Genomic Diversity of Diarrheagenic Multidrugresistant Escherichia Coli across Asymptomatic Children and Livestock in Nairobi, Kenya
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Date
2026-03
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PLOS Glob Public Health
Abstract
Diarrheagenic 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.
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Okumu 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