Decoding resistome profiles and horizontal transfer of antibiotic resistance genes across the pork production chain under One Health sectors.

The emergence of antimicrobial resistance has become a global threat to public health. Intensive antibiotic use in swine farming has accelerated the proliferation of antibiotic resistance genes (ARGs) in animal-derived foods, making the production chain a potential ARG transmission route to humans. However, shared resistome profiles and horizontal gene transfer (HGT) mechanisms along this chain remain unclear. Here, we systematically investigated the resistome profile, ARGs' host, and potential HGT of ARGs across interconnected swine farm, slaughterhouse, and retail market by metagenomic assembly and binning. From 42 metagenomes, 1354 ARG subtypes were identified, with 303 shared across all interfaces. Both microbiome and mobile genetic elements (MGEs) contributed to the variation in ARG profiles. Pseudomonadota were the dominant drivers that shape the resistome through plasmid-mediated HGT. Among the 133 reconstructed ARG-carrying genomes (ACGs), 38 of them carried multiple ARGs, indicating the potential mobility of ARGs. Notably, 3 ACGs taxonomically assigned to Pseudomonas_E alcaligenes, Serratia_J grimesii, and Escherichia coli carrying 9, 13, and 41 ARGs, respectively. Furthermore, MetaCHIP analysis uncovered 445 potential HGT events, and ARGs including CpxR, macB, fusA, and vanR were annotated as potentially transferred subtypes. This study decodes the resistome profiles and tracks horizontal ARG transfer at the community level across the entire pork supply chain - from swine farms to retail outlets. To our knowledge, few studies have explored ARG transmission subtypes and directional flows among humans, pigs, and environmental compartments in the pork production chain using metagenomic approaches. These findings highlight the important role of the pork production chain as a critical transmission vector for ARGs under One Health framework.