Antimicrobial resistance genotypes and mobile genetic elements of poultry-derived escherichia coli: A retrospective genomic study of 100 isolates from the United States

Authors: Cho, Sohyun; RAMADAN, HAZEM - Mansoura University; Hiott, Lari; Frye, Jonathan; Jackson, Charlene

Submitted to: Pathogens
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/16/2025
Publication Date: 7/23/2025
Citation: Cho, S., Ramadan, H., Hiott, L.M., Frye, J.G., Jackson, C.R. 2025. Antimicrobial resistance genotypes and mobile genetic elements of poultry-derived escherichia coli: A retrospective genomic study of 100 isolates from the United States. Pathogens. 14:726. https://doi.org/10.3390/pathogens14080726.
DOI: https://doi.org/10.3390/pathogens14080726

Interpretive Summary: E. coli are commensal bacteria but they can transfer antibiotic resistance to pathogenic bacteria, including Salmonella. In this study, the genomes of 100 antibiotic resistant E. coli isolates associated with poultry rinsate samples of chicken meat intended for human consumption were sequenced. These were the E. coli isolates previously recovered from poultry carcass rinsates and poultry diagnostic samples in the US between 2001 and 2012 and they exhibited multidrug resistance or potential extended-spectrum ß-lactam (ESBL)-producing phenotypes. The genomic data was used to study antibiotic resistance genes that can potentially be transferred to other bacteria as well as mobile genetic elements which can facilitate the transfer. This retrospective study showed the genetic variabilities among the poultry-associated E. coli with a diverse range of antibiotic resistance gene, plasmids, and phages. E. coli isolates analyzed in the current study are from our previous collection of bacterial isolates recovered between 2001 and 2012 before more strict regulations were enforced on antibiotic use on food animals. As future research, comparing the sequences of our isolates with the sequences of more recent E. coli isolates will help us understand the trends of resistance genes and the genetic elements responsible for their transmission in the poultry settings and if the regulations and guidelines have helped mitigate the problem of antibiotic resistance in food animals in the US.

Technical Abstract: The presence of antibiotic resistance in commensal Escherichia coli may be an influential factor in persistence of resistance in pathogens. This is especially critical for E. coli that consumers may be exposed to through consumption of uncooked meat. In this study, E. coli isolates previously recovered from poultry in the US between 2001 and 2012 were whole genome sequenced to identify their antibiotic resistance genes and mobile genetic elements. The genomes of 98 E. coli isolates from poultry carcass rinsates and 2 isolates from poultry diagnostic samples with multidrug resistance or potential extended-spectrum ß-lactam (ESBL)-producing phenotypes, and the genetic variabilities among the E. coli were assessed. All E. coli isolates were positive for at least one antibiotic resistance gene and plasmid replicon, with 37 resistance genes and 27 plasmid replicons detected among the isolates. While no ESBL genes were detected, blaCMY-2 was the most common ß-lactamase gene and blaTEM and blaCARB-2 were also identified. Most isolates (95%) harbored at least one intact phage and as many as seven intact phages were identified in one isolate. These results show the occurrence of antibiotic resistance genes and mobile genetic elements in these 100 poultry-associated E. coli isolates which may be responsible for the resistance phenotypes exhibited by the isolates. This retrospective study also enables comparison of resistance genes and mobile genetic elements from more recent E. coli isolates associated with poultry to aid in understanding trends of both antibiotic resistance phenotypes and genotypes in the poultry setting over time.