Resident or transient? Whole-genome approach to tracking colistin-resistant Escherichia coli in the broiler chicken processing chain

This study presents a genome-informed surveillance model to investigate the persistence and spread of colistin-resistant Escherichia coli in broiler chicken processing. The study targeted a high-throughput poultry facility—previously linked to retail meat contamination by colistin-resistant E. coli and Salmonella—where 200 carcasses were sampled across ten production batches to assess the prevalence and genomic characteristics of antimicrobial-resistant strains within the processing line. We analyzed one E. coli isolate per carcass to characterize antimicrobial resistance (AMR), and utilized whole-genome sequencing (WGS) to delineate phylogeny, virulence, AMR determinants, and plasmid content. Colistin-resistant E. coli isolates were detected in all production batches and were confirmed in 10.5 % (21/200) of the carcasses, with all isolates carrying the mcr-1.1 gene. Notably, 57.1 % of these isolates also harbored a PmrB Y358N putative colistin resistance mutation. Phylogenetic analysis revealed substantial diversity, with 31 sequence types detected; however, six isolates belonging to ST162 were identified as a resident strains cluster, persisting over four months and from multiple farms and flocks. All colistin-resistant E. coli isolates were phenotypically multidrug-resistant (MDR), carrying 10–25 AMR resistance genes per genome, including ESBL genes such as bla_CTX-M-55 (57.1 %). Virulence profiling showed a high prevalence of iron acquisition, serum resistance, and efflux-related genes, with an average of 22.5 putative virulence factors per isolate. Plasmidome analysis (n = 20 plasmids) revealed the dominance of IncI2 (60 %) and IncHI2-type replicons, with 90 % of plasmids predicted to be conjugative. Mobile genetic elements involved in horizontal gene transfer, such as MOBP relaxases and MPF-T systems, were prevalent (70 %), indicating a high potential for plasmid-mediated dissemination of AMR genes within the sampled isolates. This work offers a scalable model for processing facility-level AMR tracking and reinforces the value of WGS for industry-led food safety risk management, particularly for high-priority AMR determinants such as colistin resistance.