Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya

Background Livestock systems have been proposed as a reservoir for
antimicrobial-resistant (AMR) bacteria and AMR genetic determinants that
may infect or colonise humans, yet quantitative evidence regarding their
epidemiological role remains lacking. Here we used a combination of
genomics, epidemiology and ecology to investigate patterns of AMR gene
carriage in Escherichia coli, regarded as a sentinel organism. Methods We
conducted a structured epidemiological survey of 99 households across
Nairobi, Kenya, and whole genome sequenced E. coli isolates from 311
human, 606 livestock, and 399 wildlife faecal samples. We used statistical
models to investigate the prevalence of AMR carriage and characterise AMR
gene diversity and structure of AMR genes in different host populations
across the city. We also investigated house-hold level risk factors for
exchange of AMR genes between sympatric humans and livestock. Findings We
detected 56 unique acquired genes along with 13 point mutations present in
variable proportions in human and animal isolates, known to confer
resistance to nine antibiotic classes. We find that AMR gene community
composition is not associated with host species, but AMR genes were
frequently co-located, potentially enabling the acquisition and dispersal
of multi-drug resistance in a single step. We find that whilst keeping
livestock had no influence on human AMR gene carriage, the potential for
AMR transmission across human-livestock interfaces is greatest when manure
is poorly disposed of and in larger households. Conclusions Findings of
widespread carriage of AMR bacteria in human and animal populations,
including in long-distance wildlife species, in community settings,
highlight the value of evidence-based surveillance to address
antimicrobial resistance on a global scale. Our genomic analysis provided
in-depth understanding of AMR determinants at the interfaces of One-Health
sectors that will inform AMR prevention and control.