640: Does first-trimester clean catch urine reflect the microbiome of the vagina or lower urinary tract?

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Assess if microbes in clean catch urine of pregnant women resemble those of the vagina or the lower urinary tract. This is a prospective IRB-approved cohort study of 29 pregnant women with a singleton pregnancy <14 weeks. Exclusion criteria included recurrent UTI, antibiotic use since conception, and urinary tract anomalies. During their 1st trimester visit, consented subjects provided paired clean catch urine and vaginal swab samples. Samples were assessed by an Expanded Quantitative Culture (EQC) method that - compared to the standard urine culture method - uses more types of media and atmospheric conditions with a longer incubation period. Colony forming units (CFU) were counted for each morphologically distinct colony type; representative colonies were purified for identification using MALDI-TOF Mass Spectroscopy. Species identification and CFU counts were combined for analysis using the Bray-Curtis dissimilarity index (BC). A BC value of 0.5 was used to sort paired vaginal and urine samples as similar (<0.5) or different (≥0.5). For descriptive purposes, samples were hierarchically clustered with complete-linkage agglomeration by their vaginal culture results. The majority of the subjects were multiparous (n=20) with a mean age of 29.6 years. EQC detected live microbes in both urine and vaginal samples of all subjects. The vaginal samples clustered into 4 distinct community state structures (Figure). Based on BC indices, paired urine and vaginal samples were dissimilar (BC≥0.5) for 72% (n=21) of subjects. Of the 8 subjects with similar urine and vaginal microbiomes (BC<0.5), Lactobacillus was dominant in 88% of vaginal samples (n=7) and 100% of urine samples (n=8). In contrast, of the 21 subjects with dissimilar microbiomes (BC>0.5), a minority (24%, n=5) had a Lactobacillus-dominant urine sample (p<0.01). The clean catch urine microbiome of pregnant women in their 1st trimester is most often distinct from their vaginal microbiome, evidence that their lower urinary tract contains a unique microbiome. Women with dissimilar urine and vaginal microbiomes were less likely to have Lactobacillus-dominant urine. Given these findings, the vaginal microbiome should not be assumed to represent the lower urinary tract microbiome.