Characterizing the Urinary Microbiome in Women with UTIs Using Clean Catch and Catheterized Samples

Objectives: This study aims to characterize the urinary microbiome in those with recurrent urinary tract infection (rUTI) using PCR and to describe the difference between uropathogens found on clean catch versus catheterized urine samples.

Methods: : A non-randomized prospective cohort study was conducted of women enrolled from a urogynecology clinic who indicated a history of one UTI in the past 6 months or three in the past 1 year. Clean catch and catheterized urine samples were collected for each patient and were analyzed with PCR. A perineal swab was also collected for each patient. Paired two-sided t-test was used to determine the difference in uropathogens between the clean catch and catheterized samples. Diagnosis of bladder pain was determined by urethral or bladder pain that is present either constantly or intermittently for a period of 6 months or more.

Results: From August 2021- February 2023, 29 patients were enrolled in the study. The median age was 56 (range: 23-86). Median parity was 2 with around 30% (n=9) of participants reporting parity of 0. Around 72% (n=21) of patients are post-menopausal or perimenopausal and 41% (n=12) reported a past history of hysterectomy. Most participants in this population were White (n=23, 79%) and/or Hispanic (n=21, 72%). Four participants (14%) reported former smoking and no patients reported current smoking. Six participants (21%) had Stage 1 prolapse and one participant had Stage 2 prolapse (3%). Uropathogens were found in 83% of clean catch samples (n=24) and 59% of catheterized samples (n=17). Clean catch samples found significantly more uropathogens (mean=1.86) than catheterized samples (mean=1.10) (p=0.04). Escherichia coli (E.coli) was the most common uropathogen found in clean catch samples (n=16, 55%), whereas Enterococcus faecalis was the most common uropathogen found in catheterized samples (n=8, 28%) followed by E.coli (n=7, 24%). Of the 17 (59%) catheterized samples with a uropathogen, 8 patients (47%) had L.gasseri on perineal swab or clean catch. Of the 13 patients without a uropathogen on the catheterized sample, 6 (46%) had L.gasseri on perineal swab or clean catch. The perineal swab identified twelve patients with E.coli (41%), six with E.faecalis (21%), and three with both (10%). Seven of nine patients with bladder pain syndrome were found to have a predominance of E.coli and five had L.gasseri (55%) in either the perineal swab or clean catch.

Conclusions: Clean catch samples contain significantly more uropathogens than catheterized samples which may indicate a lack of specificity in clean catch samples in regard to diagnosis and treatment of urinary tract infection patients with PCR. Characterizing PCR can also help tailor treatments. This is an ongoing study, and future studies aim to characterize the differences in the microbes found on clean catch and catheterized samples.