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

Autor: Muloi DM; Usher Institute, University of Edinburgh, Edinburgh, UK.; International Livestock Research Institute, Nairobi, Kenya.; Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK., Wee BA; Usher Institute, University of Edinburgh, Edinburgh, UK., McClean DMH; Usher Institute, University of Edinburgh, Edinburgh, UK., Ward MJ; Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK.; Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK., Pankhurst L; Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK., Phan H; Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK., Ivens AC; Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK., Kivali V; International Livestock Research Institute, Nairobi, Kenya., Kiyong'a A; International Livestock Research Institute, Nairobi, Kenya., Ndinda C; International Livestock Research Institute, Nairobi, Kenya., Gitahi N; University of Nairobi, Nairobi, Kenya., Ouko T; Kenya Medical Research Institute, Nairobi, Kenya., Hassell JM; International Livestock Research Institute, Nairobi, Kenya.; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, UK., Imboma T; National Museums of Kenya, Nairobi, Kenya., Akoko J; International Livestock Research Institute, Nairobi, Kenya., Murungi MK; International Livestock Research Institute, Nairobi, Kenya., Njoroge SM; Kenya Medical Research Institute, Nairobi, Kenya., Muinde P; International Livestock Research Institute, Nairobi, Kenya., Nakamura Y; Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan., Alumasa L; International Livestock Research Institute, Nairobi, Kenya., Furmaga E; Department of Epidemiology, Columbia University, New York, NY, USA., Kaitho T; Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya., Öhgren EM; Uppsala University, Uppsala, Sweden., Amanya F; International Livestock Research Institute, Nairobi, Kenya., Ogendo A; International Livestock Research Institute, Nairobi, Kenya., Wilson DJ; Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK., Bettridge JM; Natural Resources Institute, University of Greenwich, Chatham, UK., Kiiru J; Kenya Medical Research Institute, Nairobi, Kenya., Kyobutungi C; African Population Health Research Centre, Nairobi, Kenya., Tacoli C; International Institute for Environment and Development, London, UK., Kang'ethe EK; University of Nairobi, Nairobi, Kenya., Davila JD; The Bartlett Development Planning Unit, Faculty of the Built Environment, University College London, London, UK., Kariuki S; Kenya Medical Research Institute, Nairobi, Kenya., Robinson TP; Food and Agriculture Organization of the United Nations, Rome, Italy., Rushton J; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, UK., Woolhouse MEJ; Usher Institute, University of Edinburgh, Edinburgh, UK. Mark.Woolhouse@ed.ac.uk., Fèvre EM; International Livestock Research Institute, Nairobi, Kenya. Eric.Fevre@liverpool.ac.uk.; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, UK. Eric.Fevre@liverpool.ac.uk.
Jazyk: angličtina
Zdroj: Nature microbiology [Nat Microbiol] 2022 Apr; Vol. 7 (4), pp. 581-589. Date of Electronic Publication: 2022 Mar 14.
DOI: 10.1038/s41564-022-01079-y
Abstrakt: 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.
(© 2022. The Author(s).)
Databáze: MEDLINE
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