A One Health perspective: Genomic insights into temporal trends of antimicrobial resistance and zoonotic transmission risks in Escherichia coli from human and swine.

Antimicrobial resistance (AMR) poses a significant challenge within the One Health framework. By integrating genomic data from 824 E. coli isolates obtained from 22 swine farms in southwestern China with 8432 publicly available genomes from human and swine sources, this study provides comprehensive insights into the temporal trends and divergence of AMR in human and swine E. coli populations, the risk of AMR transmission from swine to human, and the evolutionary mechanisms underlying the human adaptation of ST2 strains. The results revealed an overall increase in AMR until approximately 2016, followed by a subsequent decline. However, resistance to tetracyclines, quinolones, and phenicols continues to exhibit an upward trend, highlighting the urgency of enhancing regulatory measures targeting these drugs. Horizontal gene transfer play pivotal roles in shaping distinct AMR profiles in human and swine strains. ST2 E. coli was identified as a major carrier of AMR in both human and swine, and also served as the primary reservoir of blaNDM-5 within the human-associated lineage. During evolution, ST2 E. coli underwent significant genetic changes, including the enrichment of blaNDM-5 and remodeling of virulence factors, facilitating its transition from a generalist lineage colonizing both human and swine to a human-adapted lineage.