Methods for tracking the microbiome of neurogenic bladders and the effect of probiotic treatment and urinary tract infection on microbial community composition

Abstract

Long-term catheterisation, such as in spinal cord injured patients, increases the risk of urinary tract infection (UTI). Urine culture, the standard UTI diagnostic test, limits the scope of detectable microorganisms, whereas molecular methods allow for the identification of culturable and unculturable microorganisms. This study followed a cohort of patients enrolled in a probiotic clinical trial to determine how the urinary tract microflora changed as a function of probiotic treatment and UTI status. Terminal Restriction Fragment Length Polymorphism (T-RFLP) and next-generation sequencing revealed that urinary catheter biofilms were diverse and differed significantly between individuals. For a given subject, the types and relative abundances of taxa within the microbiome were altered as a result of ingesting probiotics, with significant changes in community composition pre and post probiotic therapy. The onset of symptomatic UTI was also associated with significant fluctuations in the microbial community. Disturbances in the flora associated with probiotic therapy and infection were evident when examining a single individual across time, but less clear in a cohort of individuals. Likewise, grouping patients by UTI history did not reveal distinctions between those with recurrent symptomatic infection as opposed to the asymptomatic. High inter-patient variability may make patterns in the flora difficult to detect when examining multiple subjects. For a given patient, T-RFLP and sequencing generated similar patterns in community composition. However, dominant organisms isolated by urine culture did not match those identified by sequencing urinary catheter flora. Urine cultures revealed a narrower range of organisms, and at times no bacterial growth compared to corresponding sequence data from catheters. This suggests that T-RFLP and sequencing of biofilm dwelling bacteria should be incorporated into methods of investigating urinary tract infection. Longitudinal examination of the individual over time may be the best way to monitor changes in urinary tract flora. T-RFLP is a relatively cheap and rapid technique that can be used to examine changes to the patient's urinary tract flora, which may predict infection and can be used as a diagnostic tool for UTI management.