ArticleBMC medicine2022
Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya.
Article in BMC medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 28 citations in OpenAlex.
- Wastewater Metagenomic Surveillance Reveals Socioeconomic Patterns of Pathogen Diversity and Antimicrobial Resistance in Nairobi, Kenya.Antibiotics (Basel, Switzerland) · 2026Article
- Fluoroquinolone-resistantMicrobiology spectrum · 2026Article
- Integrated poultry production as a reservoir ofMicrobial genomics · 2026Article
- Veterinary fixed-dose antibiotics in Africa: a need for evidence-based regulation.Veterinary research · 2026Article
- Antimicrobial resistantOne health (Amsterdam, Netherlands) · 2026Review
- Animal husbandry and environmental conditions are associated with cefotaxime-resistantmedRxiv : the preprint server for health sciences · 2026Article
- Prevalence and patterns of antimicrobial resistance among wildlife populations in Africa: a systematic review.npj antimicrobials and resistance · 2026Article
- Evolution and rise of antimicrobial resistance in key public health bacteria within and across the One Health sectors.Future microbiology · 2026Review
- Population Structure of Escherichia coli Isolated From the Human Bloodstream, Human and Animal Feces, and the Environment in Northern Tanzania.The Journal of infectious diseases · 2026Article
- Genomic diversity of diarrheagenic multidrug-resistant Escherichia coli across asymptomatic children and livestock in Nairobi, Kenya.PLOS global public health · 2026Article
- Pathotype-specific antimicrobial resistance in diarrheagenicFrontiers in microbiology · 2026Review
- One health analysis of antimicrobial resistance inBioinformatics advances · 2026Article
- Animal husbandry and environmental conditions are associated with cefotaxime-resistant Escherichia coli in yard soil in peri-urban Malawi.PLOS global public health · 2026Article
- Emergence of Transferable Plasmid Coharboring mcr-1.1 and blaTransboundary and emerging diseases · 2026Article
- Mobilome-driven antimicrobial resistance in a one health context: evidence and lessons from Africa.Frontiers in veterinary science · 2026Review
- Cross-domain antimicrobial resistance in poultry farming: A One Health assessment of antimicrobial use and multidrug resistance in Kiambu County, Kenya.Veterinary world · 2026Article
- Escherichia coli O157:H7 prevalence in Upper Egypt: impacts on food safety and human Health, with a protection trial using natural antibacterial Piper cubeba.World journal of microbiology & biotechnology · 2025Article
- Characterisation of Plasmid-Associated Antimicrobial Resistance Genes in Coastal MarineInternational journal of molecular sciences · 2025Article
- Human microbiome acquisition and transmission.Nature reviews. Microbiology · 2025Review
- Assessment ofJournal of water and health · 2025Article
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Authors and funding
27 authors at 10 institutions in 3 countries.
Funding
Abstract
backgroundLivestock 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.
methodsWe 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.
resultsWe 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.
conclusionsFindings 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.
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