{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T22:48:07Z","timestamp":1791586087622,"version":"4.3.4"},"reference-count":76,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2025,4,28]],"date-time":"2025-04-28T00:00:00Z","timestamp":1745798400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"WHO Advisory Group on Integrated Surveillance of Antimicrobial Resistance (AGISAR) Research Project","award":["204517"],"award-info":[{"award-number":["204517"]}]},{"name":"WHO Advisory Group on Integrated Surveillance of Antimicrobial Resistance (AGISAR) Research Project","award":["98342"],"award-info":[{"award-number":["98342"]}]},{"name":"South African Research Chairs Initiative of the Department of Science and Technology and National Research Foundation of South Africa","award":["204517"],"award-info":[{"award-number":["204517"]}]},{"name":"South African Research Chairs Initiative of the Department of Science and Technology and National Research Foundation of South Africa","award":["98342"],"award-info":[{"award-number":["98342"]}]},{"name":"South African Medical Research Council (SAMRC) under a Self-Initiated Research Grant and UK Medical Research Council awarded to Professor Sabiha Essack","award":["204517"],"award-info":[{"award-number":["204517"]}]},{"name":"South African Medical Research Council (SAMRC) under a Self-Initiated Research Grant and UK Medical Research Council awarded to Professor Sabiha Essack","award":["98342"],"award-info":[{"award-number":["98342"]}]},{"name":"College of Health Sciences, University of Kwa-Zulu Natal, South Africa","award":["204517"],"award-info":[{"award-number":["204517"]}]},{"name":"College of Health Sciences, University of Kwa-Zulu Natal, South Africa","award":["98342"],"award-info":[{"award-number":["98342"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background\/Objectives: Intensive pig farming is a critical component of food security and economic activity in South Africa; however, it also presents a risk of amplifying antimicrobial resistance (AMR). This study provides genomic insights into antibiotic-resistant Escherichia coli (E. coli) circulating across the pork production chain, using a \u2018farm-to-fork\u2019 approach. Methods: A total of 417 samples were collected from various points along the production continuum, including the farm (n = 144), transport (n = 60), and abattoir (n = 213). E. coli isolates were identified using the Colilert-18 system, and their phenotypic resistance was tested against 20 antibiotics. Thirty-one isolates were selected for further characterization based on their resistance profiles and sampling sources, utilizing whole-genome sequencing and bioinformatic analysis. Results: The isolates exhibited varying resistance to critical antibiotics used in both human and animal health, including ampicillin (31\/31, 100%), tetracycline (31\/31, 100%), amoxicillin\u2013clavulanate (29\/31, 94%), chloramphenicol (25\/31, 81%), and sulfamethoxazole\u2013trimethoprim (10\/31, 33%). Genetic analysis revealed the presence of resistance genes for \u03b2-lactams (blaEC, blaTEM), trimethoprim\/sulfonamides (dfrA1, dfrA5, dfrA12, sul2, sul3), tetracyclines (tetA, tetB, tetR, tet34), aminoglycosides (aadA, strA, aph variants), and phenicols (catB4, floR, cmlA1), most of which were plasmid-borne. Virulome analysis identified 24 genes, including toxins and adhesion factors. Mobile genetic elements included 24 plasmid replicons, 43 prophages, 19 insertion sequence families, and 7 class 1 integrons. The E. coli isolates belonged to a diverse range of sequence types, demonstrating significant genetic variability. Further phylogenomic analysis revealed eight major clades, with isolate clustering by sequence type alongside South African environmental and clinical E. coli strains, regardless of their sampling source. Conclusions: The genetic complexity observed across the pork production continuum threatens food safety and may impact human health. These findings underscore the need for enhanced AMR monitoring in livestock systems and support the integration of AMR surveillance into food safety policy frameworks.<\/jats:p>","DOI":"10.3390\/antibiotics14050446","type":"journal-article","created":{"date-parts":[[2025,4,29]],"date-time":"2025-04-29T07:49:36Z","timestamp":1745912976000},"page":"446","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Genomic Insights of Antibiotic-Resistant Escherichia coli Isolated from Intensive Pig Farming in South Africa Using \u2018Farm-to-Fork\u2019 Approach"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9225-3897","authenticated-orcid":false,"given":"Shima E.","family":"Abdalla","sequence":"first","affiliation":[{"name":"Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5726-681X","authenticated-orcid":false,"given":"Linda A.","family":"Bester","sequence":"additional","affiliation":[{"name":"Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5194-2810","authenticated-orcid":false,"given":"Akebe L. K.","family":"Abia","sequence":"additional","affiliation":[{"name":"Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa"},{"name":"Environmental Research Foundation, Westville 3630, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9875-6716","authenticated-orcid":false,"given":"Mushal","family":"Allam","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates"},{"name":"Sequencing Core Facility, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg 2193, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4672-5915","authenticated-orcid":false,"given":"Arshad","family":"Ismail","sequence":"additional","affiliation":[{"name":"Sequencing Core Facility, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg 2193, South Africa"},{"name":"Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3357-2761","authenticated-orcid":false,"given":"Sabiha Y.","family":"Essack","sequence":"additional","affiliation":[{"name":"Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3551-3458","authenticated-orcid":false,"given":"Daniel G.","family":"Amoako","sequence":"additional","affiliation":[{"name":"Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa"},{"name":"Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,4,28]]},"reference":[{"key":"ref_1","unstructured":"World Health Organization (WHO) (2015). 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