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
cg.authorship.typesCGIAR and advanced research instituteen
cg.contributor.affiliationInternational Livestock Research Instituteen
cg.contributor.affiliationUniversity of Edinburghen
cg.contributor.affiliationJohn Radcliffe Hospitalen
cg.contributor.affiliationUniversity of Nairobien
cg.contributor.affiliationKenya Medical Research Instituteen
cg.contributor.affiliationUniversity of Liverpoolen
cg.contributor.affiliationNational Museums of Kenyaen
cg.contributor.affiliationHokkaido Universityen
cg.contributor.affiliationColumbia Universityen
cg.contributor.affiliationKenya Wildlife Serviceen
cg.contributor.affiliationUppsala Universityen
cg.contributor.affiliationUniversity of Oxforden
cg.contributor.affiliationUniversity of Greenwichen
cg.contributor.affiliationAfrican Population and Health Research Centeren
cg.contributor.affiliationInternational Institute for Environment and Developmenten
cg.contributor.affiliationUniversity College Londonen
cg.contributor.affiliationFood and Agriculture Organization of the United Nationsen
cg.contributor.crpAgriculture for Nutrition and Health
cg.contributor.donorBiotechnology and Biological Sciences Research Council, United Kingdomen
cg.contributor.donorCGIAR Trust Funden
cg.contributor.donorMedical 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.donorRoyal Society, United Kingdomen
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 Akoko: 0000-0001-5730-4505en
cg.creator.identifierMaurice Murungi: 0000-0001-6467-4352en
cg.creator.identifierDeirdre McClean: 0000-0002-5857-9081en
cg.creator.identifierEric M. Fèvre: 0000-0001-8931-4986en
cg.creator.identifierJames Hassell: 0000-0002-4710-2827en
cg.creator.identifierVelma Kivali: 0000-0003-0797-4484en
cg.creator.identifierPatrick Muinde: 0000-0003-3907-7710en
cg.creator.identifierLorren Alumasa: 0000-0002-1723-0510en
cg.creator.identifierJudy Bettridge: 0000-0002-3917-4660en
cg.creator.identifierTimothy Robinson: 0000-0002-4266-963Xen
cg.creator.identifierMark Woolhouse: 0000-0003-3765-8167en
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.1038/s41564-022-01079-yen
cg.isijournalISI Journalen
cg.issn2058-5276en
cg.issue4en
cg.journalNature Microbiologyen
cg.reviewStatusPeer Reviewen
cg.subject.actionAreaResilient Agrifood Systems
cg.subject.ilriEPIDEMIOLOGYen
cg.subject.ilriLIVESTOCKen
cg.subject.impactAreaNutrition, health and food security
cg.subject.sdgSDG 3 - Good health and well-beingen
cg.volume7en
dc.contributor.authorMuloi, Dishon M.en
dc.contributor.authorWee, B.A.en
dc.contributor.authorMcClean, D.M.H.en
dc.contributor.authorWard, M.J.en
dc.contributor.authorPankhurst, L.en
dc.contributor.authorPhan, H.en
dc.contributor.authorIvens, A.C.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.authorHassell, James M.en
dc.contributor.authorImboma, Titusen
dc.contributor.authorAkoko, James M.en
dc.contributor.authorKarani, Maurice K.en
dc.contributor.authorNjoroge, Samuel M.en
dc.contributor.authorMuinde, Patricken
dc.contributor.authorNakamura, Y.en
dc.contributor.authorAlumasa, Lorrenen
dc.contributor.authorFurmaga, E.en
dc.contributor.authorKaitho, T.en
dc.contributor.authorÖhgren, E.M.en
dc.contributor.authorAmanya, Fredricken
dc.contributor.authorOgendo, Allanen
dc.contributor.authorWilson, D.J.en
dc.contributor.authorBettridge, Judy M.en
dc.contributor.authorKiiru, J.en
dc.contributor.authorKyobutungi, C.en
dc.contributor.authorTacoli, C.en
dc.contributor.authorKang'ethe, Erastus K.en
dc.contributor.authorDavila, J.D.en
dc.contributor.authorKariuki, S.en
dc.contributor.authorRobinson, Timothy P.en
dc.contributor.authorRushton, J.en
dc.contributor.authorWoolhouse, Mark E.J.en
dc.contributor.authorFèvre, Eric M.en
dc.date.accessioned2022-03-15T20:14:20Zen
dc.date.available2022-03-15T20:14:20Zen
dc.identifier.urihttps://hdl.handle.net/10568/118384
dc.titlePopulation genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscapeen
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
dcterms.accessRightsOpen Access
dcterms.audienceAcademicsen
dcterms.audienceScientistsen
dcterms.available2022-03-14en
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
dcterms.extentp. 581-589en
dcterms.issued2022-04en
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherSpringeren
dcterms.subjectgenomicsen
dcterms.subjectlivestocken
dcterms.subjectepidemiologyen
dcterms.subjecturban areasen
dcterms.typeJournal Article

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Epidemiology, ecology and socio-economics of disease emergence in Nairobi (Urban Zoo)
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