@article{c3bb96550759434b84f1275396abb1e8,
title = "Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape",
abstract = "Quantitative 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.",
keywords = "Animals, Escherichia coli Infections/epidemiology, Escherichia coli/genetics, Kenya/epidemiology, Livestock, Metagenomics",
author = "Dishon Muloi and Wee, {Bryan A} and Deirdre Mcclean and Melissa Ward and Louise Pankhurst and Hang Phan and Alasdair Ivens and Velma Kivali and Alice Kiyonga and Christine Ndinda and Nduhiu Gitahi and Tom Ouko and Hassell, {James M} and Titus Imboma and James Akoko and Murungi, {Maurice K} and Njoroge, {Samuel M} and Patrick Muinde and Yukiko Nakamura and Lorren Alumasa and Erin Furmaga and Titus Kaitho and Elin {\"O}hgren and Fredrick Amanya and Allan Ogendo and Daniel Wilson and Judy Bettridge and John Kiiru and Catherine Kyobutungi and Cecila Tacoli and Erastus Kang'ethe and Julio Davila and Samuel Kariuki and Timothy Robinson and Jonathan Rushton and Mark Woolhouse and F{\`e}vre, {Eric M.}",
note = "Funding Information: We are grateful to the residents of our 99 sampling locations in Nairobi for taking part in the study. We thank B. van Bunnik for insightful discussions and help with statistical analysis; P. Alarcon, P. Dominguez-Salas, L. Mad{\'e}, S. Ahmed and C. Pfeifer for assistance with questionnaire design; A. Kihara and J. Rogena for support with implementing the data collection tool and database design; and students on the Kenya Field Epidemiology and Laboratory Training Program (K-FELTP) for assistance with fieldwork. We thank the City of Nairobi authorities, the Department of Veterinary Services and the Department of Health Services for their cooperation in this study. This study was supported by the UK Medical Research Council, Biotechnology and Biological Science Research Council (UK), the Economic and Social Research Council (UK) and the Natural Environment Research Council (UK), through the Environmental & Social Ecology of Human Infectious Diseases Initiative (ESEI), grant reference: G1100783/1. This work was also supported, in part, by the CGIAR Research Program on Agriculture for Nutrition and Health (A4NH), led by the International Food Policy Research Institute (IFPRI). We acknowledge the CGIAR Fund Donors ( https://www.cgiar.org/funders/ ). The High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics in Oxford (funded by Wellcome Trust grant reference 090532/Z/09/Z) generated the sequencing data. We thank the Modernizing Medical Microbiology Informatics Group for bioinformatics assistance; T. Davies, T. Peto, S. Walker and D. Crook for helpful discussions. D.J.W. is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (grant 101237/Z/13/B) and is supported by a Big Data Institute Robertson Fellowship. D.M.M. was supported by the Darwin Trust of Edinburgh and Centre for Immunology, Infection and Evolution (CIIE), University of Edinburgh. B.A.W. was funded through the project {\textquoteleft}Selection and Transmission of Antimicrobial Resistance in Complex Systems (STARCS){\textquoteright} in the Joint Programming Initiative on Antimicrobial Resistance, grant reference MR/R000093/1. M.J.W. was supported by a Sir Henry Wellcome Postdoctoral Fellowship from the Wellcome Trust (grant reference WT103953MA) and by a Junior Research Fellowship as part of a Wellcome Trust Strategic grant to the Centre for Immunity, Infection and Evolution at the University of Edinburgh (grant reference 095831). The views expressed are those of the authors and are not necessarily those of CGIAR, the Government of Kenya, the Food and Agriculture Organization of the United Nations or other institutions to which the authors are affiliated. Funding Information: We are grateful to the residents of our 99 sampling locations in Nairobi for taking part in the study. We thank B. van Bunnik for insightful discussions and help with statistical analysis; P. Alarcon, P. Dominguez-Salas, L. Mad?, S. Ahmed and C. Pfeifer for assistance with questionnaire design; A. Kihara and J. Rogena for support with implementing the data collection tool and database design; and students on the Kenya Field Epidemiology and Laboratory Training Program (K-FELTP) for assistance with fieldwork. We thank the City of Nairobi authorities, the Department of Veterinary Services and the Department of Health Services for their cooperation in this study. This study was supported by the UK Medical Research Council, Biotechnology and Biological Science Research Council (UK), the Economic and Social Research Council (UK) and the Natural Environment Research Council (UK), through the Environmental & Social Ecology of Human Infectious Diseases Initiative (ESEI), grant reference: G1100783/1. This work was also supported, in part, by the CGIAR Research Program on Agriculture for Nutrition and Health (A4NH), led by the International Food Policy Research Institute (IFPRI). We acknowledge the CGIAR Fund Donors (https://www.cgiar.org/funders/). The High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics in Oxford (funded by Wellcome Trust grant reference 090532/Z/09/Z) generated the sequencing data. We thank the Modernizing Medical Microbiology Informatics Group for bioinformatics assistance; T. Davies, T. Peto, S. Walker and D. Crook for helpful discussions. D.J.W. is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (grant 101237/Z/13/B) and is supported by a Big Data Institute Robertson Fellowship. D.M.M. was supported by the Darwin Trust of Edinburgh and Centre for Immunology, Infection and Evolution (CIIE), University of Edinburgh. B.A.W. was funded through the project ?Selection and Transmission of Antimicrobial Resistance in Complex Systems (STARCS)? in the Joint Programming Initiative on Antimicrobial Resistance, grant reference MR/R000093/1. M.J.W. was supported by a Sir Henry Wellcome Postdoctoral Fellowship from the Wellcome Trust (grant reference WT103953MA) and by a Junior Research Fellowship as part of a Wellcome Trust Strategic grant to the Centre for Immunity, Infection and Evolution at the University of Edinburgh (grant reference 095831). The views expressed are those of the authors and are not necessarily those of CGIAR, the Government of Kenya, the Food and Agriculture Organization of the United Nations or other institutions to which the authors are affiliated. Publisher Copyright: {\textcopyright} 2022, The Author(s).",
year = "2022",
month = mar,
day = "14",
doi = "10.1038/s41564-022-01079-y",
language = "English",
volume = "7",
pages = "581--589",
journal = "Nature Microbiology",
issn = "2058-5276",
publisher = "Nature Publishing Group",
number = "4",
}