Antibiotics Use in Farms, 3rd Edition

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

Deadline for manuscript submissions: closed (30 April 2026) | Viewed by 1186

Special Issue Editor


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Guest Editor
Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
Interests: bacteria epidemiology; foodborne disease surveillance; molecular surveillance of bacteria; farm-to-fork studies; laboratory animal sciences; animal ethics and welfare education
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Special Issue Information

Dear Colleagues,

We have published two successful editions of the Special Issue titled “Antibiotics Use in Farms” and are now launching a third edition on the same topic.

We are especially interested in studies addressing additional drivers of resistance, such as the influence of ancient clonal lineages and innovative antibiotic strategies in production farms. We also welcome reports on urban farming communities, as these systems contribute to community protein sources, welfare, and health. The third edition will build on the rationale established in the previous Special Issues, highlighting research that fills ongoing gaps in understanding how antibiotic strategies influence resistance in various farming environments. Given the complex interplay between animals, humans, and the environment, we seek submissions presenting new epidemiological data, responses to policy changes, and evidence that advances effective antibiotic stewardship. This approach will drive practical progress based on insights gained from earlier editions and address unresolved challenges in resistance containment and sustainable antibiotic practices.

Dr. Linda Bester
Guest Editor

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.

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Keywords

  • non-antibiotic
  • alternative therapeutic options (to antibiotics)
  • alternative production strategies
  • vaccines
  • farm-sourced surveillance of antibiotic resistance
  • clonal lineages

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Published Papers (1 paper)

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Research

17 pages, 710 KB  
Article
Genomic Characterisation of Antibiotic-Resistant Escherichia coli from an Intensive Poultry Production System in the uMgungundlovu District, KwaZulu-Natal, South Africa: A Snapshot
by Nelisiwe S. Gumede, Joshua Mbanga, Charles Hunter, Melissa Ramtahal, Sabiha Y. Essack and Linda A. Bester
Antibiotics 2026, 15(2), 174; https://doi.org/10.3390/antibiotics15020174 - 5 Feb 2026
Viewed by 979
Abstract
Background: Intensive poultry production systems can act as reservoirs for antibiotic-resistant and multidrug-resistant (MDR) Escherichia coli, posing a public health risk through food and environmental transmission. Methods: This study investigated the genomic characteristics of antibiotic-resistant E. coli isolated from an intensive [...] Read more.
Background: Intensive poultry production systems can act as reservoirs for antibiotic-resistant and multidrug-resistant (MDR) Escherichia coli, posing a public health risk through food and environmental transmission. Methods: This study investigated the genomic characteristics of antibiotic-resistant E. coli isolated from an intensive poultry production system in the uMgungundlovu District, KwaZulu-Natal, South Africa. Chicken litter, wastewater, and floor swab samples were collected over three consecutive production cycles. Putative E. coli isolates were detected using the Colilert-18 system, cultured on eosin methylene blue agar, and genomically confirmed by quantitative PCR (q-PCR) targeting the uidA gene. Whole genome sequencing was performed using the Illumina MiSeq platform, followed by bioinformatic analyses to assess resistance genes, mobile genetic elements, and phylogenetic relationships. Results: Of 150 presumptive E. coli, 70 were genomically confirmed as E. coli and resistant to at least one antibiotic, with 74% exhibiting multidrug resistance. Resistance was highest to tetracycline (100%), ampicillin (94%), and trimethoprim–sulfamethoxazole (76%), while ciprofloxacin resistance was rare (3%). Genomic analysis identified multiple antibiotic resistance genes conferring resistance to fluoroquinolones, β-lactams, aminoglycosides, amphenicols, fosfomycin, and sulfonamides, as well as the disinfectant resistance gene qacI. These genes were frequently associated with mobile genetic elements, including plasmids, integrons, transposons, and insertion sequences. Predominant sequence types included ST155, ST48, ST1286, and ST602, with phylogenetic relatedness to poultry-associated isolates from Cameroon, Ghana, Nigeria, and Tanzania, as well as environmental E. coli strains previously identified in South Africa and Ghana. Conclusions: The detection of diverse, mobile MDR E. coli lineages in poultry environments clearly signals a substantial risk for resistance gene dissemination into the food chain and surrounding ecosystems. Immediate attention and intervention are warranted to mitigate public health threats. Full article
(This article belongs to the Special Issue Antibiotics Use in Farms, 3rd Edition)
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