Genomic diversity and virulence potential of high-priority critically important antimicrobial-resistant Escherichia coli from pork and chicken retail meat

Abstract

The occurrence of Escherichia coli resistant to high-priority critically important antimicrobials(HPCIA) in the food chain is a growing concern for food safety and public health. This study aimedto evaluate whether HPCIA-resistant E. coli isolated from pork and chicken meat at retail markets inLa Plata, Buenos Aires, Argentina, exhibit source-associated genomic differentiation through wholegenome sequencing. The isolates displayed a polyclonal population structure, encompassingmultiple phylogenetic groups and sequence types. Virulence gene profiles were highly diverse, withchicken-derived isolates harbouring a substantially higher number of virulence genes than porkisolates. Notably, one pork isolate carried a complete set of virulence genes characteristic ofdiarrheagenic E. coli. single Nucleotide Polymorphism-based phylogenetic analysis revealed severalclosely related subclusters, including strains recovered from both pork and chicken meat from thesame retail markets, suggesting recent clonal sharing or cross-contamination at the point of sale.These findings highlight the circulation of genetically diverse HPCIA-resistant E. coli in retail meat,underscoring the potential public health risk and the importance of monitoring resistance andvirulence determinants throughout the food production chain.