Genomic epidemiology of enteropathogenic Escherichia coli in southwestern Nigeria

作者：Olabisi C. Akinlabi, Rotimi Ayodeji Dada, Ademola A Olayinka, Ibukunoluwa O. Oginni-Falajiki, Oyeniyi S. Bejide, Pelumi Daniel Adewole, Nicholas R. Thomson, Aaron O. Aboderin, Iruka N. Okeke · 发表于：PLoS neglected tropical diseases · 年份：2025 · DOI：10.1371/journal.pntd.0013442 · 被引用次数：3 · 研究领域：Escherichia coli research studies、Antibiotic Resistance in Bacteria、Viral gastroenteritis research and epidemiology

BACKGROUND: Enteropathogenic Escherichia coli (EPEC) are etiological agents of diarrhea. We studied the genetic diversity and virulence factors of EPEC in southwestern Nigeria, where this pathotype is rarely characterized. METHODOLOGY/PRINCIPAL FINDINGS: EPEC isolates (n = 96) recovered from recent southwestern Nigeria diarrhea case-control studies were whole genome-sequenced using Illumina technology. Genomes were assembled using SPAdes and quality was evaluated using QUAST. Virulencefinder, Ectyper, and ResFinder were used to identify virulence genes, serotypes, and resistance genes. Multilocus sequence typing was done by STtyping. Single nucleotide polymorphisms (SNPs) were called out of whole genome alignment using SNP-sites and a phylogenetic tree was constructed using IQtree. Thirty-nine of the 96(40.6%) EPEC isolates were from diarrhea cases diarrhea. Nine isolates from diarrhea patients and four from healthy controls were typical EPEC, harboring bundle-forming pilus (bfp) genes whilst the rest were atypical EPEC. There were 15 EPEC-EAEC hybrids. Atypical serotypes O71:H19 (16, 16.6%), O108:H21 (6, 6.3%), O157:H39 (5, 5.2%), and O165:H9 (4, 4.2%) were the most prevalent; only 8 (8.3%) isolates belonged to classical EPEC serovars. The largest, ST517 clade harbored multiple siderophore and serine protease autotransporter genes and included an O71:H19 subclade <10 SNPs apart, representing a likely outbreak involving 15 children, four with diarrhea. Likely outbreaks, of ty...