Genomic diversity of Escherichia coli from healthy children in rural Gambia

Foster-Nyarko, Ebenezer, Alikhan, Nabil-Fareed, Ikumapayi, Usman N, Sarwar, Golam, Okoi, Catherine, Tientcheu, Peggy-Estelle Maguiagueu, Defernez, Marianne, O'Grady, Justin, Antonio, Martin and Pallen, Mark J (2021) Genomic diversity of Escherichia coli from healthy children in rural Gambia. PeerJ, 9. ISSN 2167-8359

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Abstract

Little is known about the genomic diversity of Escherichia coli in healthy children from sub-Saharan Africa, even though this is pertinent to understanding bacterial evolution and ecology and their role in infection. We isolated and whole-genome sequenced up to five colonies of faecal E. coli from 66 asymptomatic children aged three-to-five years in rural Gambia (n = 88 isolates from 21 positive stools). We identified 56 genotypes, with an average of 2.7 genotypes per host. These were spread over 37 seven-allele sequence types and the E. coli phylogroups A, B1, B2, C, D, E, F and Escherichia cryptic clade I. Immigration events accounted for three-quarters of the diversity within our study population, while one-quarter of variants appeared to have arisen from within-host evolution. Several isolates encode putative virulence factors commonly found in Enteropathogenic and Enteroaggregative E. coli, and 53% of the isolates encode resistance to three or more classes of antimicrobials. Thus, resident E. coli in these children may constitute reservoirs of virulence- and resistance-associated genes. Moreover, several study strains were closely related to isolates that caused disease in humans or originated from livestock. Our results suggest that within-host evolution plays a minor role in the generation of diversity compared to independent immigration and the establishment of strains among our study population. Also, this study adds significantly to the number of commensal E. coli genomes, a group that has been traditionally underrepresented in the sequencing of this species.

Item Type: Article
Additional Information: ©2021 Foster-Nyarko et al.
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School

Faculty of Science > School of Chemistry
Faculty of Science > School of Biological Sciences
Depositing User: LivePure Connector
Date Deposited: 09 Feb 2021 01:03
Last Modified: 12 Jun 2021 12:04
URI: https://ueaeprints.uea.ac.uk/id/eprint/79190
DOI: 10.7717/peerj.10572

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