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Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia

Chickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of Escherichia coli from 10 chickens and 9 guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types...

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Autores principales: Foster-Nyarko, Ebenezer, Alikhan, Nabil-Fareed, Ravi, Anuradha, Thomson, Nicholas M., Jarju, Sheikh, Kwambana-Adams, Brenda A., Secka, Arss, O’Grady, Justin, Antonio, Martin, Pallen, Mark John
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8115903/
https://www.ncbi.nlm.nih.gov/pubmed/33253086
http://dx.doi.org/10.1099/mgen.0.000484
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author Foster-Nyarko, Ebenezer
Alikhan, Nabil-Fareed
Ravi, Anuradha
Thomson, Nicholas M.
Jarju, Sheikh
Kwambana-Adams, Brenda A.
Secka, Arss
O’Grady, Justin
Antonio, Martin
Pallen, Mark John
author_facet Foster-Nyarko, Ebenezer
Alikhan, Nabil-Fareed
Ravi, Anuradha
Thomson, Nicholas M.
Jarju, Sheikh
Kwambana-Adams, Brenda A.
Secka, Arss
O’Grady, Justin
Antonio, Martin
Pallen, Mark John
author_sort Foster-Nyarko, Ebenezer
collection PubMed
description Chickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of Escherichia coli from 10 chickens and 9 guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types were detected in the isolates (4 of them novel), of which ST155 was the most common (22/68, 32 %). These strains span four of the eight main phylogroups of E. coli, with phylogroups B1 and A being most prevalent. Nearly a third of the isolates harboured at least one antimicrobial resistance gene, while most of the ST155 isolates (14/22, 64 %) encoded resistance to ≥3 classes of clinically relevant antibiotics, as well as putative virulence factors, suggesting pathogenic potential in humans. Furthermore, hierarchical clustering revealed that several Gambian poultry strains were closely related to isolates from humans. Although the ST155 lineage is common in poultry from Africa and South America, the Gambian ST155 isolates belong to a unique cgMLST cluster comprising closely related (38–39 alleles differences) isolates from poultry and livestock from sub-Saharan Africa – suggesting that strains can be exchanged between poultry and livestock in this setting. Continued surveillance of E. coli and other potential pathogens in rural backyard poultry from sub-Saharan Africa is warranted.
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spelling pubmed-81159032021-05-13 Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia Foster-Nyarko, Ebenezer Alikhan, Nabil-Fareed Ravi, Anuradha Thomson, Nicholas M. Jarju, Sheikh Kwambana-Adams, Brenda A. Secka, Arss O’Grady, Justin Antonio, Martin Pallen, Mark John Microb Genom Research Article Chickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of Escherichia coli from 10 chickens and 9 guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types were detected in the isolates (4 of them novel), of which ST155 was the most common (22/68, 32 %). These strains span four of the eight main phylogroups of E. coli, with phylogroups B1 and A being most prevalent. Nearly a third of the isolates harboured at least one antimicrobial resistance gene, while most of the ST155 isolates (14/22, 64 %) encoded resistance to ≥3 classes of clinically relevant antibiotics, as well as putative virulence factors, suggesting pathogenic potential in humans. Furthermore, hierarchical clustering revealed that several Gambian poultry strains were closely related to isolates from humans. Although the ST155 lineage is common in poultry from Africa and South America, the Gambian ST155 isolates belong to a unique cgMLST cluster comprising closely related (38–39 alleles differences) isolates from poultry and livestock from sub-Saharan Africa – suggesting that strains can be exchanged between poultry and livestock in this setting. Continued surveillance of E. coli and other potential pathogens in rural backyard poultry from sub-Saharan Africa is warranted. Microbiology Society 2020-11-30 /pmc/articles/PMC8115903/ /pubmed/33253086 http://dx.doi.org/10.1099/mgen.0.000484 Text en © 2021 The Authors https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
spellingShingle Research Article
Foster-Nyarko, Ebenezer
Alikhan, Nabil-Fareed
Ravi, Anuradha
Thomson, Nicholas M.
Jarju, Sheikh
Kwambana-Adams, Brenda A.
Secka, Arss
O’Grady, Justin
Antonio, Martin
Pallen, Mark John
Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia
title Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia
title_full Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia
title_fullStr Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia
title_full_unstemmed Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia
title_short Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia
title_sort genomic diversity of escherichia coli isolates from backyard chickens and guinea fowl in the gambia
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8115903/
https://www.ncbi.nlm.nih.gov/pubmed/33253086
http://dx.doi.org/10.1099/mgen.0.000484
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