Dataset Information

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.

SUBMITTER: Muloi DM

PROVIDER: S-EPMC8975746 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Muloi Dishon M DM Wee Bryan A BA McClean Deirdre M H DMH Ward Melissa J MJ Pankhurst Louise L Phan Hang H Ivens Alasdair C AC Kivali Velma V Kiyong'a Alice A Ndinda Christine C Gitahi Nduhiu N Ouko Tom T Hassell James M JM Imboma Titus T Akoko James J Murungi Maurice K MK Njoroge Samuel M SM Muinde Patrick P Nakamura Yukiko Y Alumasa Lorren L Furmaga Erin E Kaitho Titus T Öhgren Elin M EM Amanya Fredrick F Ogendo Allan A Wilson Daniel J DJ Bettridge Judy M JM Kiiru John J Kyobutungi Catherine C Tacoli Cecila C Kang'ethe Erastus K EK Davila Julio D JD Kariuki Samuel S Robinson Timothy P TP Rushton Jonathan J Woolhouse Mark E J MEJ Fèvre Eric M EM

Nature microbiology 20220314 4

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 stru ...[more]

PMID: 35288654

Similar Datasets

Project description:Urban livestock keeping in developing cities have an important role in food security and livelihoods but can also pose a significant threat to the environment and health of urban dwellers. The aim of this study was to identify the different livestock systems in Nairobi, their supply chains, and their management and food safety risks. Seven focus group discussions with livestock production officers in charge of each major Nairobi sub-county were conducted. Data were collected on the type of systems existing for each livestock species and their supply chains, disease management, food safety risks, and general husbandry and gender factors. Supply chain flow diagrams and thematic analysis of the data was done. Results of the study show a large variability of livestock keeping in Nairobi. The majority were small scale with: <5 dairy cows, 1-6 dairy goats, <10 small ruminants, <20 pigs, 200-500 broilers, 300-500 layers, <10 indigenous chickens, or <20 rabbits. Beef keeping was mainly described as a "by the way" system or done by traders to fatten animals for 3 month. Supply chain analysis indicated that most dairy farmers sold milk directly to consumers due to "lack of trust" of these in traders. Broiler and pig farmers sold mainly to traders but are dependent on few large dominating companies for their replacement or distribution of products. Selling directly to retailers or consumers (including own consumption), with backyard slaughtering, were important chains for small-scale pig, sheep and goat, and indigenous chicken keepers. Important disease risk practices identified were associated with consumption of dead and sick animals, with underground network of brokers operating for ruminant products. Qualified trained health managers were used mainly by dairy farmers, and large commercial poultry and pig farmers, while use of unqualified health managers or no treatment were common in small-scale farming. Control of urban livestock keepers was reported difficult due to their "feeling of being outlaws," "lack of trust" in government, "inaccessibility" in informal settlements, "lack of government funding," or "understaffing." Findings are useful for designing policies to help to control urban livestock production and minimize its associated health and environment risks.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets