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Antibiotics
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When Communities Matter: Interplay between Mobile Genetic Elements and Antibiotic Resistance
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When Communities Matter: Interplay between Mobile Genetic Elements and Antibiotic Resistance

A special issue of Antibiotics (ISSN 2079-6382).

Deadline for manuscript submissions: closed (30 April 2024) | Viewed by 18045

Special Issue Editor

Prof. Dr. Antony T. Vincent

E-Mail Website
Guest Editor
Département des Sciences Animales, Université Laval, Quebec, QC G1V 0A6, Canada
Interests: pathogen adaptation; microbial network; microbiome; mobile genetic elements; antibiotic resistance; alternative treatments; swine; poultry; fish
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Antibiotic resistance is a significant issue worldwide. One of the biggest challenges associated with this phenomenon is that many resistance-conferring genes can be transferred horizontally between bacteria of the same ecological niche. Certain mobile genetic elements, such as plasmids, integrons, and transposons, participate in the mobilization of genes involved in antibiotic resistance. In addition to adopting a “One Health” vision, it is crucial to understand the molecular mechanisms responsible for the spread of antibiotic resistance genes. By having a better idea of the molecular mechanisms and determinants responsible for horizontal transfer of antibiotic resistance genes, and of the propensity of bacteria to carry out these transfers, we will be able to develop more efficient control and surveillance methods.

This Special Issue will center on horizontal transfers of antibiotic resistance genes and aims to bring together articles that deal with molecular determinants involved in this process. It will focus on but is not limited to the discovery and contribution of new mobile genetic elements that carry antibiotic resistance genes; on the study of gene exchanges in complex systems, such as the microbiota or the environment; and on the impact of human or agricultural activities on the spread of antibiotic resistance. Articles dealing with ways to limit the spread of antibiotic resistance genes are also particularly welcome.

Prof. Dr. Antony T. Vincent
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
  • bacterial community
  • horizontal transfers
  • integrons
  • microbiota
  • mobile genetic elements
  • plasmids
  • transposons

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Published Papers (5 papers)

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Research

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20 pages, 3595 KiB  
Article
Horizontal Gene Transfer and Drug Resistance Involving Mycobacterium tuberculosis
by Xuhua Xia
Antibiotics 2023, 12(9), 1367; https://doi.org/10.3390/antibiotics12091367 - 25 Aug 2023
Cited by 9 | Viewed by 2521
Abstract
Mycobacterium tuberculosis (Mtb) acquires drug resistance at a rate comparable to that of bacterial pathogens that replicate much faster and have a higher mutation rate. One explanation for this rapid acquisition of drug resistance in Mtb is that drug resistance may evolve in [...] Read more.
Mycobacterium tuberculosis (Mtb) acquires drug resistance at a rate comparable to that of bacterial pathogens that replicate much faster and have a higher mutation rate. One explanation for this rapid acquisition of drug resistance in Mtb is that drug resistance may evolve in other fast-replicating mycobacteria and then be transferred to Mtb through horizontal gene transfer (HGT). This paper aims to address three questions. First, does HGT occur between Mtb and other mycobacterial species? Second, what genes after HGT tend to survive in the recipient genome? Third, does HGT contribute to antibiotic resistance in Mtb? I present a conceptual framework for detecting HGT and analyze 39 ribosomal protein genes, 23S and 16S ribosomal RNA genes, as well as several genes targeted by antibiotics against Mtb, from 43 genomes representing all major groups within Mycobacterium. I also included mgtC and the insertion sequence IS6110 that were previously reported to be involved in HGT. The insertion sequence IS6110 shows clearly that the Mtb complex participates in HGT. However, the horizontal transferability of genes depends on gene function, as was previously hypothesized. HGT is not observed in functionally important genes such as ribosomal protein genes, rRNA genes, and other genes chosen as drug targets. This pattern can be explained by differential selection against functionally important and unimportant genes after HGT. Functionally unimportant genes such as IS6110 are not strongly selected against, so HGT events involving such genes are visible. For functionally important genes, a horizontally transferred diverged homologue from a different species may not work as well as the native counterpart, so the HGT event involving such genes is strongly selected against and eliminated, rendering them invisible to us. In short, while HGT involving the Mtb complex occurs, antibiotic resistance in the Mtb complex arose from mutations in those drug-targeted genes within the Mtb complex and was not gained through HGT. Full article
(This article belongs to the Special Issue When Communities Matter: Interplay between Mobile Genetic Elements and Antibiotic Resistance)
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12 pages, 723 KiB  
Article
Studying the Association between Antibiotic Resistance Genes and Insertion Sequences in Metagenomes: Challenges and Pitfalls
by Lucie Galiot, Xavier C. Monger and Antony T. Vincent
Antibiotics 2023, 12(1), 175; https://doi.org/10.3390/antibiotics12010175 - 14 Jan 2023
Cited by 7 | Viewed by 2465
Abstract
Antibiotic resistance is an issue in many areas of human activity. The mobilization of antibiotic resistance genes within the bacterial community makes it difficult to study and control the phenomenon. It is known that certain insertion sequences, which are mobile genetic elements, can [...] Read more.
Antibiotic resistance is an issue in many areas of human activity. The mobilization of antibiotic resistance genes within the bacterial community makes it difficult to study and control the phenomenon. It is known that certain insertion sequences, which are mobile genetic elements, can participate in the mobilization of antibiotic resistance genes and in the expression of these genes. However, the magnitude of the contribution of insertion sequences to the mobility of antibiotic resistance genes remains understudied. In this study, the relationships between insertion sequences and antibiotic resistance genes present in the microbiome were investigated using two public datasets. The first made it possible to analyze the effects of different antibiotics in a controlled mouse model. The second dataset came from a study of the differences between conventional and organic-raised cattle. Although it was possible to find statistically significant correlations between the insertion sequences and antibiotic resistance genes in both datasets, several challenges remain to better understand the contribution of insertion sequences to the motility of antibiotic resistance genes. Obtaining more complete and less fragmented metagenomes with long-read sequencing technologies could make it possible to understand the mechanisms favoring horizontal transfers within the microbiome with greater precision. Full article
(This article belongs to the Special Issue When Communities Matter: Interplay between Mobile Genetic Elements and Antibiotic Resistance)
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12 pages, 1721 KiB  
Article
Discovery of Highly Trimethoprim-Resistant DfrB Dihydrofolate Reductases in Diverse Environmental Settings Suggests an Evolutionary Advantage Unrelated to Antibiotic Resistance
by Stella Cellier-Goetghebeur, Kiana Lafontaine, Claudèle Lemay-St-Denis, Princesse Tsamo, Alexis Bonneau-Burke, Janine N. Copp and Joelle N. Pelletier
Antibiotics 2022, 11(12), 1768; https://doi.org/10.3390/antibiotics11121768 - 7 Dec 2022
Cited by 3 | Viewed by 2238
Abstract
Type B dihydrofolate reductases (DfrB) are intrinsically highly resistant to the widely used antibiotic trimethoprim, posing a threat to global public health. The ten known DfrB family members have been strongly associated with genetic material related to the application of antibiotics. Several dfrB [...] Read more.
Type B dihydrofolate reductases (DfrB) are intrinsically highly resistant to the widely used antibiotic trimethoprim, posing a threat to global public health. The ten known DfrB family members have been strongly associated with genetic material related to the application of antibiotics. Several dfrB genes were associated with multidrug resistance contexts and mobile genetic elements, integrated both in chromosomes and plasmids. However, little is known regarding their presence in other environments. Here, we investigated the presence of dfrB beyond the traditional areas of enquiry by conducting metagenomic database searches from environmental settings where antibiotics are not prevalent. Thirty putative DfrB homologues that share 62 to 95% identity with characterized DfrB were identified. Expression of ten representative homologues verified trimethoprim resistance in all and dihydrofolate reductase activity in most. Contrary to samples associated with the use of antibiotics, the newly identified dfrB were rarely associated with mobile genetic elements or antibiotic resistance genes. Instead, association with metabolic enzymes was observed, suggesting an evolutionary advantage unrelated to antibiotic resistance. Our results are consistent with the hypothesis that multiple dfrB exist in diverse environments from which dfrB were mobilized into the clinically relevant resistome. Our observations reinforce the need to closely monitor their progression. Full article
(This article belongs to the Special Issue When Communities Matter: Interplay between Mobile Genetic Elements and Antibiotic Resistance)
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18 pages, 1995 KiB  
Article
Resistance Genes, Plasmids, Multilocus Sequence Typing (MLST), and Phenotypic Resistance of Non-Typhoidal Salmonella (NTS) Isolated from Slaughtered Chickens in Burkina Faso
by Assèta Kagambèga, Elizabeth A. McMillan, Soutongnooma C. Bouda, Lari M. Hiott, Hazem Ramadan, Daniel K. Soro, Poonam Sharma, Sushim K. Gupta, Nicolas Barro, Charlene R. Jackson and Jonathan G. Frye
Antibiotics 2022, 11(6), 782; https://doi.org/10.3390/antibiotics11060782 - 8 Jun 2022
Cited by 8 | Viewed by 3570
Abstract
The emergence of antimicrobial-resistant bacteria in developing countries increases risks to the health of both such countries’ residents and the global community due to international travel. It is consequently necessary to investigate antimicrobial-resistant pathogens in countries such as Burkina Faso, where surveillance data [...] Read more.
The emergence of antimicrobial-resistant bacteria in developing countries increases risks to the health of both such countries’ residents and the global community due to international travel. It is consequently necessary to investigate antimicrobial-resistant pathogens in countries such as Burkina Faso, where surveillance data are not available. To study the epidemiology of antibiotic resistance in Salmonella, 102 Salmonella strains isolated from slaughtered chickens were subjected to whole-genome sequencing (WGS) to obtain information on antimicrobial resistance (AMR) genes and other genetic factors. Twenty-two different serotypes were identified using WGS, the most prevalent of which were Hato (28/102, 27.5%) and Derby (23/102, 22.5%). All strains analyzed possessed at least one and up to nine AMR genes, with the most prevalent being the non-functional aac(6′)-Iaa gene, followed by aph(6)-Id. Multi-drug resistance was found genotypically in 36.2% of the isolates for different classes of antibiotics, such as fosfomycin and β-lactams, among others. Plasmids were identified in 43.1% of isolates (44/102), and 25 plasmids were confirmed to carry AMR genes. The results show that chicken can be considered as a reservoir of antibiotic-resistant Salmonella strains. Due to the prevalence of these drug-resistant pathogens and the potential for foodborne illnesses, poultry processing and cooking should be performed with attention to prescribed safe handling methods to avoid cross-contamination with chicken products. Full article
(This article belongs to the Special Issue When Communities Matter: Interplay between Mobile Genetic Elements and Antibiotic Resistance)
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Review

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21 pages, 393 KiB  
Review
Pseudomonas fluorescens Complex and Its Intrinsic, Adaptive, and Acquired Antimicrobial Resistance Mechanisms in Pristine and Human-Impacted Sites
by Myllena Pereira Silverio, Gabriela Bergiante Kraychete, Alexandre Soares Rosado and Raquel Regina Bonelli
Antibiotics 2022, 11(8), 985; https://doi.org/10.3390/antibiotics11080985 - 22 Jul 2022
Cited by 14 | Viewed by 6258
Abstract
Pseudomonas spp. are ubiquitous microorganisms that exhibit intrinsic and acquired resistance to many antimicrobial agents. Pseudomonas aeruginosa is the most studied species of this genus due to its clinical importance. In contrast, the Pseudomonas fluorescens complex consists of environmental and, in some cases, [...] Read more.
Pseudomonas spp. are ubiquitous microorganisms that exhibit intrinsic and acquired resistance to many antimicrobial agents. Pseudomonas aeruginosa is the most studied species of this genus due to its clinical importance. In contrast, the Pseudomonas fluorescens complex consists of environmental and, in some cases, pathogenic opportunistic microorganisms. The records of antimicrobial-resistant P. fluorescens are quite scattered, which hinders the recognition of patterns. This review compiles published data on antimicrobial resistance in species belonging to the P. fluorescens complex, which were identified through phylogenomic analyses. Additionally, we explored the occurrence of clinically relevant antimicrobial resistance genes in the genomes of the respective species available in the NCBI database. Isolates were organized into two categories: strains isolated from pristine sites and strains isolated from human-impacted or metal-polluted sites. Our review revealed that many reported resistant phenotypes in this complex might be related to intrinsic features, whereas some of them might be ascribed to adaptive mechanisms such as colistin resistance. Moreover, a few studies reported antimicrobial resistance genes (ARGs), mainly β-lactamases. In-silico analysis corroborated the low occurrence of transferable resistance mechanisms in this Pseudomonas complex. Both phenotypic and genotypic assays are necessary to gain insights into the evolutionary aspects of antimicrobial resistance in the P. fluorescens complex and the possible role of these ubiquitous species as reservoirs of clinically important and transmissible ARGs. Full article
(This article belongs to the Special Issue When Communities Matter: Interplay between Mobile Genetic Elements and Antibiotic Resistance)
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