One Health genomic surveillance identifies potential genetic links of antimicrobial-resistant foodborne pathogens across sectors

Foodborne pathogens and antimicrobial resistance are major global health concerns. The integration and analysis of genomic surveillance data across human, animal, and environmental sectors remain a critical challenge in the study of foodborne bacteria. Here we investigate potential cross-sector genetic links between antimicrobial-resistant isolates from food (mainly chicken meat), animals (mainly cecal and rectal samples), and humans (clinical cases) by comparing whole-genome sequences of non-typhoidal Salmonella (n = 1,613), Campylobacter (n = 682), and Enterococcus (n = 72) collected from these sectors across Japan. For Salmonella, we identify closely related human- and food-derived S. Blockley isolates carrying blaCTX-M-15, with pairwise SNP distances of 6–10 SNPs, as well as S. Agona isolates carrying fosA7.2, with pairwise SNP distances of 13–15 SNPs, suggesting that resistant Salmonella strains are shared between human and food sectors. For Campylobacter, we identified closely related human- and food-derived ST-22 isolates carrying a tetracycline resistance gene and a fluoroquinolone resistance-conferring gyrA mutation, with a pairwise SNP distance of 4 SNPs. These findings highlight potential genetic links of antimicrobial-resistant foodborne bacteria between food and humans. In this study, the authors use nationwide genomic data collected across sectors in Japan to identify closely related antimicrobial-resistant Salmonella and Campylobacter isolates in food and humans, highlighting the value of integrated One Health surveillance.