DistinctEscherichia colitranscriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection

Abstract

AbstractLow-abundance members of microbial communities are difficult to study in their native habitats. This includesEscherichia coli, a minor, but common inhabitant of the gastrointestinal tract and opportunistic pathogen, including of the urinary tract, where it is the primary pathogen. While multi-omic analyses have detailed critical interactions between uropathogenicEscherichia coli(UPEC) and the bladder that mediate UTI outcome, comparatively little is known about UPEC in its pre-infection reservoir, partly due to its low abundance there (<1% relative abundance). To accurately and sensitively explore the genomes and transcriptomes of diverseE. coliin gastrointestinal communities, we developedE. coliPanSelect which uses a set of probes designed to specifically recognize and captureE. coli’s broad pangenome from sequencing libraries. We demonstrated the ability ofE. coliPanSelect to enrich, by orders of magnitude, sequencing data from diverseE. coliusing a mock community and a set of human stool samples collected as part of a cohort study investigating drivers of recurrent urinary tract infections (rUTI). Comparisons of genomes and transcriptomes betweenE. coliresiding in the gastrointestinal tracts of women with and without a history of rUTI suggest that rUTI gutE. coliare responding to increased levels of oxygen and nitrate, suggestive of mucosal inflammation, which may have implications for recurrent disease.E. coliPanSelect is well suited for investigations of nativein vivobiology ofE. coliin other environments where it is at low relative abundance, and the framework described here has broad applicability to other highly diverse, low abundance organisms.