Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya

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cg.authorship.typesCGIAR and developing country instituteen
cg.authorship.typesCGIAR and advanced research instituteen
cg.contributor.affiliationUniversity of Edinburghen
cg.contributor.affiliationInternational Livestock Research Instituteen
cg.contributor.affiliationUniversity of Liverpoolen
cg.contributor.affiliationUniversity of Oxforden
cg.contributor.affiliationUniversity of Southamptonen
cg.contributor.affiliationUniversity of Greenwichen
cg.contributor.affiliationUniversity of Nairobien
cg.contributor.affiliationKenya Medical Research Instituteen
cg.contributor.affiliationNational Museums of Kenyaen
cg.contributor.affiliationKenya Wildlife Serviceen
cg.contributor.affiliationFood and Agriculture Organization of the United Nationsen
cg.contributor.crpAgriculture for Nutrition and Health
cg.contributor.donorMedical Research Council, United Kingdomen
cg.contributor.donorCGIAR Trust Funden
cg.contributor.donorBiotechnology and Biological Sciences Research Council, United Kingdomen
cg.contributor.donorEconomic and Social Research Council, United Kingdomen
cg.contributor.donorNatural Environment Research Council, United Kingdomen
cg.contributor.donorWellcome Trusten
cg.contributor.donorDarwin Trust of Edinburghen
cg.contributor.donorJoint Programming Initiative on Antimicrobial Resistanceen
cg.contributor.initiativeOne Health
cg.coverage.countryKenya
cg.coverage.iso3166-alpha2KE
cg.coverage.regionAfrica
cg.coverage.regionEastern Africa
cg.creator.identifierDishon Muloi: 0000-0002-6236-2280en
cg.creator.identifierJames Hassell: 0000-0002-4710-2827en
cg.creator.identifierJames Akoko: 0000-0001-5730-4505en
cg.creator.identifierMaurice Murungi: 0000-0001-6467-4352en
cg.creator.identifierJudy Bettridge: 0000-0002-3917-4660en
cg.creator.identifierLorren Alumasa: 0000-0002-1723-0510en
cg.creator.identifierVelma Kivali: 0000-0003-0797-4484en
cg.creator.identifierEric M. Fèvre: 0000-0001-8931-4986en
cg.creator.identifierTimothy Robinson: 0000-0002-4266-963Xen
cg.creator.identifierPatrick Muinde: 0000-0003-3907-7710en
cg.creator.identifierSamuel Njoroge: 0000-0001-6965-3681en
cg.creator.identifierMark Woolhouse: 0000-0003-3765-8167en
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.1186/s12916-022-02677-7en
cg.isijournalISI Journalen
cg.issn1741-7015en
cg.issue1en
cg.journalBMC Medicineen
cg.reviewStatusPeer Reviewen
cg.speciesEscherichia colien
cg.subject.actionAreaResilient Agrifood Systems
cg.subject.ilriAMRen
cg.subject.ilriANIMAL HEALTHen
cg.subject.ilriEPIDEMIOLOGYen
cg.subject.ilriHUMAN HEALTHen
cg.subject.ilriONE HEALTHen
cg.subject.ilriWILDLIFEen
cg.subject.impactAreaNutrition, health and food security
cg.subject.sdgSDG 3 - Good health and well-beingen
cg.volume20en
dc.contributor.authorMuloi, Dishon M.en
dc.contributor.authorHassell, James M.en
dc.contributor.authorWee, B.A.en
dc.contributor.authorWard, M.J.en
dc.contributor.authorBettridge, Judy M.en
dc.contributor.authorKivali, Velmaen
dc.contributor.authorKiyong'a, Aliceen
dc.contributor.authorNdinda, Christineen
dc.contributor.authorGitahi, N.en
dc.contributor.authorOuko, T.T.en
dc.contributor.authorImboma, Titusen
dc.contributor.authorAkoko, James M.en
dc.contributor.authorMurungi, Maurice K.en
dc.contributor.authorNjoroge, Samuel M.en
dc.contributor.authorMuinde, Patricken
dc.contributor.authorAlumasa, Lorrenen
dc.contributor.authorKaitho, T.en
dc.contributor.authorAmanya, Fredricken
dc.contributor.authorOgendo, Allanen
dc.contributor.authorBunnik, B.A.D. vanen
dc.contributor.authorKiiru, J.en
dc.contributor.authorRobinson, Timothy P.en
dc.contributor.authorKang'ethe, Erastus K.en
dc.contributor.authorKariuki, S.en
dc.contributor.authorPedersen, A.B.en
dc.contributor.authorFèvre, Eric M.en
dc.contributor.authorWoolhouse, Mark E.J.en
dc.date.accessioned2022-12-14T10:16:11Zen
dc.date.available2022-12-14T10:16:11Zen
dc.identifier.urihttps://hdl.handle.net/10568/125962
dc.titleGenomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenyaen
dcterms.abstractBackground Livestock systems have been proposed as a reservoir for antimicrobial-resistant (AMR) bacteria and AMR genetic determinants that may infect or colonise humans, yet quantitative evidence regarding their epidemiological role remains lacking. Here, we used a combination of genomics, epidemiology and ecology to investigate patterns of AMR gene carriage in Escherichia coli, regarded as a sentinel organism. Methods We conducted a structured epidemiological survey of 99 households across Nairobi, Kenya, and whole genome sequenced E. coli isolates from 311 human, 606 livestock and 399 wildlife faecal samples. We used statistical models to investigate the prevalence of AMR carriage and characterise AMR gene diversity and structure of AMR genes in different host populations across the city. We also investigated household-level risk factors for the exchange of AMR genes between sympatric humans and livestock. Results We detected 56 unique acquired genes along with 13 point mutations present in variable proportions in human and animal isolates, known to confer resistance to nine antibiotic classes. We find that AMR gene community composition is not associated with host species, but AMR genes were frequently co-located, potentially enabling the acquisition and dispersal of multi-drug resistance in a single step. We find that whilst keeping livestock had no influence on human AMR gene carriage, the potential for AMR transmission across human-livestock interfaces is greatest when manure is poorly disposed of and in larger households. Conclusions Findings of widespread carriage of AMR bacteria in human and animal populations, including in long-distance wildlife species, in community settings highlight the value of evidence-based surveillance to address antimicrobial resistance on a global scale. Our genomic analysis provided an in-depth understanding of AMR determinants at the interfaces of One Health sectors that will inform AMR prevention and control.en
dcterms.accessRightsOpen Access
dcterms.audienceAcademicsen
dcterms.audienceScientistsen
dcterms.available2022-12-08en
dcterms.bibliographicCitationMuloi, D.M., Hassell, J.M., Wee, B.A., Ward, M.J., Bettridge, J.M., Kivali, V., Kiyong'a, A., Ndinda, C., Gitahi, N., Ouko, T., Imboma, T., Akoko, J., Murungi, M.K., Njoroge, S.M., Muinde, P., Alumasa, L., Kaitho, T., Amanya, F., Ogendo, A., Bunnik, B.A.D. van, Kiiru, J., Robinson, T.P., Kang'ethe, E.K., Kariuki, S., Pedersen, A.B., Fèvre, E.M. and Woolhouse, M.E.J. 2022. Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya. BMC Medicine 20: 471.en
dcterms.extent471en
dcterms.issued2022-12-08en
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherSpringeren
dcterms.subjectantimicrobial resistanceen
dcterms.subjectone health approachen
dcterms.subjectanimal healthen
dcterms.subjecthealthen
dcterms.subjectwildlifeen
dcterms.subjectgenomicsen
dcterms.subjectepidemiologyen
dcterms.typeJournal Article

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