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Antibiotics
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The Evolution of Plasmid-Mediated Antimicrobial Resistance
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The Evolution of Plasmid-Mediated Antimicrobial Resistance

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 (20 May 2024) | Viewed by 4981

Special Issue Editors

Dr. Marta Oliva

E-Mail Website
Guest Editor
Department of Biosciences, Biotechnology and the Environment, University of Bari, Via Orabona, 4, 70125 Bari, Italy
Interests: antimicrobial resistance; mobile and mobilisable plasmids; genetic elements associated with antimicrobial resistance; horizontal transfer
Dr. Carla Calia

E-Mail Website
Guest Editor
Department of Biosciences, Biotechnology and the Environment, University of Bari, Via Orabona, 4, 70125 Bari, Italy
Interests: antimicrobial resistance; mobile and mobilisable genetic elements; genetic elements associated with antimicrobial resistance; horizontal transfer
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Antimicrobial resistance is a global problem of great public health concern. Bacteria infections caused by multidrug-resistant bacteria have increased over the last few decades and the WHO has forecasted that, by 2050, bacterial infections could become the leading cause of death for human beings. The spread of antimicrobial resistance is mainly mediated by the intra- and inter-species horizontal transfer of resistance genes. In this regard, plasmids play a key role. Indeed, their ability to spread among different bacteria-inhabiting environments, to acquire exogenous DNA sequences from chromosomes, as well as other plasmids and genetic elements (such as insertion sequences and transposons), makes these extra-chromosomal DNA molecules ideal vectors for the wide spread of antimicrobial resistance. Plasmid classification (e.g., orphan mob-associated oriTs) and organization (e.g., mosaic plasmids) have also recently been the subject of reviews and new lines of investigation. Adjacent to their role in antimicrobial resistance, plasmids represent a major driving force of prokaryote evolution. Knowledge on plasmids is still limited, and much work remains to be carried out in the exploration of the fascinating plasmid world. This Special Issue aims to collect new insights into their evolving role in the diffusion of antimicrobial resistance, and, more generally, to further extend the overall view of plasmids.

Dr. Marta Oliva
Dr. Carla Calia
Guest Editors

Manuscript Submission Information

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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

  • plasmids
  • antimicrobial resistance genes
  • mosaic
  • horizontal gene transfer
  • evolution

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Published Papers (3 papers)

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Research

13 pages, 1619 KiB  
Article
Genomic Characterization of Carbapenemase-Producing Enterobacter hormaechei, Serratia marcescens, Citrobacter freundii, Providencia stuartii, and Morganella morganii Clinical Isolates from Bulgaria
by Stefana Sabtcheva, Ivan Stoikov, Ivan N. Ivanov, Deyan Donchev, Magdalena Lesseva, Sylvia Georgieva, Deana Teneva, Elina Dobreva and Iva Christova
Antibiotics 2024, 13(5), 455; https://doi.org/10.3390/antibiotics13050455 - 16 May 2024
Cited by 2 | Viewed by 1340
Abstract
Carbapenemase-producing Enterobacter spp. Serratia marcescens, Citrobacter freundii, Providencia spp., and Morganella morganii (CP-ESCPM) are increasingly identified as causative agents of nosocomial infections but are still not under systematic genomic surveillance. In this study, using a combination of whole-genome sequencing and conjugation [...] Read more.
Carbapenemase-producing Enterobacter spp. Serratia marcescens, Citrobacter freundii, Providencia spp., and Morganella morganii (CP-ESCPM) are increasingly identified as causative agents of nosocomial infections but are still not under systematic genomic surveillance. In this study, using a combination of whole-genome sequencing and conjugation experiments, we sought to elucidate the genomic characteristics and transferability of resistance genes in clinical CP-ESCPM isolates from Bulgaria. Among the 36 sequenced isolates, NDM-1 (12/36), VIM-4 (11/36), VIM-86 (8/36), and OXA-48 (7/36) carbapenemases were identified; two isolates carried both NDM-1 and VIM-86. The majority of carbapenemase genes were found on self-conjugative plasmids. IncL plasmids were responsible for the spread of OXA-48 among E. hormaechei, C. freundii, and S. marcescens. IncM2 plasmids were generally associated with the spread of NDM-1 in C. freundii and S. marcescens, and also of VIM-4 in C. freundii. IncC plasmids were involved in the spread of the recently described VIM-86 in P. stuartii isolates. IncC plasmids carrying blaNDM-1 and blaVIM-86 were observed too. blaNDM-1 was also detected on IncX3 in S. marcescens and on IncT plasmid in M. morganii. The significant resistance transfer rates we observed highlight the role of the ESCPM group as a reservoir of resistance determinants and stress the need for strengthening infection control measures. Full article
(This article belongs to the Special Issue The Evolution of Plasmid-Mediated Antimicrobial Resistance)
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17 pages, 2227 KiB  
Article
Insights into the Evolution of IncR Plasmids Found in the Southern European Clone of the Monophasic Variant of Salmonella enterica Serovar Typhimurium
by Xenia Vázquez, Javier Fernández, Jürgen J. Heinisch, Rosaura Rodicio and M. Rosario Rodicio
Antibiotics 2024, 13(4), 314; https://doi.org/10.3390/antibiotics13040314 - 29 Mar 2024
Viewed by 1654
Abstract
Salmonella enterica subspecies enterica serovar 4,[5],12:i:- is a monophasic variant of S. Typhimurium which has emerged as a world-wide distributed pathogen in the last decades. Several clones have been identified within this variant, the European clone, the Spanish clone, the Southern European [...] Read more.
Salmonella enterica subspecies enterica serovar 4,[5],12:i:- is a monophasic variant of S. Typhimurium which has emerged as a world-wide distributed pathogen in the last decades. Several clones have been identified within this variant, the European clone, the Spanish clone, the Southern European clone and the U.S./American clone. The present study focused on isolates of the Southern European clone that were obtained from clinical samples at Spanish hospitals. The selected isolates were multidrug resistant, with most resistance genes residing on IncR plasmids that also carried virulence genes. These plasmids had a mosaic structure, comprising a highly reduced IncR backbone, which has acquired a large amount of exogenous DNA mostly derived from pSLT and IncI1-I(alfa) plasmids. Although composed of approximately the same elements, the investigated plasmids displayed a high diversity, consistent with active evolution driven by a wealth of mobile genetic elements. They comprise multiple intact or truncated insertion sequences, transposons, pseudo-compound transposons and integrons. Particularly relevant was the role of IS26 (with six to nine copies per plasmid) in generating insertions, deletions and inversions, with many of the rearrangements uncovered by tracking the patterns of eight bp target site duplications. Most of the resistance genes detected in the analyzed isolates have been previously associated with the Southern European clone. However, erm(B), lnu(G) and blaTEM-1B are novel, with the last two carried by a second resistance plasmid found in one of the IncR-positive isolates. Thus, evolution of resistance in the Southern European clone is not only mediated by diversification of the IncR plasmids, but also through acquisition of additional plasmids. All isolates investigated in the present study have the large deletion affecting the fljBA region previously found to justify the monophasic phenotype in the Southern European and U.S./American clones. An SNP-based phylogenetic analysis revealed the close relationship amongst our isolates, and support that those sharing the large fljBA deletion could be more heterogeneous than previously anticipated. Full article
(This article belongs to the Special Issue The Evolution of Plasmid-Mediated Antimicrobial Resistance)
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10 pages, 1267 KiB  
Communication
Phylogeny of Transferable Oxazolidinone Resistance Genes and Homologs
by Gábor Kardos, Levente Laczkó, Eszter Kaszab, Bálint Timmer, Krisztina Szarka, Eszter Prépost and Krisztián Bányai
Antibiotics 2024, 13(4), 311; https://doi.org/10.3390/antibiotics13040311 - 28 Mar 2024
Viewed by 1328
Abstract
Oxazolidinone resistance, especially transmissible resistance, is a major public health concern, and the origin of this resistance mechanism is not yet resolved. This study aims to delve into the phylogenetic origin of the transmissible oxazolidinone resistance mechanisms conferring cross-resistance to other drugs of [...] Read more.
Oxazolidinone resistance, especially transmissible resistance, is a major public health concern, and the origin of this resistance mechanism is not yet resolved. This study aims to delve into the phylogenetic origin of the transmissible oxazolidinone resistance mechanisms conferring cross-resistance to other drugs of human and veterinary importance. The amino acid sequences of the five cfr ribosomal methylases and optrA and poxtA were used as queries in searches against 219,549 bacterial proteomes in the NCBI RefSeq database. Hits with >40% amino acid identity and >80% query coverage were aligned, and phylogenetic trees were reconstructed. All five cfr genes yielded highly similar trees, with rlmN housekeeping ribosomal methylases located basal to the sister groups of S-adenosyl-methionine-dependent methyltransferases from various Deltaproteobacteria and Actinomycetia, including antibiotic-producing Streptomyces species, and the monophyletic group of cfr genes. The basal branches of the latter contained paenibacilli and other soil bacteria; they then could be split into the clades [cfr(C):cfr(E)] and [[cfr:cfr(B)]:cfr(D)], always with different Bacillaceae in their stems. Lachnospiraceae were encountered in the basal branches of both optrA and poxtA trees. The ultimate origin of the cfr genes is the rlmN housekeeping ribosomal methylases, which evolved into a suicide-avoiding methylase in antibiotic producers; a soil organism (Lachnospiraceae, Paenibacilli) probably acted as a transfer organism into pathogenic bacteria. In the case of optrA, the porcine pathogenic Streptococcus suis was present in all branches, while the proteins closest to poxtA originated from Clostridia. Full article
(This article belongs to the Special Issue The Evolution of Plasmid-Mediated Antimicrobial Resistance)
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