Introduction: Improving care for urinary tract infections (UTI) in spina bifida (SB) patients requires a better understanding of the resident microbiome. This study aims to characterize the composition and diversity of the urinary and intestinal microbiomes in patients with SB.
Material and Methods: Patients ages 0-30 with SB were enrolled prospectively between 10/2023 to 1/2025 from two SB clinics. Catheterized urine and stool samples were obtained. Expanded quantitative urine culture (EQUC) and 16S rRNA amplicon sequencing were performed on these specimens. Descriptive analyses of demographic, clinical and EQUC data were performed. Sequencing reads were bioinformatically decontaminated prior to analysis.
Results: Ninety-nine subjects met inclusion with a mean age of 7.1 (range 0-27) years old. Fifty-one (50.5%) subjects were male and 91 (92%) had a diagnosis of myelomeningocele. Fifty-four (54.5%) participants performed clean intermittent catheterization and 23 (23%) had a culture-proven UTI within the past year. Of the 128 urine samples obtained, 104 (84.4%) had bacterial growth on EQUC. Bacterial DNA was detectable in 28/30 (97%) urine specimens and 28/28 (100%) stool samples on amplicon sequencing. Escherichia genera was present in 20/30 (67%) of urine specimens and was the dominant genera in 50% of samples. Subjects with a history of prior UTI had greater abundance of Escherichia in the stool than those without a history of UTI (p < 0.05). Subjects on CIC had greater abundance of Staphylococcus spp. in the urine relative to those not on CIC (p < 0.05).
Conclusion: Individuals with SB have high rates of bacteria present on both EQUC (84%) and amplicon sequencing (97%), but little diversity in their urobiome. Escherichia is abundant within the urine of individuals with SB and significantly more abundant in the stool of individuals with prior UTI.
