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

Abstract

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 household-level risk factors for the exchange of AMR genes between sympatric humans and livestock. Results 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 an in-depth understanding of AMR determinants at the interfaces of One Health sectors that will inform AMR prevention and control.

Risk factors for diarrheagenic Escherichia coli infection in children aged 6–24 months in peri-urban community, Nairobi, Kenya

“…There was no relationship between DEC carriage and number of household members which has been identified in previous studies as a risk factor together with animal feces/ manure within the premises [53,54]. Livestock keeping is a common practice in this rapidly urbanizing environment, and interactions between children and livestock is possible even with non-livestock keeping households [29,54,55]. However, there was consistence that livestock ownership had no association with DEC carriage.…”

“…This could have been due to fecal shedding that results in lower pathogen positivity as diarrhea subsides and microbiota-mediated pathogen clearance [52]. There was no relationship between DEC carriage and number of household members which has been identified in previous studies as a risk factor together with animal feces/ manure within the premises [53,54]. Livestock keeping is a common practice in this rapidly urbanizing environment, and interactions between children and livestock is possible even with non-livestock keeping households [29,54,55].…”

Detection of Escherichia coli O157: H7 from patients with Gastroenteritis

“…In Poland, Katherine et al, 18 in a study done on children complaining from gastroenteritis reported that E. coli O157:H7 serotype was not isolated at all. Similarly, Muloi et al 19 could not isolate E. coli O157:H7 from any of 606 diarrhea cases in Italy.…”

Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology

“…To address the increasing prevalence of MDR E. coli infections in humans, it is essential to gain insights into the reservoirs and origins from which humans acquire these infections. A combination of WGS, epidemiology, and ecology was employed to investigate the prevalence of AMR carriage and to characterise the diversity of AMR genes in E. coli, in Nairobi, Kenya [173]. The study pointed out that the composition of AMR gene communities was not linked to the host species.…”