Slaughtered swine as convergence hotspots for antimicrobial-resistant and disinfectant-tolerant Escherichia coli originating from humans and farm animals

This study presents regional One Health surveillance of Escherichia coli across a farm–slaughterhouse–human continuum in rural China, clarifying where hazardous strains co-carrying clinically important antimicrobial-resistance genes and disinfectant-tolerance determinants are enriched and disseminated. We analyzed 300 E. coli isolates, comprising 200 non-clinical and 100 clinical isolates. The non-clinical isolates were recovered from 526 samples collected across poultry and swine farms, a swine slaughterhouse, community carriers, and environmental matrices, while the clinical isolates were obtained from a local hospital. Populations were strongly source-structured. Clinical isolates were dominated by high-risk lineages ST1193 and ST131, while animal isolates were enriched for ST155. Third-generation cephalosporin resistance was near-universal in patients and slaughtered swine (97.7–100%) but low in farmed swine (8.3%), indicating pronounced amplification at the slaughterhouse interface. Accessory-genome profiling showed source-specific hazard signatures. Animal isolates carried the highest burden of resistance and stress response genes, whereas clinical isolates were enriched in virulence determinants ( iuc , ybt , iss ) and highly mobile, high-priority resistance features, yielding comparable resistance health-risk indices. Notably, slaughtered swine isolates co-carried bla CTX-M-14 , floR , and qac , linking 3GCR, farm-associated phenicol resistance, and disinfectant tolerance in a single hotspot. A gene-based XGBoost source-attribution model identified slaughterhouses as critical convergence nodes for high-risk E. coli and mobile resistance elements.