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Antibiotics
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The One Health Perspective: Unveiling Animal and Zoonotic Microbiota in...
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The One Health Perspective: Unveiling Animal and Zoonotic Microbiota in the Frame of Antimicrobial Resistance

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Antibiotics in Animal Health".

Deadline for manuscript submissions: 31 December 2026 | Viewed by 907

Special Issue Editors

Prof. Dr. Athina S. Tzora

E-Mail Website
Guest Editor
Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, School of Agriculture, University of Ioannina, 47150 Arta, Greece
Interests: AMR; milk and cheese microbiota; animals’ intestinal microbiota; mastitis in small ruminants; LAB (lactic acid bacteria); foodomics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Chrysoula Voidarou

E-Mail Website
Guest Editor
Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, School of Agriculture, University of Ioannina, 47150 Arta, Greece
Interests: microbiology; microbial ecology; microbiome, resistome, antimicrobial resistance, public health; food-borne diseases; food technology; food safety; nutrients; fermented foods; lactic acid bacteria
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Antimicrobial resistance (AMR) poses a serious and growing threat, endangering modern medicine, food security, and animal welfare. This Special Issue examines the critical role of both farm and companion animals, as well as animal-derived food, as sources and conduits for resistant bacteria. These reservoirs not only sustain and amplify resistant strains but also serve as vital pathways for disseminating resistance determinants across species and ecosystems, exacerbating the global public health crisis. The unregulated use of antimicrobials in veterinary practice, livestock and food production, has accelerated the emergence of multidrug-resistant pathogens compounding global health challenges. Operating under the One Health paradigm, this Special Issue emphasizes the need for interdisciplinary approaches that integrate conventional and innovative methodologies to elucidate molecular mechanisms, track environmental transmission routes and strengthen surveillance and control measures against AMR. By bridging microbiology, veterinary science, environmental research, and food safety, we aim to foster a comprehensive understanding of AMR dynamics within the One Health framework. We welcome rigorous contributions that provide actionable insights and comprehensive solutions to mitigate this escalating crisis, which is crucial for protecting health, ensuring food security, and promoting sustainability.

Prof. Dr. Athina S. Tzora
Prof. Dr. Chrysoula Voidarou
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 250 words) can be sent to the Editorial Office for assessment.

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 (AMR)
  • One Health approach
  • veterinary medicine
  • livestock production
  • foodborne pathogen reservoirs
  • epidemiological mapping
  • resistance mechanisms
  • microbiome
  • resistome
  • intervention

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Published Papers (1 paper)

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Research

26 pages, 4168 KB  
Article
Whole-Genome Analysis of Escherichia coli from One Health Sources: Evaluating Genetic Relatedness and Antimicrobial Resistance Carriage
by Alyssa Butters, Juan Jovel, Sheryl Gow, Cheryl Waldner and Sylvia L. Checkley
Antibiotics 2025, 14(11), 1151; https://doi.org/10.3390/antibiotics14111151 - 14 Nov 2025
Viewed by 651
Abstract
Background/Objectives: Due to the numerical dominance of environmental and commensal strains, understanding antimicrobial resistance (AMR) transmission in Escherichia coli requires consideration of non-clinical as well as pathogenic isolates. In this cross-sectional study, associations between the genetic context of non-clinical E. coli and [...] Read more.
Background/Objectives: Due to the numerical dominance of environmental and commensal strains, understanding antimicrobial resistance (AMR) transmission in Escherichia coli requires consideration of non-clinical as well as pathogenic isolates. In this cross-sectional study, associations between the genetic context of non-clinical E. coli and AMR carriage are examined in isolates sampled from different niches within a One Health continuum. Methods: Two hundred eighty-eight E. coli isolates collected in Alberta, Canada (2018–2019) from wastewater, well water, feces of broiler chickens and feedlot cattle, and retail beef and chicken meat were selected from existing surveillance collections using a stratified random sampling structure. Using short-read whole genome assemblies, phylogenetic relationships were inferred from pan-genome multiple sequence alignments. Principal coordinate analysis and permutational analysis of variance (PERMANOVA) of a Jaccard dissimilarity matrix derived from gene presence/absence data were used to investigate contributions of source and AMR strata to observe genetic dissimilarity. Population clustering and gene under- or over-representation by source and cluster were also explored. Results: Minimal phylogenetic segregation of isolates was noted based on source or AMR strata, and both contributed significant but small proportions of observed genetic dissimilarity, with the largest proportion attributed to phylogroup. There was notable diversity of E. coli within and between sources; however, in some larger clusters, differential gene presence/absence was potentially linked to ecological niche rather than source of isolation. Conclusions: This study highlights the ecological complexity of AMR in E. coli in non-clinical contexts, offering a novel lens on how niche-specific factors can influence population structure and AMR carriage. It also provides insight into apparent discrepancies in the literature regarding clustering of E. coli by source. These findings support a more integrative One Health approach to AMR surveillance, emphasizing the need to account for microbial diversity and niche-specific adaptation across interconnected systems. Full article
(This article belongs to the Special Issue The One Health Perspective: Unveiling Animal and Zoonotic Microbiota in the Frame of Antimicrobial Resistance)
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