Muloi, Dishon M;
Wee, Bryan A;
McClean, Deirdre MH;
Ward, Melissa J;
Pankhurst, Louise;
Hang, Phan;
Ivens, Alasdair C;
... Fevre, Eric M; + view all
(2022)
Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape.
Nature Microbiology
10.1038/s41564-022-01079-y.
(In press).
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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.
| Type: | Article |
|---|---|
| Title: | Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape |
| Location: | England |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1038/s41564-022-01079-y |
| Publisher version: | https://doi.org/10.1038/s41564-022-01079-y |
| Language: | English |
| Additional information: | Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
| Keywords: | Microbiology, ANTIMICROBIAL RESISTANCE, NAIROBI, HUMANS, TRANSMISSION, FRAMEWORK, SYSTEM, IDENTIFICATION, INTERFACE, POLICY |
| UCL classification: | UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of the Built Environment UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of the Built Environment > Development Planning Unit UCL > Provost and Vice Provost Offices > UCL BEAMS UCL |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10145939 |
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