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Genomic diversity of Escherichia coli from healthy children in rural Gambia

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 6...

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Autores principales: Foster-Nyarko, Ebenezer, Alikhan, Nabil-Fareed, Ikumapayi, Usman N., Sarwar, Golam, Okoi, Catherine, Tientcheu, Peggy-Estelle Maguiagueu, Defernez, Marianne, O’Grady, Justin, Antonio, Martin, Pallen, Mark J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7796664/
https://www.ncbi.nlm.nih.gov/pubmed/33505796
http://dx.doi.org/10.7717/peerj.10572
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author Foster-Nyarko, Ebenezer
Alikhan, Nabil-Fareed
Ikumapayi, Usman N.
Sarwar, Golam
Okoi, Catherine
Tientcheu, Peggy-Estelle Maguiagueu
Defernez, Marianne
O’Grady, Justin
Antonio, Martin
Pallen, Mark J.
author_facet Foster-Nyarko, Ebenezer
Alikhan, Nabil-Fareed
Ikumapayi, Usman N.
Sarwar, Golam
Okoi, Catherine
Tientcheu, Peggy-Estelle Maguiagueu
Defernez, Marianne
O’Grady, Justin
Antonio, Martin
Pallen, Mark J.
author_sort Foster-Nyarko, Ebenezer
collection PubMed
description 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.
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spelling pubmed-77966642021-01-26 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 Pallen, Mark J. PeerJ Ecology 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. PeerJ Inc. 2021-01-06 /pmc/articles/PMC7796664/ /pubmed/33505796 http://dx.doi.org/10.7717/peerj.10572 Text en ©2021 Foster-Nyarko et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Ecology
Foster-Nyarko, Ebenezer
Alikhan, Nabil-Fareed
Ikumapayi, Usman N.
Sarwar, Golam
Okoi, Catherine
Tientcheu, Peggy-Estelle Maguiagueu
Defernez, Marianne
O’Grady, Justin
Antonio, Martin
Pallen, Mark J.
Genomic diversity of Escherichia coli from healthy children in rural Gambia
title Genomic diversity of Escherichia coli from healthy children in rural Gambia
title_full Genomic diversity of Escherichia coli from healthy children in rural Gambia
title_fullStr Genomic diversity of Escherichia coli from healthy children in rural Gambia
title_full_unstemmed Genomic diversity of Escherichia coli from healthy children in rural Gambia
title_short Genomic diversity of Escherichia coli from healthy children in rural Gambia
title_sort genomic diversity of escherichia coli from healthy children in rural gambia
topic Ecology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7796664/
https://www.ncbi.nlm.nih.gov/pubmed/33505796
http://dx.doi.org/10.7717/peerj.10572
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