Genomic Insights of Antibiotic-Resistant Isolated from Intensive Pig Farming in South Africa Using 'Farm-to-Fork' Approach.

: 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 () circulating across the pork production chain, using a 'farm-to-fork' approach. : 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). 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. : 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-clavulanate (29/31, 94%), chloramphenicol (25/31, 81%), and sulfamethoxazole-trimethoprim (10/31, 33%). Genetic analysis revealed the presence of resistance genes for β-lactams (, ), trimethoprim/sulfonamides (, , , , ), tetracyclines (, , , ), aminoglycosides (, , variants), and phenicols (, , ), 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 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 strains, regardless of their sampling source. : 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.