Evidence of uncultivated bacteria in the adult female bladder

Abstract

Clinical urine specimens are usually considered to be sterile when they do not yield uropathogens using standard clinical cultivation procedures. Our aim was to test if the adult female bladder might contain bacteria that are not identified by these routine procedures. An additional aim was to identify and recommend the appropriate urine collection method for the study of bacterial communities in the female bladder. Consenting participants who were free of known urinary tract infection provided urine samples by voided, transurethral, and/or suprapubic collection methods. The presence of bacteria in these samples was assessed by bacterial culture, light microscopy, and 16S rRNA gene sequencing. Bacteria that are not or cannot be routinely cultivated (hereinafter called uncultivated bacteria) were common in voided urine, urine collected by transurethral catheter (TUC), and urine collected by suprapubic aspirate (SPA), regardless of whether the subjects had urinary symptoms. Voided urine samples contained mixtures of urinary and genital tract bacteria. Communities identified in parallel urine samples collected by TUC and SPA were similar. Uncultivated bacteria are clearly present in the bladders of some women. It remains unclear if these bacteria are viable and/or if their presence is relevant to idiopathic urinary tract conditions.

Fig 1

Unweighted UniFrac principal component analysis comparing vaginal swabs (S) to voided (V) and TUC (C) urine samples from patients 1 (red), 6 (yellow), 8, (blue), and 9 (magenta).

Fig 2

Comparison of the total bacterial communities in (A) TUC (blue) and SPA (red) samples and (B) in needle sticks (green) and skin swabs (purple) of culture-negative participants. Numbers of genera in each sample type were totaled, and the percentage of that total was calculated for each genus. Only the most abundant genera are shown. Error bars represent standard deviations. Note the difference in the scales of the y axes.

Fig 3

Comparison of bacterial communities from each culture-negative participant. The percentage of each genus was calculated for each sample. Only the most abundant genera are shown. TUC (blue), SPA (red), needle (yellow), and skin (green) samples are shown. C, control; P, patient.

Fig 4

The most abundant genera in TUC (A), SPA (B), needle (C), and skin (D) samples from a culture-positive patient.