Genomic Diversity of Diarrheagenic Multidrugresistant Escherichia Coli across Asymptomatic Children and Livestock in Nairobi, Kenya

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dc.contributor.authorOkumu, Noah O.
dc.contributor.authorJuma, John
dc.contributor.authorOyola, Samuel
dc.contributor.authorMoodley, Arshnee
dc.contributor.authorMwangi, Kennedy
dc.contributor.authorKibet, Gilbert
dc.contributor.authorOchieng, Linnet
dc.contributor.authorWatson, Julie
dc.contributor.authorNgeranwa, Joseph J.N.
dc.contributor.authorCumming, Oliver
dc.contributor.authorCook, Elizabeth A.J.
dc.contributor.authorMuloi, Dishon M.
dc.date.accessioned2026-04-08T08:09:20Z
dc.date.available2026-04-08T08:09:20Z
dc.date.issued2026-03
dc.descriptionArticle
dc.description.abstractDiarrheagenic Escherichia coli represents a critical public health threat, yet their genomic characteristics in community settings remain poorly described. We sequenced 77 multidrug-resistant isolates from children (n=59), livestock (n=17), and food (n=1) in peri-urban Nairobi, Kenya. Phylogenetic analysis revealed polyphyletic diversity across phylogroups and sequence types without host-specific clustering. We detected high-risk lineages ST69 (n=5) and ST131 (n=2) among children. Nearly all isolates carried extended-spectrum β-lactamase genes, including blaCTX-M-15 and blaOXA-1, with resistance spanning nine antibiotic classes. Network analysis revealed a stable multidrug-resistance cluster (blaTEM-1B, aph(3)-Ib, aph(6)-Id, sul2, tetA) shared across hosts. Virulence-associated gene profiling showed 34 entericassociated determinants, with children’s isolates carrying significantly more genes than livestock (mean 6.4 vs. 4.2, p=0.001). The presence of virulent, multidrugresistant lineages in apparently healthy community carriers highlights a potential reservoir of multidrug-resistant diarrheagenic-associated pathogenic potential outside hospitals. These findings underscore urgent need for genomic surveillance, stewardship and WASH to interrupt transmission of high-risk E. coli clones.
dc.description.sponsorshipBill & Melinda Gates Foundation (BMGF) and the Foreign, Commonwealth and Development Office (FCDO) of the UK Government (grant number INV-008449 to OC) and by the CGIAR Research Program on Agriculture for Nutrition and Health, led by the International Food Policy Research Institute (IFPRI). Additional support was provided by the Royal Society of Tropical Medicine and Hygiene (RSTMH) in partnership with Journal of Comparative Pathology Educational Trust (JCPET) through an early career research grant (grant to NOO).
dc.identifier.citationOkumu NO, Juma J, Oyola S, Moodley A, Mwangi K, Kibet G, et al. (2026) Genomic diversity of diarrheagenic multidrug-resistant Escherichia coli across asymptomatic children and livestock in Nairobi, Kenya. PLOS Glob Public Health 6(4): e0005644. https://doi. org/10.1371/journal.pgph.0005644
dc.identifier.urihttps://doi.org/10.1371/journal.pgph.0005644
dc.identifier.urihttps://ir-library.ku.ac.ke/handle/123456789/32908
dc.language.isoen
dc.publisherPLOS Glob Public Health
dc.titleGenomic Diversity of Diarrheagenic Multidrugresistant Escherichia Coli across Asymptomatic Children and Livestock in Nairobi, Kenya
dc.typeArticle
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