Molecular Epidemiology of blaNDM-Positive E. coli in Jiangsu Chicken Production Chain

The emergence of New Delhi metallo-β-lactamase (NDM)-producing Escherichia coli (E. coli) in the food production chain poses a serious public health threat. This study aimed to investigate the prevalence and molecular characteristics of blaNDM-carrying E. coli along the chicken production chain (farms, slaughterhouses, and supermarkets) in Jiangsu Province, China. Between 2023 and 2025, 408 samples were collected, recovering 39 blaNDM-positive E. coli isolates (9.56%). Isolation rates were 10.4% (26/250) in farms, 10.1% (11/108) in slaughterhouses, and 4.0% (2/50) in supermarkets. Whole-genome sequencing (WGS) identified blaNDM-5 as the dominant variant, alongside the first detection of blaNDM-13 in local farm environments. All isolates exhibited high-level resistance to meropenem (MIC: 16–128 μg/mL) and universal resistance (100%) to ampicillin, cefoxitin, ceftiofur, and sulfisoxazole. Notably, 41.03% and 7.69% of strains co-harbored the polymyxin resistance gene mcr-1.1 and the tigecycline resistance gene tet(X4), respectively. Isolates carried an average of 19.5 antimicrobial resistance genes, with IncFIB (AP001918) (82.05%) identified as the dominant plasmid replicon. Multilocus sequence typing (MLST) revealed 18 distinct sequence types (STs), with ST156 and ST155 being the most prevalent. Phylogenetic analysis confirmed slaughterhouses as critical hubs for cross-contamination, evidenced by shared STs (ST1158, ST155, ST162) and minimal SNP differences (1–11) between environment and carcass isolates. Furthermore, the detection of clinically relevant ST10 and ST69 clones in supermarket retail chicken meat underscores a direct foodborne transmission risk to humans. These findings highlight the poultry supply chain as a significant reservoir of multidrug-resistant blaNDM-positive E. coli. Accordingly, we recommend enhanced biosecurity protocols and stricter restrictions and controls on antimicrobial use in broiler farms.