Remarkable genomic diversity among Escherichia isolates recovered from healthy chickens

Thomson, Nicholas M., Gilroy, Rachel, Getino, Maria, Foster-Nyarko, Ebenezer, Van Vliet, Arnoud H. M., La Ragione, Roberto M. and Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 (2022) Remarkable genomic diversity among Escherichia isolates recovered from healthy chickens. PeerJ, 10. ISSN 2167-8359

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Abstract

The genus Escherichia has been extensively studied and it is known to encompass a range of commensal and pathogenic bacteria that primarily inhabit the gastrointestinal tracts of warm-blooded vertebrates. However, the presence of E. coli as a model organism and potential pathogen has diverted attention away from commensal strains and other species in the genus. To investigate the diversity of Escherichia in healthy chickens, we collected fecal samples from antibiotic-free Lohmann Brown layer hens and determined the genome sequences of 100 isolates, 81 of which were indistinguishable at the HC0 level of the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing scheme. Despite initial selection on CHROMagar Orientation medium, which is considered selective for E. coli, in silico phylotyping and core genome single nucleotide polymorphism analysis revealed the presence of at least one representative of all major clades of Escherichia, except for E. albertii, Shigella, and E. coli phylogroup B2 and cryptic clade I. The most frequent phylogenomic groups were E. coli phylogroups A and B1 and E. ruysiae (clades III and IV). We compiled a collection of reference strains isolated from avian sources (predominantly chicken), representing every Escherichia phylogroup and species, and used it to confirm the phylogeny and diversity of our isolates. Overall, the isolates carried low numbers of the virulence and antibiotic resistance genes typically seen in avian pathogenic E. coli. Notably, the clades not recovered are ones that have been most strongly associated with virulence by other studies.

Item Type:	Article
Faculty \ School:	Faculty of Medicine and Health Sciences > Norwich Medical School Faculty of Science > School of Biological Sciences
Related URLs:	https://peerj.com/articles/12935
Depositing User:	LivePure Connector
Date Deposited:	25 Mar 2022 13:27
Last Modified:	22 Oct 2022 17:38
URI:	https://ueaeprints.uea.ac.uk/id/eprint/84271
DOI:	10.7717/peerj.12935

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