Longitudinal Genitourinary and Fecal Microbiomes in Women with and without Recurrent UTI - pt1

Objectives: Recurrent urinary tract infections (rUTI) are a significant burden that worsen antibiotic resistance patterns. Understanding the urogenital, vaginal, and fecal microbiome in women with rUTI may guide innovative treatment to alter the microbiome. Our primary objective was to characterize the urogenital, vaginal, and fecal microbiome in women with rUTI and in control women at weekly intervals over a 1-month period. Secondary objectives were to examine differences in alpha diversity (bacterial species richness and relative abundance) between women with rUTI and controls.

Methods: This was a prospective cohort study of women with rUTI and controls. Each participant self-collected voided urine, vaginal swab, and fecal samples weekly for 4 consecutive weeks. Samples were immediately placed into DNA/RNA shield solutions and stored for analyzation in a single batch. DNA extraction, 16S amplicon sequencing, and analysis were performed on the urine, vaginal, and fecal samples. 16S sequence data were quality checked and demultipexed in Qiime2 and taxonomy tables were created. Shapiro Wilkes and Kruskal Wallis tests were performed to test significance of group (rUTI vs control) on alpha diversity, and mean species diversity within samples. Secondary analyses were performed to evaluate for correlation between age, BMI, menopausal status, and vaginal estrogen usage with microbiome differences.

Results: Fifteen women were enrolled in the study, 7 with rUTI and 8 controls. The mean age was 51 (+/- 14.5) years. 180 total samples (60 urine, 60 vaginal swabs, and 60 fecal) were collected. After DNA extraction and rarefaction, 154 samples (41 urine, 56 vaginal swabs, and 57 fecal) were analyzed. 12 urine samples resulted in no PCR product and 7 urine samples fell below the rarefaction limit. The urogenital and vaginal microbiomes were Lactobacillus predominant in both rUTI and control groups (Figure 1). Blautia was more abundant in the control urobiome. Fecal samples were not predominated by a single taxon. No significant difference was seen in alpha diversity of the voided urine samples between rUTI and control groups. The alpha diversity of vaginal samples was significantly higher in the rUTI participants as compared to the controls (p=0.003). Species richness and evenness were both higher in the rUTI group, compared to the controls (Figure 2). Alpha diversity of fecal samples was significantly higher in the control group, compared to the rUTI group. Secondary analysis examined alpha diversity by menopausal status within the rUTI group. Alpha diversity was significantly higher in the post-menopausal rUTI vaginal samples compared to pre-menopausal rUTI vaginal samples, driven by evenness (Figure 2).

Conclusions: Within-sample diversity differed significantly in vaginal and fecal samples, with the rUTI group having greater diversity in the vaginal microbiome and reduced diversity in the fecal microbiome. This may represent a dysregulation of the vaginal and fecal microbiomes in rUTI.