Genomic Analysis of Antibiotics Resistance in Pathogens, 2nd Edition

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 (30 April 2024) | Viewed by 12753

Special Issue Editor


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Guest Editor
INIAV - National Institute for Agrarian and Veterinarian Research / cE3c - Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Lisbon, Portugal
Interests: bacterial genomics; microbiome dynamics; evolution
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Special Issue Information

Dear Colleagues,

We have published one successful Special Issue, entitled "Genomic Analysis of Antibiotics Resistance in Pathogens". This result encouraged us to open a second volume on the same topic. As a continuation of the Special Issue published in 2022, this second volume will seek manuscript submissions pertaining to the horizontal transfer of antibiotic resistance genes, their dissemination and epidemiology, association with bacterial virulence, between bacterial genotypes and their phenotypes, or any related research topic. You are welcome to read the published papers in the first Special Issue “Genomic Analysis of Antibiotics Resistance in Pathogens”.

More information on the Special Issue can be found on the following website:

https://www.mdpi.com/journal/antibiotics/special_issues/Gene_pathogen.

Dr. Teresa V. Nogueira
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
  • genome analysis
  • metagenome analysis
  • horizontal gene transfer
  • clinical microbiology
  • veterinary microbiology
  • superbugs

Published Papers (5 papers)

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Research

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13 pages, 2054 KiB  
Article
Source Attribution of Antibiotic Resistance Genes in Estuarine Aquaculture: A Machine Learning Approach
by Helena Sofia Salgueiro, Ana Cristina Ferreira, Ana Sofia Ribeiro Duarte and Ana Botelho
Antibiotics 2024, 13(1), 107; https://doi.org/10.3390/antibiotics13010107 - 22 Jan 2024
Viewed by 1767
Abstract
Aquaculture located in urban river estuaries, where other anthropogenic activities may occur, has an impact on and may be affected by the environment where they are inserted, namely by the exchange of antimicrobial resistance genes. The latter may ultimately, through the food chain, [...] Read more.
Aquaculture located in urban river estuaries, where other anthropogenic activities may occur, has an impact on and may be affected by the environment where they are inserted, namely by the exchange of antimicrobial resistance genes. The latter may ultimately, through the food chain, represent a source of resistance genes to the human resistome. In an exploratory study of the presence of resistance genes in aquaculture sediments located in urban river estuaries, two machine learning models were applied to predict the source of 34 resistome observations in the aquaculture sediments of oysters and gilt-head sea bream, located in the estuaries of the Sado and Lima Rivers and in the Aveiro Lagoon, as well as in the sediments of the Tejo River estuary, where Japanese clams and mussels are collected. The first model included all 34 resistomes, amounting to 53 different antimicrobial resistance genes used as source predictors. The most important antimicrobial genes for source attribution were tetracycline resistance genes tet(51) and tet(L); aminoglycoside resistance gene aadA6; beta-lactam resistance gene blaBRO-2; and amphenicol resistance gene cmx_1. The second model included only oyster sediment resistomes, amounting to 30 antimicrobial resistance genes as predictors. The most important antimicrobial genes for source attribution were the aminoglycoside resistance gene aadA6, followed by the tetracycline genes tet(L) and tet(33). This exploratory study provides the first information about antimicrobial resistance genes in intensive and semi-intensive aquaculture in Portugal, helping to recognize the importance of environmental control to maintain the integrity and the sustainability of aquaculture farms. Full article
(This article belongs to the Special Issue Genomic Analysis of Antibiotics Resistance in Pathogens, 2nd Edition)
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23 pages, 3684 KiB  
Article
Tracing the Evolutionary Pathways of Serogroup O78 Avian Pathogenic Escherichia coli
by Eun-Jin Ha, Seung-Min Hong, Seung-Ji Kim, Sun-Min Ahn, Ho-Won Kim, Kang-Seuk Choi and Hyuk-Joon Kwon
Antibiotics 2023, 12(12), 1714; https://doi.org/10.3390/antibiotics12121714 - 9 Dec 2023
Cited by 1 | Viewed by 1486
Abstract
Avian pathogenic E. coli (APEC) causes severe economic losses in the poultry industry, and O78 serogroup APEC strains are prevalent in chickens. In this study, we aimed to understand the evolutionary pathways and relationships between O78 APEC and other E. coli strains. To [...] Read more.
Avian pathogenic E. coli (APEC) causes severe economic losses in the poultry industry, and O78 serogroup APEC strains are prevalent in chickens. In this study, we aimed to understand the evolutionary pathways and relationships between O78 APEC and other E. coli strains. To trace these evolutionary pathways, we classified 3101 E. coli strains into 306 subgenotypes according to the numbers and types of single nucleotide polymorphisms (RST0 to RST63-1) relative to the consensus sequence (RST0) of the RNA polymerase beta subunit gene and performed network analysis. The E. coli strains showed four apparently different evolutionary pathways (I-1, I-2, I-3, and II). The thirty-two Korean O78 APEC strains tested in this study were classified into RST4-4 (45.2%), RST3-1 (32.3%), RST21-1 (12.9%), RST4-5 (3.2%), RST5-1 (3.2%), and RST12-6 (3.2%), and all RSTs except RST21-1 (I-2) may have evolved through the same evolutionary pathway (I-1). A comparative genomic study revealed the highest relatedness between O78 strains of the same RST in terms of genome sequence coverage/identity and the spacer sequences of CRISPRs. The early-appearing RST3-1 and RST4-4 prevalence among O78 APEC strains may reflect the early settlement of O78 E. coli in chickens, after which these bacteria accumulated virulence and antibiotic resistance genes to become APEC strains. The zoonotic risk of the conventional O78 APEC strains is low at present, but the appearance of genetically distinct and multiple virulence gene-bearing RST21-1 O78 APEC strains may alert us to a need to evaluate their virulence in chickens as well as their zoonotic risk. Full article
(This article belongs to the Special Issue Genomic Analysis of Antibiotics Resistance in Pathogens, 2nd Edition)
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13 pages, 1046 KiB  
Article
Plasmid Costs Explain Plasmid Maintenance, Irrespective of the Nature of Compensatory Mutations
by João S. Rebelo, Célia P. F. Domingues and Francisco Dionisio
Antibiotics 2023, 12(5), 841; https://doi.org/10.3390/antibiotics12050841 - 1 May 2023
Cited by 1 | Viewed by 1943
Abstract
Conjugative plasmids often carry virulence and antibiotic-resistant genes. Therefore, understanding the behavior of these extra-chromosomal DNA elements gives insights into their spread. Bacteria frequently replicate slower after plasmids’ entry, an observation inconsistent with the plasmids’ ubiquity in nature. Several hypotheses explain the maintenance [...] Read more.
Conjugative plasmids often carry virulence and antibiotic-resistant genes. Therefore, understanding the behavior of these extra-chromosomal DNA elements gives insights into their spread. Bacteria frequently replicate slower after plasmids’ entry, an observation inconsistent with the plasmids’ ubiquity in nature. Several hypotheses explain the maintenance of plasmids among bacterial communities. However, the numerous combinations of bacterial species and strains, plasmids, and environments claim a robust elucidatory mechanism of plasmid maintenance. Previous works have shown that donor cells already adapted to the plasmid may use the plasmid as a ‘weapon’ to compete with non-adapted plasmid-free cells. Computer simulations corroborated this hypothesis with a wide range of parameters. Here we show that donor cells benefit from harboring conjugative plasmids even if compensatory mutations in transconjugant cells occur in the plasmid, not on chromosomes. The advantage’s leading causes are as follows: mutations take time to appear, many plasmids remain costly, and re-transfer of mutated plasmids usually occurs in sites distant to the original donors, implying little competition between these cells. Research in previous decades cautioned against uncritical acceptance of the hypothesis that resistance cost helps to preserve antibiotics’ effectiveness. This work gives a new twist to this conclusion by showing that costs help antibiotic-resistant bacteria to compete with plasmid-free cells even if compensatory mutations appear in plasmids. Full article
(This article belongs to the Special Issue Genomic Analysis of Antibiotics Resistance in Pathogens, 2nd Edition)
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Review

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23 pages, 1185 KiB  
Review
Dissemination of Enterococcal Genetic Lineages: A One Health Perspective
by Joana Monteiro Marques, Mariana Coelho, Andressa Rodrigues Santana, Daniel Pinto and Teresa Semedo-Lemsaddek
Antibiotics 2023, 12(7), 1140; https://doi.org/10.3390/antibiotics12071140 - 1 Jul 2023
Cited by 6 | Viewed by 2783
Abstract
Enterococcus spp. are commensals of the gastrointestinal tracts of humans and animals and colonize a variety of niches such as water, soil, and food. Over the last three decades, enterococci have evolved as opportunistic pathogens, being considered ESKAPE pathogens responsible for hospital-associated infections. [...] Read more.
Enterococcus spp. are commensals of the gastrointestinal tracts of humans and animals and colonize a variety of niches such as water, soil, and food. Over the last three decades, enterococci have evolved as opportunistic pathogens, being considered ESKAPE pathogens responsible for hospital-associated infections. Enterococci’s ubiquitous nature, excellent adaptative capacity, and ability to acquire virulence and resistance genes make them excellent sentinel proxies for assessing the presence/spread of pathogenic and virulent clones and hazardous determinants across settings of the human–animal–environment triad, allowing for a more comprehensive analysis of the One Health continuum. This review provides an overview of enterococcal fitness and pathogenic traits; the most common clonal complexes identified in clinical, veterinary, food, and environmental sources; as well as the dissemination of pathogenic genomic traits (virulome, resistome, and mobilome) found in high-risk clones worldwide, across the One Health continuum. Full article
(This article belongs to the Special Issue Genomic Analysis of Antibiotics Resistance in Pathogens, 2nd Edition)
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18 pages, 545 KiB  
Review
Three Innovations of Next-Generation Antibiotics: Evolvability, Specificity, and Non-Immunogenicity
by Hyunjin Shim
Antibiotics 2023, 12(2), 204; https://doi.org/10.3390/antibiotics12020204 - 18 Jan 2023
Cited by 7 | Viewed by 3884
Abstract
Antimicrobial resistance is a silent pandemic exacerbated by the uncontrolled use of antibiotics. Since the discovery of penicillin, we have been largely dependent on microbe-derived small molecules to treat bacterial infections. However, the golden era of antibiotics is coming to an end, as [...] Read more.
Antimicrobial resistance is a silent pandemic exacerbated by the uncontrolled use of antibiotics. Since the discovery of penicillin, we have been largely dependent on microbe-derived small molecules to treat bacterial infections. However, the golden era of antibiotics is coming to an end, as the emergence and spread of antimicrobial resistance against these antibacterial compounds are outpacing the discovery and development of new antibiotics. The current antibiotic market suffers from various shortcomings, including the absence of profitability and investment. The most important underlying issue of traditional antibiotics arises from the inherent properties of these small molecules being mostly broad-spectrum and non-programmable. As the scientific knowledge of microbes progresses, the scientific community is starting to explore entirely novel approaches to tackling antimicrobial resistance. One of the most prominent approaches is to develop next-generation antibiotics. In this review, we discuss three innovations of next-generation antibiotics compared to traditional antibiotics as specificity, evolvability, and non-immunogenicity. We present a number of potential antimicrobial agents, including bacteriophage-based therapy, CRISPR-Cas-based antimicrobials, and microbiome-derived antimicrobial agents. These alternative antimicrobial agents possess innovative properties that may overcome the inherent shortcomings of traditional antibiotics, and some of these next-generation antibiotics are not merely far-fetched ideas but are currently in clinical development. We further discuss some related issues and challenges such as infection diagnostics and regulatory frameworks that still need to be addressed to bring these next-generation antibiotics to the antibiotic market as viable products to combat antimicrobial resistance using a diversified set of strategies. Full article
(This article belongs to the Special Issue Genomic Analysis of Antibiotics Resistance in Pathogens, 2nd Edition)
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