The darkest place is under the candlestick - healthy urogenital tract as a source of UTI-related Escherichia coli lineages

Abstract

Since the discovery of the urinary microbiome, including identification of Escherichia coli in healthy hosts, its involvement in UTI development is a subject of high interest. We explored population diversity and antimicrobial resistance of E. coli from urogenital microbiome of asymptomatic and recurrent UTI (rUTI) women. We also evaluated the genomic relationship between extraintestinal pathogenic E. coli (ExPEC) strains from healthy and diseased hosts, particularly of the ST131 lineage. E. coli was highly prevalent in asymptomatic women (48%) with slightly higher prevalence in vaginal samples comparing to urine, and occasionally with multiclonal population in the same individual. B2 was the most frequent phylogenetic group, with most strains classified as ExPEC. We demonstrated that virulence associated genes profile does not allow to distinguish strains isolated from healthy and rUTI host. We identified E. coli widespread lineages e.g., sequence types (ST) 127, ST131 (asymptomatic cohort) and ST73, ST131 (rUTI), frequently resistant to at least one antibiotic. Phylogenomics of ST131 and other ExPEC lineages revealed close relatedness between healthy and diseased host. These findings demonstrate that healthy urogenital microbiome is a source of potentially pathogenic and antibiotic resistant E. coli strains, including globally spread E. coli lineages causing UTI including ST131.