Current testing to identify subacute bacterial infection coinciding with irritative lower urinary tract symptoms are limited. New testing models allow increased resolution of small microbial communities residing in our urinary tract. Our goal was to characterize the treatment response of culture negative patients with irritative urinary symptoms to Next Generation Sequencing (NGS) technology suggested antibiotic therapy.

Patients presenting with chronic or recurrent irritative lower urinary tract symptoms with either a negative urinalysis or standard culture with <10,000 colony forming units (CFU’s) were prospectively recruited for characterization. On enrollment, patients completed the validated UTI-SIQ 8 symptom questionnaire, to assess urinary symptoms. Urine was submitted for NGS, which provided speciation of bacterial species present, and recommendations for antibiotic therapy. If patients had an abnormal urinalysis, antibiotic therapy was initiated per recommendations of the technology. At 3-4 weeks follow up, women repeated the validated questionnaire and a clean-catch urine specimen for repeat NGS testing. We used paired samples T-test to assess for changes in symptomatic questionnaires before and after treatment, and Chi Square tests to assess for demographic and clinical factors associated with symptomatic response.

Between July 2023 and 2025 a total of 63 women were assessed for eligibility, 15 had positive urine cultures, and 9 were lost to follow up. Mean age was 52. Baseline urinalysis revealed pyuria in 58.9%, nitrite positive in 0%, and microscopic hematuria in 33.3%. Baseline NGS revealed high, medium, and low levels of bacteria in 23 (59%), 12 (30.8%), and 4 (10.3%) respectively. The most common organisms identified were E. Coli (68%), K. Pneumoniae (38%) and E. Faecalis (21%). Only 2 patients were found to have no significant pathogenic bacteria on their NGS testing, and an additional 1 patient had only non-pathogenic bacteria (lactobacillus), leaving 36/39 with pathogenic bacteria. 27 had a positive urinalysis with treatment data available, and 24/27 with pathogenic bacteria who underwent treatment via NGS directed antibiotic therapy. Mean symptom scores improved from 16.30 (+/-8.02) to 10.56 (+/-7.97), p=0.005. 18 (66.67%) reported >2 point improvement in their symptom scores. Total clearance of pathogenic species occurred in 29.6%, with an additional 29.6% reducing number of species of pathogenic bacteria. There was no association with preliminary pathogenic bacterial species, or clearance of pathogenic species and symptom improvement (Table 1).

NGS identified pathogenic bacteria in 92% women with irritative urinary symptoms and a negative standard urine culture. Directed antibiotic therapy improved irritative lower urinary tract symptoms in 67% of these patients.

NGS detects bacterial colonies in the vast majority of symptomatic women. Directed antibiotic therapy may be associated with improvements in symptoms. Sterilization of urine, or patient factors predictive of response with NGS directed therapy, remain elusive. Future, placebo controlled trials and in depth testing should be pursued.

Continence 19S (2026) 102691
DOI: 10.1016/j.cont.2026.102691