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Genomic diversity of Escherichia coli from healthy children in rural Gambia

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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.

In: PeerJ, Vol. 9, e10572, 06.01.2021.

Research output: Contribution to journalArticle

Harvard

Foster-Nyarko, E, Alikhan, N-F, Ikumapayi, UN, Sarwar, G, Okoi, C, Tientcheu, P-EM, Defernez, M, O'Grady, J, Antonio, M & Pallen, MJ 2021, 'Genomic diversity of Escherichia coli from healthy children in rural Gambia', PeerJ, vol. 9, e10572. https://doi.org/10.7717/peerj.10572

APA

Foster-Nyarko, E., Alikhan, N-F., Ikumapayi, U. N., Sarwar, G., Okoi, C., Tientcheu, P-E. M., Defernez, M., O'Grady, J., Antonio, M., & Pallen, M. J. (2021). Genomic diversity of Escherichia coli from healthy children in rural Gambia. PeerJ, 9, [e10572]. https://doi.org/10.7717/peerj.10572

Vancouver

Foster-Nyarko E, Alikhan N-F, Ikumapayi UN, Sarwar G, Okoi C, Tientcheu P-EM et al. Genomic diversity of Escherichia coli from healthy children in rural Gambia. PeerJ. 2021 Jan 6;9. e10572. https://doi.org/10.7717/peerj.10572

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. / Genomic diversity of Escherichia coli from healthy children in rural Gambia. In: PeerJ. 2021 ; Vol. 9.

Bibtex- Download

@article{4b09a2c1fdd6416cb8784dd8f75f32c3,
title = "Genomic diversity of Escherichia coli from healthy children in rural Gambia",
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.",
author = "Ebenezer Foster-Nyarko and Nabil-Fareed Alikhan and Ikumapayi, {Usman N} and Golam Sarwar and Catherine Okoi and Tientcheu, {Peggy-Estelle Maguiagueu} and Marianne Defernez and Justin O'Grady and Martin Antonio and Pallen, {Mark J}",
note = "{\textcopyright}2021 Foster-Nyarko et al.",
year = "2021",
month = jan,
day = "6",
doi = "10.7717/peerj.10572",
language = "English",
volume = "9",
journal = "PeerJ",
issn = "2167-8359",
publisher = "PeerJ",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Genomic diversity of Escherichia coli from healthy children in rural Gambia

AU - Foster-Nyarko, Ebenezer

AU - Alikhan, Nabil-Fareed

AU - Ikumapayi, Usman N

AU - Sarwar, Golam

AU - Okoi, Catherine

AU - Tientcheu, Peggy-Estelle Maguiagueu

AU - Defernez, Marianne

AU - O'Grady, Justin

AU - Antonio, Martin

AU - Pallen, Mark J

N1 - ©2021 Foster-Nyarko et al.

PY - 2021/1/6

Y1 - 2021/1/6

N2 - 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.

AB - 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.

U2 - 10.7717/peerj.10572

DO - 10.7717/peerj.10572

M3 - Article

C2 - 33505796

VL - 9

JO - PeerJ

JF - PeerJ

SN - 2167-8359

M1 - e10572

ER -

ID: 186064949