Recurrent urinary tract infection and estrogen shape the taxonomic ecology and functional potential of the postmenopausal urobiome

Abstract

Community-acquired urinary tract infection (UTI) is among the most common bacterial infections observed in humans. Postmenopausal women are a rapidly growing and underserved demographic group who are severely affected by rUTI with a >50% recurrence rate. In this population, rUTI can persist for years, reducing quality of life and imposing a significant healthcare burden. rUTI is most often treated by long-term antibiotic therapy, but development of antibiotic resistance and allergy leave physicians with fewer treatment options. The female urobiome has been identified as a key component of the urogenital environment. However, structural and functional changes in the urobiome underlying rUTI susceptibility in postmenopausal women are not well understood. Here, we used strictly curated, controlled cross-sectional human cohorts of postmenopausal women, urobiome whole genome (shotgun) metagenomic sequencing (WGMS), advanced urine culturing techniques, extensive biobanking of >900 patient-derived urinary bacterial and fungal isolates, and mass spectrometry-based estrogen profiling to survey the urobiome in rUTI patients during infection relapse and remission as well as healthy comparators with no lifetime history of UTI. Our results suggest that a history of rUTI strongly shapes the taxonomic and functional ecology of the urobiome. We also find a putative protective commensal population, consisting of species known to convey protection against bacterial vaginosis such as Lactobacillus crispatus, within the urobiome of women who do not experience UTI. Integration of clinical metadata detected an almost exclusive enrichment of putative protective species belonging to the genus, Lactobacillus, in women taking estrogen hormone therapy (EHT). We further show that the urobiome taxonomic ecology is shaped by EHT, with strong enrichments of putatively protective lactobacilli, such as L. crispatus and L. vaginalis. Integrating quantitative metabolite profiling of urinary estrogens with WGMS, we observed robust associations between urobiome taxa, such as Bifidobacterium breve and L. crispatus, and urinary estrogen conjugate concentrations, suggesting that EHT strongly alters the taxonomic composition of the female urobiome. We have further used functional metagenomic profiling and patient-derived isolate phenotyping to identify microbial metabolic pathways, antimicrobial resistance genes (ARGs), and clinically relevant antimicrobial resistance phenotypes enriched between disease-states. Our data suggest distinct metabolic and ARG signatures of the urobiome associated with current rUTI status and history. Taken together, our data suggests that rUTI history and estrogen use strongly shape the functional and taxonomic composition of the urobiome in postmenopausal women.

Bladder-resident bacteria associated with increased risk of recurrence after electrofulguration in women with antibiotic-recalcitrant urinary tract infection

“…Furthermore, it is a limitation that 16S rRNA probes can only provide genus or familylevel identification and few genus-specific few probe sets have been validated in bladder tissue (42). Future studies should develop more probe sets that can identify other uropathogenic genera as well as genera that comprise the urinary microbiota (43,44). Once these new probe sets are developed, it will be important to determine the association between the genera information of bacteria embedded within the bladder and those identified in urine cultures from future UTI episodes.…”

Commensal Urinary Lactobacilli Inhibit Major Uropathogens In Vitro With Heterogeneity at Species and Strain Level

“…Interestingly, L. crispatus has been previously associated with a healthy host urinary tract in some urinary microbiome studies (Pearce et al, 2014;Neugent et al, 2022) but no difference in abundance of this species was found in others (Komesu et al, 2020;Vaughan et al, 2021). Urinary L. crispatus isolates recently were found to inhibit E. coli CFT073 and E. faecalis in TSB medium via accumulation of phenyl-lactic acid (Abdul-Rahim et al, 2021).…”

“…In this study, we conducted initial functional characterization of urinary lactobacilli from seven species under uniform conditions. Three of those species (eight strains) are from the abundant and frequently identified species in the female urinary tract: L. crispatus, L. gasseri and L. jensenii ( Ma et al., 2012 ; Komesu et al., 2020 ; Neugent et al., 2022 ). While lactobacilli inhabiting other ecological niches have been previously studied, urinary lactobacilli have not previously been characterized, despite their potential for direct interactions with uropathogens and potential clinical implications regarding urinary tract infections.…”

“…While we tested several isolates of lactobacilli, it possible that any isolates from postmenopausal women are less protective in vivo against UTI, potentially explaining the documented susceptibility of this patient population to rUTI ( Pearce et al., 2014 ; Komesu et al., 2020 ; Vaughan et al., 2021 ; Neugent et al., 2022 ; Zeng et al., 2022 ). Therefore, to advance our understanding of the urinary microbiome interactions with uropathogens, it will be essential to compare the behavior of urinary lactobacilli from healthy and rUTI cohorts of pre-menopausal women.…”