ArticlePLOS global public health2026
Genomic diversity of diarrheagenic multidrug-resistant Escherichia coli across asymptomatic children and livestock in Nairobi, Kenya.
Article in PLOS global public health, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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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 enteric-associated determinants, with children's isolates carrying significantly more genes than livestock (mean 6.4 vs. 4.2, p = 0.001). The presence of virulent, multidrug-resistant 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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