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 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. Phylogeography and phylogenomic analyses of E. coli isolates collected from humans and domesticated and wild animals across 99 households in Nairobi reveal strong intra-household, and lower but detectable inter-household and inter-host, strain-sharing patterns.

Automated summary

This study investigates the distribution and sharing patterns of Escherichia coli among humans, livestock, and peri-domestic wildlife in Nairobi, Kenya, using whole-genome sequencing. The results show that the diversity and sharing patterns of E. coli are influenced by household and host type, with evidence of inter-household and inter-host sharing, especially between humans and animals. The findings highlight the importance of a large-scale sampling framework and whole-genome sequencing in understanding strain-sharing events and pathways contributing to zoonotic disease emergence and antimicrobial resistance spread.