Genotypic Characterization of Virulence Factors in Extended-Spectrum Beta-Lactamase (ESBL)-Producing Escherichia coli Strains from Chickens in Hungary

TL;DR

This study identifies virulence genes in E. coli from Hungarian chickens, showing they have zoonotic potential but lack gut-specific pathotypes.

Contribution

The study provides new insights into the genotypic characteristics of ExPEC pathotypes in poultry-derived E. coli strains in Hungary.

Findings

Most isolates contained virulence genes associated with ExPEC pathotypes like UPEC, APEC, and NMEC.

Fitness-related genes for iron acquisition were highly prevalent.

Enteric pathotype markers were completely absent in all isolates.

Abstract

Background: The increasing attention on extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strains isolated from poultry flocks stems from concerns about their virulence potential and zoonotic risk. Of particular significance is the identification of extraintestinal pathogenic E. coli (ExPEC) pathotypes in poultry, as these strains pose not only animal health concerns but also serious threats to food safety and public health. Mapping the genetic background of pathogenicity and antimicrobial resistance is essential for risk assessment and the development of effective control strategies. Methods: A total of 87 E. coli isolates were isolated from tracheal and cloacal swab samples collected from healthy chickens between 2022 and 2023. Whole-genome sequencing was performed using Illumina and MGI next-generation sequencing platforms. Bioinformatic analyses were conducted to identify virulence-associated genes and pathotype markers using multiple reference databases, including VirulenceFinder. The frequency of virulence genes was summarized both in tabular form and visualized through graphical representations. Results: A substantial proportion of the isolates harbored virulence genes linked to various ExPEC pathotypes, particularly uropathogenic E. coli (UPEC), avian pathogenic E. coli (APEC), and neonatal meningitis-causing E. coli (NMEC). The most frequently detected colonization factors included members of the fim, pap, ecp, and fae gene families. Among fitness-related genes, iron acquisition systems—ent, chu, iro, iuc, fep, and ybt—were especially prevalent. Classic UPEC-associated genes such as pap and fimH, along with the APEC-related iutA and vat, were found at high frequencies. Four isolates exhibited a virulence gene profile characteristic of the NMEC pathotype (ibeA, kpsD/M/T, fimH). In contrast, hallmark genes of enteric pathotypes were absent from all isolates. Conclusions: The predominance of extraintestinal virulence factors in the examined poultry-derived E. coli strains underscores their zoonotic potential. The complete absence of enteric pathotype markers indicates that the studied poultry populations primarily harbor ExPEC-like strains. These findings highlight the critical need for ongoing genomic surveillance and targeted preventive strategies within poultry production systems.

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