Whole-genome sequence-based comparison of antimicrobial resistant diarrheagenic Escherichia coli in pork and chicken production chains in Korea

Abstract

Diarrheagenic Escherichia coli (DEC) is a serious public health threat. We investigated the distribution, antimicrobial resistance, and molecular characteristics of DEC in pork and chicken production chains following the “One Health” approach. We collected 1567 pig- and 771 chicken-associated samples from animal farms, slaughterhouses, and retail markets. Of these samples, we identified 150 DEC isolates, with 73 (4.7 %) originating from pigs and 77 (10 %) from chickens. DEC risk of contamination in the final product (meat) was significantly higher in chickens (27.3 %) compared to pigs (0.5 %). In addition, carryover meat contamination was observed by clones originating from slaughterhouses in the chicken meat production chain. The resistance of chicken-associated isolates compared to pig-associated isolates to most antimicrobial agents was higher. Phylogenetic analysis following whole-genome sequencing of 150 DEC showed distinct lineages based on the host species, resulting in 20 clusters and 16 singletons. Multilocus sequence typing and serotyping revealed 25 and 30 different sequence types (STs) and serotypes, respectively. Human infection-related STs, including ST10 (11 %), ST23 (2.3 %), and ST48 (6.8 %), along with serotypes O89 (12.3 %), O26 (6.8 %), O103 (5.5 %), O121 (2.7 %), and O145 (2.7 %), were commonly detected in pig-associated isolates, emphasizing a zoonotic risk. Furthermore, the presence of various plasmids containing antimicrobial resistance and virulence genes was evident, posing a risk of spreading these genes to clinically important pathogens. Therefore, implementing effective control programs to reduce the prevalence of antimicrobial-resistant DEC in food production systems is important.