Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape

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cg.authorship.typesCGIAR and developing country instituteen_US
cg.authorship.typesCGIAR and advanced research instituteen_US
cg.contributor.affiliationInternational Livestock Research Instituteen_US
cg.contributor.affiliationUniversity of Edinburghen_US
cg.contributor.affiliationJohn Radcliffe Hospitalen_US
cg.contributor.affiliationUniversity of Nairobien_US
cg.contributor.affiliationKenya Medical Research Instituteen_US
cg.contributor.affiliationUniversity of Liverpoolen_US
cg.contributor.affiliationNational Museums of Kenyaen_US
cg.contributor.affiliationHokkaido Universityen_US
cg.contributor.affiliationColumbia Universityen_US
cg.contributor.affiliationKenya Wildlife Serviceen_US
cg.contributor.affiliationUppsala Universityen_US
cg.contributor.affiliationUniversity of Oxforden_US
cg.contributor.affiliationUniversity of Greenwichen_US
cg.contributor.affiliationAfrican Population and Health Research Centeren_US
cg.contributor.affiliationInternational Institute for Environment and Developmenten_US
cg.contributor.affiliationUniversity College Londonen_US
cg.contributor.affiliationFood and Agriculture Organization of the United Nationsen_US
cg.contributor.crpAgriculture for Nutrition and Healthen_US
cg.contributor.donorBiotechnology and Biological Sciences Research Council, United Kingdomen_US
cg.contributor.donorCGIAR Trust Funden_US
cg.contributor.donorMedical 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.donorRoyal Society, United Kingdomen_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 Akoko: 0000-0001-5730-4505en_US
cg.creator.identifierMaurice Murungi: 0000-0001-6467-4352en_US
cg.creator.identifierDeirdre McClean: 0000-0002-5857-9081en_US
cg.creator.identifierEric M. Fèvre: 0000-0001-8931-4986en_US
cg.creator.identifierJames Hassell: 0000-0002-4710-2827en_US
cg.creator.identifierVelma Kivali: 0000-0003-0797-4484en_US
cg.creator.identifierPatrick Muinde: 0000-0003-3907-7710en_US
cg.creator.identifierLorren Alumasa: 0000-0002-1723-0510en_US
cg.creator.identifierJudy Bettridge: 0000-0002-3917-4660en_US
cg.creator.identifierTimothy Robinson: 0000-0002-4266-963Xen_US
cg.creator.identifierMark Woolhouse: 0000-0003-3765-8167en_US
cg.howPublishedFormally Publisheden_US
cg.identifier.doihttps://doi.org/10.1038/s41564-022-01079-yen_US
cg.isijournalISI Journalen_US
cg.issn2058-5276en_US
cg.issue4en_US
cg.journalNature Microbiologyen_US
cg.reviewStatusPeer Reviewen_US
cg.subject.actionAreaResilient Agrifood Systemsen_US
cg.subject.ilriEPIDEMIOLOGYen_US
cg.subject.ilriLIVESTOCKen_US
cg.subject.impactAreaNutrition, health and food securityen_US
cg.subject.sdgSDG 3 - Good health and well-beingen_US
cg.volume7en_US
dc.contributor.authorMuloi, Dishon M.en_US
dc.contributor.authorWee, B.A.en_US
dc.contributor.authorMcClean, D.M.H.en_US
dc.contributor.authorWard, M.J.en_US
dc.contributor.authorPankhurst, L.en_US
dc.contributor.authorPhan, H.en_US
dc.contributor.authorIvens, A.C.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.authorHassell, James M.en_US
dc.contributor.authorImboma, Titusen_US
dc.contributor.authorAkoko, James M.en_US
dc.contributor.authorKarani, Maurice K.en_US
dc.contributor.authorNjoroge, Samuel M.en_US
dc.contributor.authorMuinde, Patricken_US
dc.contributor.authorNakamura, Y.en_US
dc.contributor.authorAlumasa, Lorrenen_US
dc.contributor.authorFurmaga, E.en_US
dc.contributor.authorKaitho, T.en_US
dc.contributor.authorÖhgren, E.M.en_US
dc.contributor.authorAmanya, Fredricken_US
dc.contributor.authorOgendo, Allanen_US
dc.contributor.authorWilson, D.J.en_US
dc.contributor.authorBettridge, Judy M.en_US
dc.contributor.authorKiiru, J.en_US
dc.contributor.authorKyobutungi, C.en_US
dc.contributor.authorTacoli, C.en_US
dc.contributor.authorKang'ethe, Erastus K.en_US
dc.contributor.authorDavila, J.D.en_US
dc.contributor.authorKariuki, S.en_US
dc.contributor.authorRobinson, Timothy P.en_US
dc.contributor.authorRushton, J.en_US
dc.contributor.authorWoolhouse, Mark E.J.en_US
dc.contributor.authorFèvre, Eric M.en_US
dc.date.accessioned2022-03-15T20:14:20Zen_US
dc.date.available2022-03-15T20:14:20Zen_US
dc.identifier.urihttps://hdl.handle.net/10568/118384en_US
dc.titlePopulation genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscapeen_US
dcterms.abstractQuantitative evidence for the risk of zoonoses and the spread of antimicrobial resistance remains lacking. Here, as part of the UrbanZoo project, we sampled Escherichia coli from humans, livestock and peri-domestic wildlife in 99 households across Nairobi, Kenya, to investigate its distribution among host species in this rapidly developing urban landscape. We performed whole-genome sequencing of 1,338 E. coli isolates and found that the diversity and sharing patterns of E. coli were heavily structured by household and strongly shaped by host type. We also found evidence for inter-household and inter-host sharing and, importantly, between humans and animals, although this occurs much less frequently. Resistome similarity was differently distributed across host and household, consistent with being driven by shared exposure to antimicrobials. Our results indicate that a large, epidemiologically structured sampling framework combined with WGS is needed to uncover strain-sharing events among different host populations in complex environments and the major contributing pathways that could ultimately drive the emergence of zoonoses and the spread of antimicrobial resistance.en_US
dcterms.accessRightsOpen Accessen_US
dcterms.audienceAcademicsen_US
dcterms.audienceScientistsen_US
dcterms.available2022-03-14en_US
dcterms.bibliographicCitationMuloi, D.M., Wee, B.A., McClean, D.M.H., Ward, M.J., Pankhurst, L., Phan, H., Ivens, A.C., Kivali, V., Kiyong'a, A., Ndinda, C., Gitahi, N., Ouko, T., Hassell, J.M., Imboma, T., Akoko, J., Karani, M.K., Njoroge, S.M., Muinde, P., Nakamura, Y., Alumasa, L., Furmaga, E., Kaitho, T., Öhgren, E.M., Amanya, F., Ogendo, A., Wilson, D.J., Bettridge, J.M., Kiiru, J., Kyobutungi, C., Tacoli, C., Kang’ethe, E.K., Davila, J.D., Kariuki, S., Robinson, T.P., Rushton, J., Woolhouse, M.E.J. and Fèvre, E.M. 2022. Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape. Nature Microbiology 7: 581–589.en_US
dcterms.extentp. 581-589en_US
dcterms.issued2022-04en_US
dcterms.languageenen_US
dcterms.licenseCC-BY-4.0en_US
dcterms.publisherSpringeren_US
dcterms.subjectgenomicsen_US
dcterms.subjectlivestocken_US
dcterms.subjectepidemiologyen_US
dcterms.subjecturban areasen_US
dcterms.typeJournal Articleen_US

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