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_US
cg.authorship.typesCGIAR and advanced research instituteen_US
cg.contributor.affiliationUniversity of Edinburghen_US
cg.contributor.affiliationInternational Livestock Research Instituteen_US
cg.contributor.affiliationUniversity of Liverpoolen_US
cg.contributor.affiliationUniversity of Oxforden_US
cg.contributor.affiliationUniversity of Southamptonen_US
cg.contributor.affiliationUniversity of Greenwichen_US
cg.contributor.affiliationUniversity of Nairobien_US
cg.contributor.affiliationKenya Medical Research Instituteen_US
cg.contributor.affiliationNational Museums of Kenyaen_US
cg.contributor.affiliationKenya Wildlife Serviceen_US
cg.contributor.affiliationFood and Agriculture Organization of the United Nationsen_US
cg.contributor.crpAgriculture for Nutrition and Healthen_US
cg.contributor.donorMedical Research Council, United Kingdomen_US
cg.contributor.donorCGIAR Trust Funden_US
cg.contributor.donorBiotechnology and Biological Sciences Research Council, United Kingdomen_US
cg.contributor.donorEconomic and Social Research Council, United Kingdomen_US
cg.contributor.donorNatural Environment Research Council, United Kingdomen_US
cg.contributor.donorWellcome Trusten_US
cg.contributor.donorDarwin Trust of Edinburghen_US
cg.contributor.donorJoint Programming Initiative on Antimicrobial Resistanceen_US
cg.contributor.initiativeOne Healthen_US
cg.coverage.countryKenyaen_US
cg.coverage.iso3166-alpha2KEen_US
cg.coverage.regionAfricaen_US
cg.coverage.regionEastern Africaen_US
cg.creator.identifierDishon Muloi: 0000-0002-6236-2280en_US
cg.creator.identifierJames Hassell: 0000-0002-4710-2827en_US
cg.creator.identifierJames Akoko: 0000-0001-5730-4505en_US
cg.creator.identifierMaurice Murungi: 0000-0001-6467-4352en_US
cg.creator.identifierJudy Bettridge: 0000-0002-3917-4660en_US
cg.creator.identifierLorren Alumasa: 0000-0002-1723-0510en_US
cg.creator.identifierVelma Kivali: 0000-0003-0797-4484en_US
cg.creator.identifierEric M. Fèvre: 0000-0001-8931-4986en_US
cg.creator.identifierTimothy Robinson: 0000-0002-4266-963Xen_US
cg.creator.identifierPatrick Muinde: 0000-0003-3907-7710en_US
cg.creator.identifierSamuel Njoroge: 0000-0001-6965-3681en_US
cg.creator.identifierMark Woolhouse: 0000-0003-3765-8167en_US
cg.howPublishedFormally Publisheden_US
cg.identifier.doihttps://doi.org/10.1186/s12916-022-02677-7en_US
cg.isijournalISI Journalen_US
cg.issn1741-7015en_US
cg.issue1en_US
cg.journalBMC Medicineen_US
cg.reviewStatusPeer Reviewen_US
cg.speciesEscherichia colien_US
cg.subject.actionAreaResilient Agrifood Systemsen_US
cg.subject.ilriAMRen_US
cg.subject.ilriANIMAL HEALTHen_US
cg.subject.ilriEPIDEMIOLOGYen_US
cg.subject.ilriHUMAN HEALTHen_US
cg.subject.ilriONE HEALTHen_US
cg.subject.ilriWILDLIFEen_US
cg.subject.impactAreaNutrition, health and food securityen_US
cg.subject.sdgSDG 3 - Good health and well-beingen_US
cg.volume20en_US
dc.contributor.authorMuloi, Dishon M.en_US
dc.contributor.authorHassell, James M.en_US
dc.contributor.authorWee, B.A.en_US
dc.contributor.authorWard, M.J.en_US
dc.contributor.authorBettridge, Judy M.en_US
dc.contributor.authorKivali, Velmaen_US
dc.contributor.authorKiyong'a, Aliceen_US
dc.contributor.authorNdinda, Christineen_US
dc.contributor.authorGitahi, N.en_US
dc.contributor.authorOuko, T.T.en_US
dc.contributor.authorImboma, Titusen_US
dc.contributor.authorAkoko, James M.en_US
dc.contributor.authorMurungi, Maurice K.en_US
dc.contributor.authorNjoroge, Samuel M.en_US
dc.contributor.authorMuinde, Patricken_US
dc.contributor.authorAlumasa, Lorrenen_US
dc.contributor.authorKaitho, T.en_US
dc.contributor.authorAmanya, Fredricken_US
dc.contributor.authorOgendo, Allanen_US
dc.contributor.authorBunnik, B.A.D. vanen_US
dc.contributor.authorKiiru, J.en_US
dc.contributor.authorRobinson, Timothy P.en_US
dc.contributor.authorKang'ethe, Erastus K.en_US
dc.contributor.authorKariuki, S.en_US
dc.contributor.authorPedersen, A.B.en_US
dc.contributor.authorFèvre, Eric M.en_US
dc.contributor.authorWoolhouse, Mark E.J.en_US
dc.date.accessioned2022-12-14T10:16:11Zen_US
dc.date.available2022-12-14T10:16:11Zen_US
dc.identifier.urihttps://hdl.handle.net/10568/125962en_US
dc.titleGenomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenyaen_US
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_US
dcterms.accessRightsOpen Accessen_US
dcterms.audienceAcademicsen_US
dcterms.audienceScientistsen_US
dcterms.available2022-12-08en_US
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_US
dcterms.extent471en_US
dcterms.issued2022-12-08en_US
dcterms.languageenen_US
dcterms.licenseCC-BY-4.0en_US
dcterms.publisherSpringeren_US
dcterms.subjectantimicrobial resistanceen_US
dcterms.subjectone health approachen_US
dcterms.subjectanimal healthen_US
dcterms.subjecthealthen_US
dcterms.subjectwildlifeen_US
dcterms.subjectgenomicsen_US
dcterms.subjectepidemiologyen_US
dcterms.typeJournal Articleen_US

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