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Antibiotics
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Antibiotic Resistance and Virulence in Bacterial Isolates: A Genomic Perspective...
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Antibiotic Resistance and Virulence in Bacterial Isolates: A Genomic Perspective from Human and Animal Sources

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 June 2025 | Viewed by 563

Special Issue Editors

Dr. Sónia Ramos

E-Mail Website
Guest Editor
Faculty of Veterinary Medicine, Centro Universitário Lisboa, Campo Grande, 376, 1749-024 Lisboa, Portugal
Interests: antibiotic resistance; multidrug-resistant isolates; genomic; food safety; one health
Special Issues, Collections and Topics in MDPI journals
Dr. Alexandra Nunes

E-Mail Website
Guest Editor
Portuguese National Institute of Health, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
Interests: microbial genomics; bioinformatics; microbiology; antibiotic resistance; virulence; transcriptomics; infectious diseases; public health
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Antibiotic resistance is a growing concern that affects not only human health but also veterinary medicine and agriculture. The ability of bacteria to develop resistance to multiple antibiotics can be attributed to various genetic mechanisms, including the acquisition of resistance genes through horizontal gene transfer. This Special Issue seeks to shed light on the genomic factors contributing to antibiotic resistance and the increased virulence of bacterial pathogens, which can lead to more severe infections and reduced treatment options.

This issue will cover a range of topics, including, but not limited to the following:

  1. Genomic characterization of multidrug resistant bacteria (MDRB) isolates from human and animal sources.
  2. Identification and analysis of novel resistance genes and mobile genetic elements.
  3. Comparative genomics to understand the evolution and spread of resistance mechanisms.
  4. The role of virulence factors in the pathogenesis of resistant infections.
  5. The impact of antibiotic use in agriculture on the emergence of resistance in zoonotic pathogens.
  6. Genomic surveillance and tracking of resistance genes in environmental reservoirs.
  7. Development of novel diagnostic tools and therapeutic strategies targeting resistant bacteria.

We invite original research articles, reviews, and perspectives that address the genomic aspects of antibiotic resistance and virulence in bacterial isolates from human and animal sources. Submissions should provide new insights into the mechanisms of resistance, the genomic basis of virulence, or the development of strategies to mitigate the spread of MDRB.

Dr. Sónia Ramos
Dr. Alexandra Nunes
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

  • MDRB
  • antimicrobial resistance
  • one health
  • mobile genetic elements
  • AMR
  • antimicrobial resistance gene

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Published Papers (1 paper)

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Research

16 pages, 1933 KiB  
Article
Mapping Integron-Associated AMR Genes in Whole Genome Sequences of Salmonella Typhimurium from Dairy Cattle
by Sami Ullah Khan Bahadur, Nora Jean Nealon, Joshua B. Daniels, Muhammad Usman Zaheer, Mo Salman and Sangeeta Rao
Antibiotics 2025, 14(7), 633; https://doi.org/10.3390/antibiotics14070633 - 21 Jun 2025
Viewed by 327
Abstract
Background: Antimicrobial resistance (AMR) is a critical global health threat, with AMR Salmonella enterica serovar Typhimurium strains being a major foodborne pathogen. Integrons, a type of mobile genetic element, capture and transfer resistance genes, thereby playing a role in the spread of AMR. Objectives: [...] Read more.
Background: Antimicrobial resistance (AMR) is a critical global health threat, with AMR Salmonella enterica serovar Typhimurium strains being a major foodborne pathogen. Integrons, a type of mobile genetic element, capture and transfer resistance genes, thereby playing a role in the spread of AMR. Objectives: This study aimed to characterize the locations of integrons carrying AMR genes within the whole genomes of 32 Salmonella Typhimurium isolates collected from dairy cattle by two U.S. Veterinary Diagnostic Laboratories between 2009 and 2012. Methods: Class I integrons were sequenced from PCR-amplified products. DNA was extracted, quantified, barcoded, and sequenced on the Illumina MiSeq platform. Whole genome sequences were trimmed and assembled using the SPAdes assembler in Geneious Prime®, and plasmids were identified with the PlasmidFinder pipeline in Linux. Integron locations were determined by aligning their sequences with whole genome contigs and plasmids, while AMR genes were identified through BLAST with the MEGARes 3.0 database and confirmed by alignment with isolate, plasmid, and integron sequences. Statistical analysis was applied to compare the proportions of isolates harboring integrons on their chromosome versus plasmids and also to examine the associations between integron presence and AMR gene presence. Results: Seven plasmid types were identified from all isolates: IncFII(S) (n = 14), IncFIB(S) (n = 13), IncC (n = 7), Inc1-I(Alpha) (n = 3), and ColpVC, Col(pAHAD28), and Col8282 (1 isolate each). Of the 32 isolates, 16 (50%) carried at least one size of integron. Twelve of them carried both 1000 and 1200 bp; 3 carried only 1000 bp and 1 carried 1800 bp integrons. Of the 15 isolates that carried 1000 bp integron, 12 harbored it on IncFIB(S) plasmids, 2 on IncC plasmids, and 1 on the chromosome. The 1200 bp integrons from all 12 isolates were located on chromosomes. There were significant positive associations between the presence of integrons and the presence of several AMR genes including sul1, aadA2, blaCARB-2, qacEdelta1, tet(G), and floR (p < 0.05). AMR genes were located as follows: aadA2 on IncFIB(S) and IncC plasmids; blaCMY-2 on IncC plasmid; qacEdelta1 on IncFIB(S), IncC, and chromosome; blaCARB-2, floR, tet(A) and tet(G) on the chromosome. Conclusions: The findings highlight the genomic and plasmid complexity of Salmonella Typhimurium which is impacted by the presence and location of integrons, and this study provides genomic insights that can inform efforts to enhance food safety and protect both animal and public health. Full article
(This article belongs to the Special Issue Antibiotic Resistance and Virulence in Bacterial Isolates: A Genomic Perspective from Human and Animal Sources)
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