Genomic diversity of pathogenic multidrug-resistant Escherichia coli across asymptomatic children and livestock in Nairobi, Kenya

Abstract Pathogenic 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 bla CTX-M-15 and bla OXA-1 , with resistance spanning nine antibiotic classes. Network analysis revealed a stable multidrug-resistance cluster ( bla TEM-1B , aph(3)-Ib, aph(6)-Id, sul2, tetA ) shared across hosts. Virulence 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 healthy community carriers highlights a cryptic reservoir of pathogenic potential outside hospitals. These findings underscore urgent need for genomic surveillance, stewardship and WASH to interrupt transmission of high-risk E. coli clones.