Special Issue "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: 30 September 2023 | Viewed by 2311

Special Issue 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
Special Issues, Collections and Topics in MDPI journals

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 2200 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 (2 papers)

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Research

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Article
Plasmid Costs Explain Plasmid Maintenance, Irrespective of the Nature of Compensatory Mutations
Antibiotics 2023, 12(5), 841; https://doi.org/10.3390/antibiotics12050841 - 01 May 2023
Cited by 1 | Viewed by 741
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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Review
Three Innovations of Next-Generation Antibiotics: Evolvability, Specificity, and Non-Immunogenicity
Antibiotics 2023, 12(2), 204; https://doi.org/10.3390/antibiotics12020204 - 18 Jan 2023
Cited by 2 | Viewed by 1121
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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