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ARS Home » Northeast Area » Wyndmoor, Pennsylvania » Eastern Regional Research Center » Characterization and Interventions for Foodborne Pathogens » Research » Publications at this Location » Publication #411824

Research Project: Molecular Analysis of Foodborne Pathogen Responses to Stressors

Location: Characterization and Interventions for Foodborne Pathogens

Title: Comparative genomics of extra intestinal pathogenic E. coli from human clinical and food samples

item Guragain, Manita
item Kanrar, Siddhartha
item Bosilevac, Joseph - Mick
item Dickey, Aaron
item Liu, Yanhong

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 3/18/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Introduction: Extraintestinal pathogenic Escherichia coli (ExPEC) causes a range of serious human diseases and complications, however, understanding of the sources of ExPEC is poor. Purpose: Comparative genomic analyses of ExPEC from human clinical and food (poultry) samples to assess the risk of poultry as a potential reservoir of high risk ExPEC. Methods: Forty human clinical and 33 poultry (chicken or turkey meat) isolates were confirmed to be ExPEC by multiplex PCR. Genomes were sequenced using long- or short-read technologies. Long read sequences were assembled using Flye 2.9.2. Assembly of short read sequences and characterization of all genome assemblies were performed using the GEAbash bioinformatic pipeline. Prevalence was compared using Fisher’s exact test. Results: Overall whole genome sequencing of ExPEC strains identified 94 virulence genes, 7 phylogroups, 32 sequence types (ST), and 29 antibiotic resistance genes (ARGs). Most of the virulence genes (65/94) were detected in both human and poultry isolates, with some virulence factors unique to each sample source. The majority of the human isolates (34/40) and poultry isolates (9/33) belonged to phylogroup B2 known for better persistence in the human gut and high virulence. Another predominant phylogroup among poultry isolates was phylogroup F (10/33), a group associated with devastating poultry diseases and potential zoonotic risk. Highly virulent ST95 was represented among strains from both sources. Prevalence of ARGs were higher in poultry (24/33) as compared to human isolates (18/40). Resistance against six different classes of antibiotics was identified in both poultry and human isolates. Significance: Distribution of poultry isolates across highly virulent phylogroups and STs, together with abundance of virulence factors and ARGs suggest that poultry may act as a source of high risk ExPEC leading to serious human diseases.