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. 2025 Jan;26(1):e1.
doi: 10.4142/jvs.24225. Epub 2024 Dec 2.

Whole genome sequencing analysis of enteropathogenic Escherichia coli from human and companion animals in Korea

Jae Young Oh #  1   2 , Kyung-Hyo Do #  3 , Jae Hong Jeong  1 , SuMin Kwak  1 , Sujin Choe  3 , Dongheui An  4 , Jong-Chan Chae  1   2 , Kwangjun Lee  5 , Kwang-Won Seo  6
Affiliations

Whole genome sequencing analysis of enteropathogenic Escherichia coli from human and companion animals in Korea

Jae Young Oh et al. J Vet Sci. 2025 Jan.

Abstract

Importance: This study is essential for comprehending the zoonotic transmission, antimicrobial resistance, and genetic diversity of enteropathogenic Escherichia coli (EPEC).

Objective: To improve our understanding of EPEC, this study focused on analyzing and comparing the genomic characteristics of EPEC isolates from humans and companion animals in Korea.

Methods: The whole genome of 26 EPEC isolates from patients with diarrhea and 20 EPEC isolates from companion animals in Korea were sequenced using the Illumina HiSeq X (Illumina, USA) and Oxford Nanopore MinION (Oxford Nanopore Technologies, UK) platforms.

Results: Most isolates were atypical EPEC, and did not harbor the bfpA gene. The most prevalent virulence genes were found to be ompT (humans: 61.5%; companion animals: 60.0%) followed by lpfA (humans: 46.2%; companion animals: 60.0%). Although pan-genome analyses showed no apparent correlation among the origin of the strains, virulence profiles, and antimicrobial resistance profiles, isolates included in clade A obtained from both humans and companion animals exhibited high similarity. Additionally, all the isolates included in clade A encoded the ompT gene and did not encode the hlyE gene. The two isolates from companion animals harbored an incomplete bundle-forming pilus region encoding bfpA and bfpB. Moreover, the type IV secretion system-associated genes tra and trb were found in the bfpA-encoding isolates from humans.

Conclusions and relevance: Whole-genome sequencing enabled a more accurate analysis of the phylogenetic structure of EPEC and provided better insights into the understanding of EPEC epidemiology and pathogenicity.

Keywords: Enteropathogenic Escherichia coli; companion animal; human; one health; whole genome sequencing.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Fig. 1
Fig. 1. Genomic epidemiology among 46 enteropathogenic Escherichia coli strains from humans and companion animals. Black boxes indicate the presence of virulence and antimicrobial resistance genes, and resistance phenotypes to each antimicrobial agent.
SRF, serum resistance factors; AG, aminoglycosides; Q, quinolones; FPI, folate-pathway inhibitors; Te, tetracyclines; Te, tetracyclines; Pc, phenicols, Mb, monobactams; Cp, carbapenems; Pm, polymyxins.
Fig. 2
Fig. 2. Circular comparison for sequence of plasmid encoding bfpA gene from three enteropathogenic Escherichia coli strains from humans and companion animals.
The E2348_69_plasmid_pMAR7 was compared with three bfpA encoding plasmids. The outer ring shows annotated genes.
Fig. 3
Fig. 3. Multiple genome alignments of the bundle-forming pilus region of bfpA encoding plasmids from three enteropathogenic Escherichia coli strains from humans and companion animals.
cgST, core-genome multilocus sequence type.
See this image and copyright information in PMC

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