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Antibiotics
Special Issues
Genomic Characterization of Antimicrobial Resistance and Evolution Mechanism of Bacteria
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Genomic Characterization of Antimicrobial Resistance and Evolution Mechanism of Bacteria

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 June 2024) | Viewed by 2368

Special Issue Editors

Dr. Daniel Gyamfi Amoako

E-Mail Website
Guest Editor
1. Department of Pathobiology, University of Guelph, Guelph, ON, Canada
2. Antimicrobial Research Unit, College of Health Sciences, University of KwaZuluNatal, Durban 4000, South Africa
Interests: antimicrobial resistance; molecular genetics; one-health genomics; pathogenomics; applied bioinformatics; machine learning analytics
Special Issues, Collections and Topics in MDPI journals
Dr. Linda Bester

E-Mail Website
Guest Editor
1. College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
2. Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
Interests: bacteria epidemiology; molecular surveillance of bacteria; one-health genomics; zoonotic pathogens; human health risk
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the ever-evolving battle against antimicrobial resistance (AMR), our understanding of the genomic landscape of bacteria and their mechanisms of evolution has become pivotal. In bacteria, resistance to antibiotics is determined by genetic factors such as chromosomes, plasmids or other movable genetic elements. Although antimicrobial resistance genes (ARGs) typically exhibit significant sequence variability, such as the impact of different concentrations of antibiotics on their genomic dynamics, the impact of this diversity on AMR is still unclear. Therefore, understanding the dynamic changes and mobilization of antibiotic resistance genes in humans, animals, plants and environmental microorganisms through genomics and metagenomics methods is crucial.

This Special Issue seeks to foster a comprehensive understanding of the genetic underpinnings of bacterial antimicrobial resistance and the evolutionary dynamics that underlie these adaptations.

Dr. Daniel Gyamfi Amoako
Dr. Linda Bester
Guest Editors

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

  • antimicrobial resistance mechanism
  • mobile genetic element
  • horizontal gene transfer
  • resistome
  • evolution
  • molecular phylogenetics
  • genomics
  • bioinformatics analysis
  • next-generation sequencing

Published Papers (2 papers)

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Research

14 pages, 1508 KiB  
Article
Genomic Characterization of Multidrug-Resistant Enterobacteriaceae Clinical Isolates from Southern Thailand Hospitals: Unraveling Antimicrobial Resistance and Virulence Mechanisms
by Thunchanok Yaikhan, Sirikan Suwannasin, Kamonnut Singkhamanan, Sarunyou Chusri, Rattanaruji Pomwised, Monwadee Wonglapsuwan and Komwit Surachat
Antibiotics 2024, 13(6), 531; https://doi.org/10.3390/antibiotics13060531 - 6 Jun 2024
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Abstract
The emergence and spread of antimicrobial resistance (AMR) among Enterobacteriaceae pose significant threats to global public health. In this study, we conducted a short-term surveillance effort in Southern Thailand hospitals to characterize the genomic diversity, AMR profiles, and virulence factors of Enterobacteriaceae strains. [...] Read more.
The emergence and spread of antimicrobial resistance (AMR) among Enterobacteriaceae pose significant threats to global public health. In this study, we conducted a short-term surveillance effort in Southern Thailand hospitals to characterize the genomic diversity, AMR profiles, and virulence factors of Enterobacteriaceae strains. We identified 241 carbapenem-resistant Enterobacteriaceae, of which 12 were selected for whole-genome sequencing (WGS) and genome analysis. The strains included Proteus mirabilis, Serratia nevei, Klebsiella variicola, Klebsiella aerogenes, Klebsiella indica, Klebsiella grimontii, Phytobacter ursingii, Phytobacter palmae, Kosakonia spp., and Citrobacter freundii. The strains exhibited high levels of multidrug resistance, including resistance to carbapenem antibiotics. Whole-genome sequencing revealed a diverse array of antimicrobial resistance genes (ARGs), with strains carrying genes for ß-lactamase, efflux pumps, and resistance to other antibiotic classes. Additionally, stress response, metal tolerance, and virulence-associated genes were identified, highlighting the adaptability and pathogenic potential of these strains. A plasmid analysis identified several plasmid replicons, including IncA/C2, IncFIB(K), and Col440I, as well as several plasmids identical to those found globally, indicating the potential for the horizontal gene transfer of ARGs. Importantly, this study also identified a novel species of Kosakonia spp. PSU27, adding to the understanding of the genetic diversity and resistance mechanisms of Enterobacteriaceae in Southern Thailand. The results reported in this study highlight the critical importance of implementing effective antimicrobial management programs and developing innovative treatment approaches to urgently tackle AMR. Full article
(This article belongs to the Special Issue Genomic Characterization of Antimicrobial Resistance and Evolution Mechanism of Bacteria)
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18 pages, 2320 KiB  
Article
Genomic Epidemiology of C2/H30Rx and C1-M27 Subclades of Escherichia coli ST131 Isolates from Clinical Blood Samples in Hungary
by Kinga Tóth, Ivelina Damjanova, Levente Laczkó, Lilla Buzgó, Virág Lesinszki, Erika Ungvári, Laura Jánvári, Adrienn Hanczvikkel, Ákos Tóth and Dóra Szabó
Antibiotics 2024, 13(4), 363; https://doi.org/10.3390/antibiotics13040363 - 16 Apr 2024
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Abstract
Extended-spectrum β-lactamase-producing Escherichia coli ST131 has become widespread worldwide. This study aims to characterize the virulome, resistome, and population structure of E. coli ST131 isolates from clinical blood samples in Hungary. A total of 30 C2/H30Rx and 33 C1-M27 ST131 isolates were selected [...] Read more.
Extended-spectrum β-lactamase-producing Escherichia coli ST131 has become widespread worldwide. This study aims to characterize the virulome, resistome, and population structure of E. coli ST131 isolates from clinical blood samples in Hungary. A total of 30 C2/H30Rx and 33 C1-M27 ST131 isolates were selected for Illumina MiSeq sequencing and 30 isolates for MinION sequencing, followed by hybrid de novo assembly. Five C2/H30Rx and one C1-M27 cluster were identified. C1-M27 isolates harbored the F1:A2:B20 plasmid in 93.9% of cases. Long-read sequencing revealed that blaCTX-M-27 was on plasmids. Among the C2/H30Rx isolates, only six isolates carried the C2-associated F2:A1:B- plasmid type. Of 19 hybrid-assembled C2/H30Rx genomes, the blaCTX-M-15 gene was located on plasmid only in one isolate, while in the other isolates, ISEcp1 or IS26-mediated chromosomal integration of blaCTX-M-15 was detected in unique variations. In one isolate a part of F2:A1:B- plasmid integrated into the chromosome. These results suggest that CTX-M-15-producing C2/H30Rx and CTX-M-27-producing C1-M27 subclades may have emerged and spread in different ways in Hungary. While blaCTX-M-27 was carried mainly on the C1/H30R-associated F1:A2:B20 plasmid, the IncF-like plasmids of C2/H30Rx or its composite transposons have been incorporated into the chromosome through convergent evolutionary processes. Full article
(This article belongs to the Special Issue Genomic Characterization of Antimicrobial Resistance and Evolution Mechanism of Bacteria)
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