Genetic structure and antimicrobial resistance of foodborne Escherichia coli in Australia

Abstract

Poultry meat is thought to harbour the most “human-like” E. coli strains, capable of causing both intestinal and extra-intestinal infections in humans. Furthermore, poultry meat is also known to harbour multi-drug resistant E. coli strains. In this study, extensive sampling of retail poultry meat products sold in major supermarkets and independent butchers in Canberra was undertaken. Phenotyping and genotyping of the E. coli isolated from the meat samples was then performed to better understand the evolution and diversity of these strains and their significance to human health. Using a whole genome sequence based approach, the strains were then compared to clinical and commensal human E. coli isolates to determine if there is transmission between the two hosts. A highly diverse population of E. coli in poultry meat was identified in this study. Although the exact contamination route is hard to determine, our findings suggest that poultry meat is frequently contaminated, not only with E. coli isolates from poultry birds but also significantly from other sources, possibly during processing chains and transport. In addition, the genetic structure comparison of human and poultry meat E. coli strains indicate that there is cross-transmission between the two hosts, but at low levels. Therefore, poultry meat serves as a low risk transmission route for zoonotic E. coli strains that can cause extra-intestinal infections. Our findings also suggest that the risk of exposure to intestinal or diarrheal pathogenic E. coli strains through poultry meat consumption and handling is even lower than exposure to extra-intestinal pathogenic E. coli (ExPEC) strains. Furthermore, poultry meat in Canberra region does not serve as a highly significant carrier of antimicrobial resistant E. coli unlike several other countries. Resistance was commonly observed to antibiotic classes approved for use in poultry industries (like ampicillin and tetracycline), but was low for critically important antibiotics to humans which are banned in the industry (like fluoroquinolone and 3rd generation cephalosporins). In addition, no carbapenem and colistin resistance was observed, which has recently been identified in poultry meat products in many countries including China, United Kingdom, Denmark. Poultry meat in Canberra is therefore more frequently contaminated with E. coli strains from the birds rather than from other contamination sources. Show more