Introduction: In postmenopausal women, urinary tract infection (UTI) commonly develops into recurrent UTI (rUTI). Enterococcus faecalis, part of the normal flora of the gastrointestinal tract, is frequently associated with UTI. The presence of E. faecalis in the gastrointestinal tract has been proposed as a predisposing factor for UTI. Although E. faecalis is commonly found in urine of both healthy women and those with rUTI, factors E. faecalis utilizes to colonize the urinary tract remain unclear. The goal of this work is to use comparative genomics to identify adaptations that enable E. faecalis persistence in the urinary niche.
Methods: We completed Illumina and Nanopore sequencing of 37 urinary and 15 gut E. faecalis strains. Generated hybrid genome assemblies provided complete chromosome and plasmid sequences. We curated a database of additional 93 E. faecalis reference genomes (34 gut, 13 urine, 46 blood) and performed Pangenome analysis to assess genetic diversity. Bioinformatic analyses of Multilocus Sequence Typing, Plasmid Typing, Antimicrobial Resistance Gene (ARG) predictions, and pan-Genome Wide Association Studies were done to identify genetic factors associated with urinary strains.
Results: Pangenome analysis of 146 E. faecalis genomes revealed diversity among urine strains. Gene enrichment analysis identified enrichment of csp, a gene encoding a cold shock protein (CSP) in urine isolates (86%) compared to gut (51%) and blood (72%). Plasmid types were not significantly different among urinary and gut strains. Urinary strains demonstrated stronger similarity to gut strains in terms of mean genome size, plasmid types, and prevalence of ARGs apart from Vancomycin resistance which was absent in all strains.
Conclusions: Urinary isolates are genetically diverse and no strong clonal cluster was associated with urinary E. faecalis. This suggests multiple E. faecalis lineages may colonize the urinary tract in opportune circumstances. Finding that urinary and gut E. faecalis strains are most similar supports the hypothesis that urinary strains arise from gut reservoirs of E. faecalis. Finally, we have identified csp as an intriguing candidate gene that may be involved in adaptation of E. faecalis to the urinary niche.
Source of Funding: The Welch Foundation to NJD, NIH grant R01AI116610 and the Cecil H. and Ida Green Chair to KLP.