Characterization of the Interstitial Cystitis/Bladder Pain Syndrome Microbiome in Clinically Diagnosed Patients

Aim: Ongoing research in the urinary disease field suggests that a subset of patients with bladder pain and incontinence may have an infection as the cause of those clinical features, which may be difficult to diagnose by standard testing. Shotgun metagenomics sequencing (smNGS) provides a comprehensive way to identify infectious agents, namely, viruses, fungi, or bacteria, one possible cause that may be responsible for Interstitial Cystitis/Bladder Pain Syndrome (IC/BPS). Methods: DNA was extracted from these samples and sequenced by combining KAPA HyperPlus library construction with next generation sequencing (Nextseq500, Illumina). Reads were analyzed using Xplore-Patho®, an analytical system that permits the detection of 37,000+ microorganisms, including over 12,000 known pathogens. Results: Urine samples were collected from 49 clinically diagnosed IC/BPS. Additionally, controls urine samples were collected from 13 individuals without chronic lower urinary tract symptoms. Comparisons in diversity between the IC/ BPS and control groups were performed. Of the 41 female patients who were diagnosed with IC/BPS, 35 had signs of infection with a microbial signature for IC/BPS, including the presence of Proteobacterium, BK and JC viruses (Betapolyomavirus), and higher fungal loads. The alpha diversity differences between the female IC/BPS and female control groups were not statistically significant (p = 0.18). In contrast, the beta diversity was found to be different between female IC/BPS and control groups using Kruskal-Wallis ANOVA (p = 2.33e-14). Conclusion: Culture, PCR, antigen, or antibody-based standard urine tests cannot comprehensively screen for the infectious causes of IC/BPS. We present an all-inclusive, unbiased smNGS approach that helped unravel the infectious causes of IC/BPS. This new tool can help clinicians treat their patients in a more timely and effective manner.