. Full article

(This article belongs to the Special Issue Antibiotic Resistance Genes: Spread and Evolution)

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7 pages, 224 KiB

Open AccessCommunication

Antimicrobial Resistance of Escherichia coli and Pseudomonas aeruginosa from Companion Birds

by Lorena Varriale, Ludovico Dipineto, Tamara Pasqualina Russo, Luca Borrelli, Violante Romano, Stefano D’Orazio, Antonino Pace, Lucia Francesca Menna, Alessandro Fioretti and Antonio Santaniello

Antibiotics 2020, 9(11), 780; https://doi.org/10.3390/antibiotics9110780 - 6 Nov 2020

Cited by 10 | Viewed by 2629

Abstract

Antimicrobial resistance is a public health concern worldwide and it is largely attributed to the horizontal exchange of transferable genetic elements such as plasmids carrying integrons. Several studies have been conducted on livestock showing a correlation between the systemic use of antibiotics and the onset of resistant bacterial strains. In contrast, although companion birds are historically considered as an important reservoir for human health threats, little information on the antimicrobial resistance in these species is available in the literature. Therefore, this study was aimed at evaluating the antimicrobial resistance of Escherichia coli and Pseudomonasaeruginosa isolated from 755 companion birds. Cloacal samples were processed for E. coli and P. aeruginosa isolation and then all isolates were submitted to antimicrobial susceptibility testing. P. aeruginosa was isolated in 59/755 (7.8%) samples, whereas E. coli was isolated in 231/755 (30.7%) samples. Most strains showed multidrug resistance. This study highlights that companion birds may act as substantial reservoirs carrying antimicrobial resistance genes which could transfer directly or indirectly to humans and animals, and from a One Health perspective this risk should not be underestimated. Full article

(This article belongs to the Special Issue Antibiotic Resistance Genes: Spread and Evolution)

7 pages, 856 KiB

Open AccessCommunication

First Report of an Escherichia coli Strain Carrying the Colistin Resistance Determinant mcr-1 from a Dog in South Korea

by Dong Chan Moon, Abraham Fikru Mechesso, Hee Young Kang, Su-Jeong Kim, Ji-Hyun Choi, Mi Hyun Kim, Hyun-Ju Song, Soon-Seek Yoon and Suk-Kyung Lim

Antibiotics 2020, 9(11), 768; https://doi.org/10.3390/antibiotics9110768 - 2 Nov 2020

Cited by 8 | Viewed by 2029

Abstract

We studied the presence of the mobile colistin resistance gene mcr-1 in Escherichia coli isolates recovered from fecal and urine samples of companion animals, that were collected from South Korea in 2018 and 2019. The mcr-1 gene was detected in one colistin-resistant E. coli isolated from a diarrheic dog. The isolate exhibited additional resistance to multiple antimicrobials, including fluoroquinolones and third-generation cephalosporins. The mcr-1 carrying isolate belonged to ST160. The pulsed-field gel electrophoresis pattern of our strain differed from those ST160 E. coli strains previously identified from chickens in Korea. The mcr-1 gene was identified in the IncI2 plasmid. It was also transferred to E. coli J53 recipient strain, with a conjugation efficiency of 2.8 × 10⁻⁴. Average nucleotide identity analysis demonstrated that the mcr-1-carrying plasmid in this study was closely related to those from patients in Korea. To the best of our knowledge, this is the first report of mcr-1 carrying E. coli from a companion animal in South Korea. Our findings support One Health approach is necessary to prevent the dissemination of this high-risk gene. Full article

(This article belongs to the Special Issue Antibiotic Resistance Genes: Spread and Evolution)

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14 pages, 1323 KiB

Open AccessArticle

Molecular Characterization and Comparative Genomics of IncQ-3 Plasmids Conferring Resistance to Various Antibiotics Isolated from a Wastewater Treatment Plant in Warsaw (Poland)

by Marta Piotrowska, Lukasz Dziewit, Rafał Ostrowski, Cora Chmielowska and Magdalena Popowska

Antibiotics 2020, 9(9), 613; https://doi.org/10.3390/antibiotics9090613 - 17 Sep 2020

Cited by 9 | Viewed by 3501

Abstract

As small, mobilizable replicons with a broad host range, IncQ plasmids are widely distributed among clinical and environmental bacteria. They carry antibiotic resistance genes, and it has been shown that they confer resistance to β-lactams, fluoroquinolones, aminoglycosides, trimethoprim, sulphonamides, and tetracycline. The previously proposed classification system divides the plasmid group into four subgroups, i.e., IncQ-1, IncQ-2, IncQ-3, and IncQ-4. The last two subgroups have been poorly described so far. The aim of this study was to analyze five newly identified IncQ-3 plasmids isolated from a wastewater treatment plant in Poland and to compare them with all known plasmids belonging to the IncQ-3 subgroup whose sequences were retrieved from the NCBI database. The complete nucleotide sequences of the novel plasmids were annotated and bioinformatic analyses were performed, including identification of core genes and auxiliary genetic load. Furthermore, functional experiments testing plasmid mobility were carried out. Phylogenetic analysis based on three core genes (repA, mobA/repB, and mobC) revealed the presence of three main clusters of IncQ-3 replicons. Apart from having a highly conserved core, the analyzed IncQ-3 plasmids were vectors of antibiotic resistance genes, including (I) the qnrS2 gene that encodes fluoroquinolone resistance and (II) β-lactam, trimethoprim, and aminoglycoside resistance genes within integron cassettes. Full article

(This article belongs to the Special Issue Antibiotic Resistance Genes: Spread and Evolution)

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10 pages, 503 KiB

Open AccessCommunication

Molecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii Isolated from War-Injured Patients from the Eastern Ukraine

by Paul G. Higgins, Ralf Matthias Hagen, Andreas Podbielski, Hagen Frickmann and Philipp Warnke

Antibiotics 2020, 9(9), 579; https://doi.org/10.3390/antibiotics9090579 - 5 Sep 2020

Cited by 19 | Viewed by 3468

Abstract

Recently, a total of 32 carbapenem- and fluoroquinolone-resistant Acinetobacter baumannii (Ab) isolates was isolated from war-injured patients who were treated at German Bundeswehr Hospitals, and preliminarily typed by “DiversiLab” repetitive elements sequence-based (rep-) PCR. Core genome-based sequence typing was also used to provide more detailed epidemiological information. From the clusters observed by rep-PCR, selected Ab strains were subjected to Next Generation Sequencing (NGS) in order to compare them with international outbreak-associated Ab strains and to identify MLST (multi-locus sequence type) lineages, as well as to identify known resistance genes. Accordingly, NGS indicated higher diversity than rep-PCR, but also confirmed likely transmission events. The identified acquired carbapenem-resistant genes comprised bla_OXA-23, bla_OXA-72 and bla_GES-12, as well as various other intrinsic and acquired resistance-associated genetic elements. All isolates clustered with the previously identified international clonal lineages IC1, IC2, IC6 and IC7, with corresponding Pasteur sequence types ST1, ST2, ST78 and ST25, respectively. In conclusion, the assessment confirmed a broad spectrum of resistance-associated genes in Ab isolated from war-injured patients from the Eastern Ukraine, and provided the first insights into locally abundant clonal lineages. Full article

(This article belongs to the Special Issue Antibiotic Resistance Genes: Spread and Evolution)

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15 pages, 4770 KiB

Open AccessArticle

Involvement of hpap2 and dgkA Genes in Colistin Resistance Mediated by mcr Determinants

by Alejandro Gallardo, María Ugarte-Ruiz, Marta Hernández, Pedro Miguela-Villoldo, David Rodríguez-Lázaro, Lucas Domínguez and Alberto Quesada

Antibiotics 2020, 9(9), 531; https://doi.org/10.3390/antibiotics9090531 - 22 Aug 2020

Cited by 8 | Viewed by 3786

Abstract

Plasmid-mediated colistin resistance (mcr) determinants are challenging the efficacy of polymyxins against Gram-negative pathogens. Among 10 mcr genes described so far, the major determinants mcr-1 and mcr-3 are found closely linked to hpap2 or dgkA genes, encoding a hypothetical phosphatidic acid phosphatase of type 2 (PAP2) and a diacylglycerol kinase, respectively, whose functions are still unknown. In this study, mcr-1, mcr-1–hpap2, mcr-3, and mcr-3–dgkA were expressed in Escherichia coli, and recombinant strains were analyzed to detect antimicrobial susceptibility and changes in the expression of genes involved in phospholipid metabolism. The mcr-1 or mcr-3 single genes were enough to drive growth on colistin selective media, although co-expression of linked genes conferred maximal antibiotic resistance. Expression of mcr determinants downregulated endogenous genes involved in lipopolysaccharide (LPS) modification or phospholipid recycling, although to different extents of repression: strong for arnB, ybjG, and pmrR; medium for eptA, lpxT, and dgkA; small for bacA and pgpB. Four of these genes (bacA, lpxT, pgpB, and ybjG) encode undecaprenyl pyrophosphate (UPP) phosphatases. In these conditions, cells presented resistance against bacitracin, an antibiotic that sequesters UPP from PAP2 enzymes. The hpap2 and dgkA genes might play a role in colistin resistance by compensating for phospholipid metabolism functions altered during LPS modification by colistin resistance determinants. Full article

(This article belongs to the Special Issue Antibiotic Resistance Genes: Spread and Evolution)

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