The Urinary Microbiome in Postmenopausal Women with Recurrent Urinary Tract Infections

ABSTRACT Recurrent urinary tract infections (UTI) are highly prevalent in postmenopausal women, where vaginal estrogen and prophylactic antibiotics are used for treatment. The etiology of recurrent UTIs is not completely known, but the urinary microbiome is thought to be implicated. Thus, we aimed to compare the “steady state” urinary microbiome in three groups of menopausal women who were all using topically-applied vaginal estrogen: 1) women with recurrent UTIs on daily antibiotic prophylaxis; 2) women with recurrent UTIs not on antibiotic prophylaxis; and 3) age-matched controls without recurrent UTIs. Here we present a cross-sectional analysis of baseline data from 64 women enrolled in a longitudinal cohort study. Catheterized urine samples were collected > 4 weeks after last treatment for UTI. Samples were evaluated using expanded quantitative urine culture (EQUC) and 16S rRNA gene sequencing. With EQUC techniques, there were no significant differences in the median numbers of microbial species isolated among groups (p=0.96), even when considering Lactobacilli (p=0.72). However, there were trends towards different Lactobacillus species between groups. With sequencing the overwhelming majority of urinary samples contained Lactobacilli , with non-significant trends in relative abundance of Lactobacilli among groups. Using a Bayesian regression analysis for compositional data, we identified significant differences in anaerobic taxa that were associated with phenotypic groups. Most of these differences centered on Bacteroidales and the family Prevotellaceae , though differences were also noted in Actinobacteria and certain genera of Clostridiales. Associations between anaerobes within the urinary microbiome and recurrent UTI warrants further investigation. IMPORTANCE In menopausal women with recurrent urinary tract infections (UTIs) compared to those without, the abundance of Lactobacillus within the urinary microbiome is not significantly different when vaginal estrogen is regularly used. In this population, Lactobacillaceae were identified in 97% of urine samples using culture-independent techniques. However, with expanded urine cultures, women with recurrent UTIs taking daily antibiotics had a disproportionately low amount of L. gasseri / L. acidophilus compared to the other phenotypic groups. These findings support the theory that certain Lactobacillus species may be more important than others in the pathophysiology of postmenopausal recurrent UTIs. Furthermore, when using culture-independent techniques to explore urinary microbiota across phenotypic groups, we identified differences in multiple anaerobic taxa. Taken together, these results suggest that altered ratios of anaerobes and certain Lactobacillus species within the urinary microbiome may be implicated in postmenopausal recurrent UTI.