Genomic epidemiology and antimicrobial resistance dynamics of Salmonella in Jiangxi poultry/pork supply chains.

Abstract

This study investigated the genomic epidemiology, contamination hotspots, and antimicrobial resistance (AMR) profiles of Salmonella across the poultry and pork supply chains in Jiangxi Province, China, using 216 isolates (2015-2021). We observed distinct temporal dynamics, with S. typhimurium increasing by 67.5&#xa0;% (p&#xa0;<&#xa0;0.01) and S. enteritidis declining by 46&#xa0;% (p&#xa0;<&#xa0;0.05). Live poultry stalls showed significantly higher contamination (32.4&#xa0;% chicken, 28.7&#xa0;% pork) than supermarkets (p&#xa0;<&#xa0;0.001). Network analysis identified farms to slaughterhouses (weight&#xa0;=&#xa0;45) and live poultry markets (weight&#xa0;=&#xa0;35) as critical transmission interfaces. Alarming AMR rates were found for tetracycline (75.2-82.4&#xa0;%), ampicillin (70.3-79.8&#xa0;%), and sulfamethoxazole-trimethoprim (60.2-64.5&#xa0;%). Ciprofloxacin resistance was significantly higher in clinical isolates (55.3&#xa0;%) compared to food sources (p&#xa0;<&#xa0;0.01). Multidrug resistance affected 58-67.6&#xa0;% of isolates, with 25.3&#xa0;% of clinical isolates resistant to 6-9 drug classes. High-risk clonal lineages, particularly ST34-Typhimurium, exhibited extensive resistance. Geospatial mapping revealed Shangrao as a Typhimurium hotspot (p&#xa0;<&#xa0;0.01). A strong correlation between serotype prevalence and resistance (&#x3c1;&#xa0;=&#xa0;0.78, p&#xa0;<&#xa0;0.001) suggested co-selection. These findings provide actionable insights for mitigating Salmonella transmission and combating AMR in food production.