Bacterial DNA and live bacteria have been detected in human urine in the absence of clinical infection, challenging the prevailing dogma that urine is normally sterile. Urgency urinary incontinence (UUI) is a poorly understood urinary condition characterized by symptoms that overlap urinary infection, including urinary urgency and increased frequency with urinary incontinence. The recent discovery of the urinary microbiome warrants investigation into whether bacteria contribute to UUI. In this study, we used 16S rRNA gene sequencing to classify bacterial DNA and expanded quantitative urine culture (EQUC) techniques to isolate live bacteria in urine collected by using a transurethral catheter from women with UUI and, in comparison, a cohort without UUI. For these cohorts, we demonstrated that the UUI and non-UUI urinary microbiomes differ by group based on both sequence and culture evidences. Compared to the non-UUI microbiome, sequencing experiments revealed that the UUI microbiome was composed of increased Gardnerella and decreased Lactobacillus. Nine genera (Actinobaculum, Actinomyces, Aerococcus, Arthrobacter, Corynebacterium, Gardnerella, Oligella, Staphylococcus, and Streptococcus) were more frequently cultured from the UUI cohort. Although Lactobacillus was isolated from both cohorts, distinctions existed at the species level, with Lactobacillus gasseri detected more frequently in the UUI cohort and Lactobacillus crispatus most frequently detected in controls. Combined, these data suggest that potentially important differences exist in the urinary microbiomes of women with and without UUI, which have strong implications in prevention, diagnosis, or treatment of UUI.

Enhanced quantitative urine culture (EQUC) detects live microorganisms in the vast majority of urine specimens reported as "no growth" by the standard urine culture protocol. Here, we evaluated an expanded set of EQUC conditions (expanded-spectrum EQUC) to identify an optimal version that provides a more complete description of uropathogens in women experiencing urinary tract infection (UTI)-like symptoms. One hundred fifty adult urogynecology patient-participants were characterized using a self-completed validated UTI symptom assessment (UTISA) questionnaire and asked "Do you feel you have a UTI?" Women responding negatively were recruited into the no-UTI cohort, while women responding affirmatively were recruited into the UTI cohort; the latter cohort was reassessed with the UTISA questionnaire 3 to 7 days later. Baseline catheterized urine samples were plated using both standard urine culture and expanded-spectrum EQUC protocols: standard urine culture inoculated at 1 l onto 2 agars incubated aerobically; expanded-spectrum EQUC inoculated at three different volumes of urine onto 7 combinations of agars and environments. Compared to expanded-spectrum EQUC, standard urine culture missed 67% of uropathogens overall and 50% in participants with severe urinary symptoms. Thirty-six percent of participants with missed uropathogens reported no symptom resolution after treatment by standard urine culture results. Optimal detection of uropathogens could be achieved using the following: 100 l of urine plated onto blood (blood agar plate [BAP]), colistin-nalidixic acid (CNA), and MacConkey agars in 5% CO 2 for 48 h. This streamlined EQUC protocol achieved 84% uropathogen detection relative to 33% detection by standard urine culture. The streamlined EQUC protocol improves detection of uropathogens that are likely relevant for symptomatic women, giving clinicians the opportunity to receive additional information not currently reported using standard urine culture techniques.T he diagnostic gold standard for clinically relevant urinary tract infection (UTI) continues to be questioned for both clinical and research purposes. Since the 1950s, clinical practice has relied on detecting Ն105 CFU/ml of a known uropathogen using the standard clinical urine culture protocol (1). The standard urine culture was initially described for detection of patients at risk for pyelonephritis (2); interpretation has been generalized to diagnose lower urinary tract infection despite studies reporting limitations of the Ն10 5 -CFU/ml threshold (3-6). While the clinical focus has centered on various cutoff thresholds, the basic uropathogen detection method remains unchanged.Given emerging evidence that documents the presence of urinary microbiota in many adult women (7-15), it is clear that the mere presence of an organism should not prompt antibiotic treatment. However, clinicians are likely to benefit from a more complete report of organisms present within a symptomatic patient's urine. Recent evidence reports bacteria in ϳ90% of "no-growth" st...

Metagenomic analyses have indicated that the female bladder harbors an indigenous microbiota. However, there are few cultured reference strains with sequenced genomes available for functional and experimental analyses. Here we isolate and genome-sequence 149 bacterial strains from catheterized urine of 77 women. This culture collection spans 78 species, representing approximately two thirds of the bacterial diversity within the sampled bladders, including Proteobacteria, Actinobacteria, and Firmicutes. Detailed genomic and functional comparison of the bladder microbiota to the gastrointestinal and vaginal microbiotas demonstrates similar vaginal and bladder microbiota, with functional capacities that are distinct from those observed in the gastrointestinal microbiota. Whole-genome phylogenetic analysis of bacterial strains isolated from the vagina and bladder in the same women identifies highly similar Escherichia coli, Streptococcus anginosus, Lactobacillus iners, and Lactobacillus crispatus, suggesting an interlinked female urogenital microbiota that is not only limited to pathogens but is also characteristic of health-associated commensals.

Objectives To characterize the urinary microbiota in women 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 female multi-site randomized trial participants without clinical evidence of urinary tract infection and 16S rRNA 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 Over half [51.1% (93/182)] of the participants’ urine samples were sequence-positive. Sequence-positive participants were younger (55.8 vs. 61.3, p=0.0007), had a higher body mass index (33.7 vs. 30.1, p=0.0009), had a higher mean baseline daily urgency urinary incontinence episodes (5.7 vs. 4.2, p<0.0001), responded better to treatment (decrease in urgency urinary incontinence episodes −4.4 vs. −3.3, p=0.0013) and were less likely to develop urinary tract infection (9% vs. 27%, p=0.0011). In sequence-positive samples, eight major bacterial clusters were identified; seven clusters were dominated by a single genus, most commonly Lactobacillus (45%) or Gardnerella (17%), but also other taxa (25%). The remaining cluster had no dominant genus (13%). Conclusions DNA sequencing confirmed urinary bacterial DNA in many women without signs of infection and with urgency urinary incontinence. Sequence status was associated with baseline urgency urinary incontinence episodes, treatment response and post-treatment urinary tract infection risk.

Introduction Many adult women have resident urinary bacteria (urinary microbiome/microbiota). In adult women affected by urinary urgency incontinence (UUI), the etiologic and/or therapeutic role of the urinary microbiome/microbiota remains unknown. Hypothesis Microbiome/microbiota characteristics will relate to clinically relevant treatment response to oral UUI medication. Methods Adult women initiating oral medication treatment for UUI and a comparator group of unaffected women were recruited in a tertiary care health care system. All participants provided baseline clinical data and urine. Women with UUI were given 5mg solifenacin with potential dose escalation to 10mg for inadequate UUI symptoms control at 4 weeks. Additional data and urine samples were collected from women with UUI at 4 and 12 weeks. The samples were assessed by 16S rRNA gene sequencing and enhanced quantitative urine culturing. The primary outcome was treatment response as measured by the validated Patient Global Symptom Control (PGSC) questionnaire. Clinically relevant UUI symptom control was defined as a 4 or 5 score on the PGSC. Results The diversity and composition of the urinary microbiome/microbiota of women with and without UUI differed at baseline. Women with UUI had more bacteria and a more diverse microbiome/microbiota. The clinical response to solifenacin in UUI participants was related to baseline microbiome/microbiota, with responders more likely to have fewer bacteria and a less diverse community at baseline. Non-responders had a more diverse community that often included bacteria not typically found in responders. Conclusions Knowledge of an individual’s urinary microbiome/microbiota may help refine UUI treatment. Complementary tools, DNA sequencing and expanded urine culture, provide information about bacteria that appear related to UUI incontinence status and UUI treatment response in this population of adult women.