Elizabethtemiloluwa/AMR_Big_data_2026_ST410

ST410 Escherichia coli from human bloodstream infections and wastewater in Nigeria # ST410 Escherichia coli from human bloodstream infections and wastewater in Nigeria ### Authors: Elizabeth Temiloluwa Akande, Oluwadamilare I. Olatunbosun, Ademola A Olayinka, Aaron O. Aboderin, and Iruka N. Okeke. ## Background Escherichia coli sequence type 410 (ST410) is an emerging high-risk, multidrug-resistant clone that has been reported from multiple continents to carry extended-spectrum beta lactamase and carbapenemase genes on IncF plasmids. ST410 has been detected in Nigeria but its population structure and transmission pathways have not been studied. We recently completed the WHO Tricycle protocol in Ile-Ife Nigeria, during which we identified ST410 isolates from bloodstream infections and from wastewater. The isolates were whole genome sequenced with the goal of understanding ST410 inter-relatedness in Nigeria and carriage of antimicrobial resistance genes. ## Methods Twenty-nine ST410 isolates from Ile-Ife were Illumina-sequenced and their genomes quality assured using FastQC. A core-genome phylogenetic tree (variants-only) (snp phylogeny and IQ-TREE) was constructed. Genomes were screened for antibiotic resistance genes (AMRFinderPlus), plasmid replicons (PlasmidFinder), and virulence factors (VirulenceFinder). ## Results The isolates segregated into four ST410 subclades, by isolation niche. These included a wastewater specific (C), human clinical isolate specific (D), predominantly human (5/8) isolate clade (B) and a predominantly wastewater (7/8) clade (A). Clades A and B are aerobactin positive and the predominantly human clade B carried afa adhesin genes. All human (10/10) and 6/19 wastewater isolates carried blaCTX-M-15 extended-spectrum beta-lactamase gene. blaNDM-5 was found in 11/19 wastewater isolates but in none of the human isolates with all but one clade C isolate, and all environmental clade B isolates, carrying this carbapenemase gene, while 2/10 of the human isolates carried blaOXA-181. Other resistance genes (including AmpC …