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

View ORCID ProfileEbenezer Foster-Nyarko, View ORCID ProfileNabil-Fareed Alikhan, View ORCID ProfileAnuradha Ravi, View ORCID ProfileNicholas M. Thomson, View ORCID ProfileSheikh Jarju, View ORCID ProfileBrenda Anna Kwambana-Adams, Arss Secka, View ORCID ProfileJustin O’Grady, View ORCID ProfileMartin Antonio, View ORCID ProfileMark J. Pallen
doi: https://doi.org/10.1101/2020.05.14.096289
Ebenezer Foster-Nyarko
1Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, United Kingdom
2Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard Road, Fajara, the Gambia
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  • ORCID record for Ebenezer Foster-Nyarko
Nabil-Fareed Alikhan
1Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, United Kingdom
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Anuradha Ravi
1Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, United Kingdom
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Nicholas M. Thomson
1Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, United Kingdom
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Sheikh Jarju
2Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard Road, Fajara, the Gambia
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Brenda Anna Kwambana-Adams
2Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard Road, Fajara, the Gambia
5NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, United Kingdom
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Arss Secka
3West Africa Livestock Innovation Centre (WALIC), MB 14, Banjul, the Gambia
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Justin O’Grady
1Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, United Kingdom
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Martin Antonio
2Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard Road, Fajara, the Gambia
4Warwick Medical School, University of Warwick, Coventry, United Kingdom
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Mark J. Pallen
1Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, United Kingdom
6School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
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  • For correspondence: M.Pallen@uea.ac.uk
  • Abstract
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Abstract

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 ten chickens and nine guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types were detected in the isolates (four 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 comprised of 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.

Author notes All supporting data and protocols have been provided within the article or as supplementary data files. Eleven supplementary figures and eight supplementary files are available with the online version of this article.

Data summary The genomic assemblies for the isolates reported here are available for download from EnteroBase (http://enterobase.warwick.ac.uk/species/index/ecoli) and the EnteroBase assembly barcodes are provided in File S2.

Sequences have been deposited in the NCBI SRA, under the BioProject ID: PRJNA616250 and accession numbers SAMN14485281 to SAMN14485348 (File S2). Assemblies have been deposited in GenBank under the BioProject ID: PRJNA616250 and accession numbers CP053258 and CP053259.

Impact statement Domestic birds play a crucial role in human society, in particular contributing to food security in low-income countries. Many households in Sub-Saharan Africa rear free-range chickens and guinea fowl, which are often left to scavenge for feed in and around the family compound, where they are frequently exposed to humans, other animals and the environment. Such proximity between backyard poultry and humans is likely to facilitate transmission of pathogens such as Escherichia coli or antimicrobial resistance between the two host species. Little is known about the population structure of E. coli in rural chickens and guinea fowl, although this information is needed to contextualise the potential risks of transmission of bacterial strains between humans and rural backyard poultry. Thus, we sought to investigate the genomic diversity of E. coli in backyard poultry from rural Gambia.

Competing Interest Statement

The authors have declared no competing interest.

  • Abbreviations

    APEC
    Avian Pathogenic E. coli;
    ExPEC
    Extraintestinal pathogenic E. coli;
    ST
    Sequence type;
    AMR
    Antimicrobial resistance;
    MDR
    Multiple-drug resistance;
    MLST
    Multi-locus sequence typing;
    cgMLST
    core-genome multi-locus sequence typing;
    ARIBA
    Antimicrobial resistance identification by assembly;;
    VFDB
    Virulence factors database;
    SNP
    single nucleotide polymorphism;
    STGG
    Skimmed milk tryptone glucose glycerol;
    SDS
    Sodium dodecyl-sulphate;
    EDTA
    Ethylenediaminetetraacetic acid;
    ESBL
    Expanded-spectrum beta-lactamase;
    MIC
    minimum inhibitory concentrations.
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    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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    Posted May 15, 2020.
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    Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia
    Ebenezer Foster-Nyarko, Nabil-Fareed Alikhan, Anuradha Ravi, Nicholas M. Thomson, Sheikh Jarju, Brenda Anna Kwambana-Adams, Arss Secka, Justin O’Grady, Martin Antonio, Mark J. Pallen
    bioRxiv 2020.05.14.096289; doi: https://doi.org/10.1101/2020.05.14.096289
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    Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia
    Ebenezer Foster-Nyarko, Nabil-Fareed Alikhan, Anuradha Ravi, Nicholas M. Thomson, Sheikh Jarju, Brenda Anna Kwambana-Adams, Arss Secka, Justin O’Grady, Martin Antonio, Mark J. Pallen
    bioRxiv 2020.05.14.096289; doi: https://doi.org/10.1101/2020.05.14.096289

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