Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape
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 amon...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2022
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/118384 |
| _version_ | 1855521231337422848 |
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| author | Muloi, Dishon M. Wee, B.A. McClean, D.M.H. Ward, M.J. Pankhurst, L. Phan, H. Ivens, A.C. Kivali, Velma Kiyong'a, Alice Ndinda, Christine Gitahi, N. Ouko, T.T. Hassell, James M. Imboma, Titus Akoko, James M. Karani, Maurice K. Njoroge, Samuel M. Muinde, Patrick Nakamura, Y. Alumasa, Lorren Furmaga, E. Kaitho, T. Öhgren, E.M. Amanya, Fredrick Ogendo, Allan Wilson, D.J. Bettridge, Judy M. Kiiru, J. Kyobutungi, C. Tacoli, C. Kang'ethe, Erastus K. Davila, J.D. Kariuki, S. Robinson, Timothy P. Rushton, J. Woolhouse, Mark E.J. Fèvre, Eric M. |
| author_browse | Akoko, James M. Alumasa, Lorren Amanya, Fredrick Bettridge, Judy M. Davila, J.D. Furmaga, E. Fèvre, Eric M. Gitahi, N. Hassell, James M. Imboma, Titus Ivens, A.C. Kaitho, T. Kang'ethe, Erastus K. Karani, Maurice K. Kariuki, S. Kiiru, J. Kivali, Velma Kiyong'a, Alice Kyobutungi, C. McClean, D.M.H. Muinde, Patrick Muloi, Dishon M. Nakamura, Y. Ndinda, Christine Njoroge, Samuel M. Ogendo, Allan Ouko, T.T. Pankhurst, L. Phan, H. Robinson, Timothy P. Rushton, J. Tacoli, C. Ward, M.J. Wee, B.A. Wilson, D.J. Woolhouse, Mark E.J. Öhgren, E.M. |
| author_facet | Muloi, Dishon M. Wee, B.A. McClean, D.M.H. Ward, M.J. Pankhurst, L. Phan, H. Ivens, A.C. Kivali, Velma Kiyong'a, Alice Ndinda, Christine Gitahi, N. Ouko, T.T. Hassell, James M. Imboma, Titus Akoko, James M. Karani, Maurice K. Njoroge, Samuel M. Muinde, Patrick Nakamura, Y. Alumasa, Lorren Furmaga, E. Kaitho, T. Öhgren, E.M. Amanya, Fredrick Ogendo, Allan Wilson, D.J. Bettridge, Judy M. Kiiru, J. Kyobutungi, C. Tacoli, C. Kang'ethe, Erastus K. Davila, J.D. Kariuki, S. Robinson, Timothy P. Rushton, J. Woolhouse, Mark E.J. Fèvre, Eric M. |
| author_sort | Muloi, Dishon M. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace118384 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1183842024-11-07T09:51:36Z Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape Muloi, Dishon M. Wee, B.A. McClean, D.M.H. Ward, M.J. Pankhurst, L. Phan, H. Ivens, A.C. Kivali, Velma Kiyong'a, Alice Ndinda, Christine Gitahi, N. Ouko, T.T. Hassell, James M. Imboma, Titus Akoko, James M. Karani, Maurice K. Njoroge, Samuel M. Muinde, Patrick Nakamura, Y. Alumasa, Lorren Furmaga, E. Kaitho, T. Öhgren, E.M. Amanya, Fredrick Ogendo, Allan Wilson, D.J. Bettridge, Judy M. Kiiru, J. Kyobutungi, C. Tacoli, C. Kang'ethe, Erastus K. Davila, J.D. Kariuki, S. Robinson, Timothy P. Rushton, J. Woolhouse, Mark E.J. Fèvre, Eric M. genomics livestock epidemiology urban areas 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. 2022-04 2022-03-15T20:14:20Z 2022-03-15T20:14:20Z Journal Article https://hdl.handle.net/10568/118384 en Open Access Springer Muloi, 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. |
| spellingShingle | genomics livestock epidemiology urban areas Muloi, Dishon M. Wee, B.A. McClean, D.M.H. Ward, M.J. Pankhurst, L. Phan, H. Ivens, A.C. Kivali, Velma Kiyong'a, Alice Ndinda, Christine Gitahi, N. Ouko, T.T. Hassell, James M. Imboma, Titus Akoko, James M. Karani, Maurice K. Njoroge, Samuel M. Muinde, Patrick Nakamura, Y. Alumasa, Lorren Furmaga, E. Kaitho, T. Öhgren, E.M. Amanya, Fredrick Ogendo, Allan Wilson, D.J. Bettridge, Judy M. Kiiru, J. Kyobutungi, C. Tacoli, C. Kang'ethe, Erastus K. Davila, J.D. Kariuki, S. Robinson, Timothy P. Rushton, J. Woolhouse, Mark E.J. Fèvre, Eric M. Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape |
| title | Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape |
| title_full | Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape |
| title_fullStr | Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape |
| title_full_unstemmed | Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape |
| title_short | Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape |
| title_sort | population genomics of escherichia coli in livestock keeping households across a rapidly developing urban landscape |
| topic | genomics livestock epidemiology urban areas |
| url | https://hdl.handle.net/10568/118384 |
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