The female urinary microbiome in urgency urinary incontinence

Abstract

Objective: The purpose of this study was to characterize the urinary microbiota in women who are planning treatment for urgency urinary incontinence and to describe clinical associations with urinary symptoms, urinary tract infection, and treatment outcomes.

Study design: Catheterized urine samples were collected from multisite randomized trial participants who had no clinical evidence of urinary tract infection; 16S ribosomal RNA gene sequencing was used to dichotomize participants as either DNA sequence-positive or sequence-negative. Associations with demographics, urinary symptoms, urinary tract infection risk, and treatment outcomes were determined. In sequence-positive samples, microbiotas were characterized on the basis of their dominant microorganisms.

Results: More than one-half (51.1%; 93/182) of the participants' urine samples were sequence-positive. Sequence-positive participants were younger (55.8 vs 61.3 years old; P = .0007), had a higher body mass index (33.7 vs 30.1 kg/m(2); P = .0009), had a higher mean baseline daily urgency urinary incontinence episodes (5.7 vs 4.2 episodes; P < .0001), responded better to treatment (decrease in urgency urinary incontinence episodes, -4.4 vs -3.3; P = .0013), and were less likely to experience urinary tract infection (9% vs 27%; P = .0011). In sequence-positive samples, 8 major bacterial clusters were identified; 7 clusters were dominated not only by a single genus, most commonly Lactobacillus (45%) or Gardnerella (17%), but also by other taxa (25%). The remaining cluster had no dominant genus (13%).

Conclusion: DNA sequencing confirmed urinary bacterial DNA in many women with urgency urinary incontinence who had no signs of infection. Sequence status was associated with baseline urgency urinary incontinence episodes, treatment response, and posttreatment urinary tract infection risk.

Keywords: bacteria; microbiome; microbiota; urgency urinary incontinence; urinary tract infection.

Figure 1. The urinary microbiota profile of sequence positive participants

The urinary microbiota profiles of sequence positive participants cluster together, as demonstrated in the dendrogram (top), and by the dominant bacterial taxa present, as depicted in the histogram (bottom). The dendrogram was based on clustering of the Euclidean distance between urine samples and each line represents a separate individual. Urine samples that possessed the same dominant bacterial taxa grouped together in the dendrogram and were classified into the following urotypes, as shown by the dashed horizontal line: Lactobacillus, Gardnerella, Gardnerella/Prevotella, Enterobacteriaceae, Staphylococcus, Aerococcus and Diverse. The placement of the urotype grouping line provided clear distinction of urine samples by the dominant genera, while maintaining clusters that contain at least 2 urine samples. The histogram displays the bacterial taxa detected by sequencing as the percentage of sequences per urine by sequence positive participants (N=93). Each bar on the x-axis represents the urinary microbiota sequence-based composition of a single participant. The y-axis represents the percentage of sequences per participant with each color corresponding to a particular bacterial taxon. Bacteria were classified to the genus level with the exception of Enterobacteriaceae and Lachnospiraceae, which could only be classified to the family level. The 15 most sequence abundant bacterial taxa were displayed and the remainder of the taxa, including unclassified sequences, were grouped into the category “Other”.

Figure 2. Distribution of dominant taxa in urine of all sequence positive participants

The sequence proportion of dominant taxa (taxa that accounted for greater than 45% of the sequences in at least one sample) were graphed for the sequence positive samples (N=93). The boxplots represent the 25^th, 50^th and 75^th percentile of the sequence proportion, while points represent outliers. Lactobacillus was detected in the majority of urine samples and the sequence abundance ranged from 0 to 100% of the total sequences per sample. The median amount of Lactobacillus sequences detected per urine was 20%. Gardnerella was the second most frequently detected genus, with 43% of samples containing >1% Gardnerella sequences Whereas Staphylocccus, Aerococcus, Enterobacteriaceae and Bifidobacterium were detected in high abundance in a few samples, they were present at very low levels or not at all in the remainder of samples. For example, Staphylococcus and Aerococcus were detected at >45% of total sequences in only 3 and 2 samples, respectively. Lacto, Lactobacillus; Gard, Gardnerella; Prev, Prevotella; Staph, Staphylococcus; Aero, Aerococcus, Entero, Enterobacteriaceae, and Bifido, Bifidobacterium.

Figure 3. Demographic variable distribution by urotype, including the sequence-negative group

Boxplots are shown comparing each urotype and the sequence negative group to A) age, B) weight, BMI and C) the number of UUI episodes at baseline for each participant. Aero=Aerococcus, Bif=Bifidobacterium, Ent=Enterobacteriaceae, Gard=Gardnerella, Lac=Lactobacillus, Div = diverse, G/P =Gardnerella/Prevotella, Staph=Staphylococcus and Neg = sequence-negative group. N stands for the number of samples within each group.

Figure 4. Comparison of average bacterial sequence abundance in urine by treatment group and UTI outcome

The average amount of bacterial sequences detected in the sequence positive urine of each randomized treatment cohort (anticholinergic versus botox) and UTI outcome cohort (positive versus negative) was calculated. The average bacterial sequence abundance profiles were similar between treatment cohorts, whereas the profiles differed between UTI outcome cohorts.

Figure 5. Urinary microbiota profiles by UTI outcome

The 15 most abundant bacteria detected by sequencing were displayed as the percentage of sequences per sample on the y-axis. The vertical bars along the x-axis represent the microbiota profile of individual participants separated by UTI outcome. The urinary microbiota profiles of the eight UTI positive participants consist of the following urotypes: 1 Lactobacillus, 1 Gardnerella, 2 Enterobacteriaceae, 1 Staphylococcus, 1 Aerococcus, 1 Bifidobacterium and 1 diverse. The proportion of Lactobacillus-dominant urines and diverse urines is less in the UTI positive group compared to the UTI negative group.