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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Egg and Poultry Production Safety Research Unit » Research » Publications at this Location » Publication #395317

Research Project: Reduction of Foodborne Pathogens and Antimicrobial Resistance in Poultry Production Environments

Location: Egg and Poultry Production Safety Research Unit

Title: Chicken production and human clinical Escherichia coli isolates differ in their carriage of antimicrobial resistance and virulence factors

item WOYDA, REED - Colorado State University
item Oladeinde, Adelumola - Ade
item ABDO, ZAID - Colorado State University

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/17/2022
Publication Date: 1/18/2023
Citation: Woyda, R., Oladeinde, A., Abdo, Z. 2023. Chicken production and human clinical Escherichia coli isolates differ in their carriage of antimicrobial resistance and virulence factors. Applied and Environmental Microbiology.

Interpretive Summary: Pathogenic Escherichia coli causes disease in both humans and food-producing animals. E. coli etiology is dependent on a repertoire of virulence factors and antimicrobial resistance genes. Food-borne outbreaks are highly associated with the consumption of under cooked and contaminated food products. This association highlights the need to understand the genetic factors that make E. coli virulent and pathogenic in humans and poultry. This research shows that E. coli isolates originating from human clinical settings and chicken production harbor different antimicrobial resistance genes and virulence factors that can be used to classify them into phylogroups and host origins. In addition, to aid in the repeatability and reproducibility of the results presented in this study, we have made a public repository of the bioinformatic tool developed for the analyses performed and have provided the National Center for Biotechnology Information associated with the E. coli genomes analyzed.

Technical Abstract: Contamination of food animal products by Escherichia coli (E. coli) is a leading cause of food-borne disease outbreaks, hospitalizations, and deaths in humans. Chicken is currently the most consumed meat both in the United States and across the globe according to the United States Department of Agriculture. Although E. coli is a ubiquitous commensal bacterium of the gut of humans and animals, its ability to acquire antimicrobial resistance (AMR) genes and virulence factors (VF) can lead to the emergence of pathogenic strains that are resistant to critically important antibiotics. Thus, it is important to identify the genetic factors that contribute to the virulence and AMR of E. coli. In this study, we performed an in-depth genomic evaluation of the AMR genes and VF of E. coli genomes available through National Antimicrobial Resistance Monitoring System GenomeTrackr database. Our objective was to determine the genetic relatedness of chicken production isolates and human clinical isolates. To achieve this aim, we first developed a massively parallel analytical pipeline (Reads2Resistome) to accurately characterize the resistome of each E. coli genome including the AMR and VF harbored. We used Random Forests and hierarchical clustering to show that AMR genes and VF are sufficient to classify isolates into different pathogenic phylogroups and host origin. We found that the presence of key type III secretion system and AMR genes differentiated human clinical isolates from chicken production isolates. These results further improve our understanding of the interconnected role AMR and VF play in shaping the evolution of pathogenic E. coli strains.