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.

Investigating risks for human colonisation with extended spectrum beta-lactamase producing E. coli and K. pneumoniae in Malawian households: a one health longitudinal cohort study

“…Despite low rates of reported ABU, we observed high rates of ESBL-E colonisation in animals, especially in the urban region, consistent with evidence from other LMIC settings where sharing of ESBL-producing bacteria between household members and domestic animals / livestock (19,20) have been reported (21,22). Local animal husbandry practices including the proximity and location of animal co-habitation (23–25), household attitudes to animal and human waste management in the shared environment and animal interactions with key external environments are likely to promote ESBL transmission.…”

Multidrug-Resistant Enteropathogenic Escherichia coli Isolated from Diarrhoeic Calves, Milk, and Workers in Dairy Farms: A Potential Public Health Risk

“…Interestingly, isolates of the same serotype that shared the same farm showed higher genetic similarity than isolates of this serotype in another farm (for example, O26 isolates in Farm 2 displayed 85–95% similarity, although they shared only 75% similarity with O26 isolates from Farm 3). This farm (location)-associated genetic similarity was previously reported worldwide [ 15 , 28 ]. These findings prove vertical and horizontal clonal dissemination of EPEC serovars between different sources within the farm, as previously reported [ 14 , 15 , 28 ].…”

“…This farm (location)-associated genetic similarity was previously reported worldwide [ 15 , 28 ]. These findings prove vertical and horizontal clonal dissemination of EPEC serovars between different sources within the farm, as previously reported [ 14 , 15 , 28 ].…”

“…This may highlight potential interspecies zoonotic transmission of these pathogens between workers and calves within the farm, as reported in other studies [ 14 , 23 ]. This means that dairy farm workers are at constant occupational risk and may also play a role in reverse transmission of MDR E. coli isolates and/or their AMR genes within the farm [ 14 , 15 ]. Furthermore, Silvestro et al [ 23 ] provided genetic evidence of infection transmission from the dairy workers to their families; therefore, they may also pose a health risk to their contacts.…”

“…Cattle and their milk are important reservoirs of E. coli -carrying AMR genes [ 11 , 12 , 13 ]; multidrug resistance (MDR) selection in this host is driven by the excess, non-prescribed use of antibiotics for the prevention or treatment of bacterial infections of economic importance, such as neonatal calf diarrhoea [ 11 , 12 ]. MDR E. coli carried by cattle can pass to humans through contact with live carrier animals or through consumption of their food products [ 14 , 15 ].…”