Urinary Tract Microbiome Analysed Despite Low Bacterial Load

Although the urinary tract is considered to provide harsh conditions for the growth of bacteria and fungi, the introduction of medical devices as urinary stents offers surfaces for microbial growth leading to the formation of biofilms and encrustations.

In total, 89 patients treated for kidney and ureteral stones who received a stenting for three to six weeks without urinary tract infection at stenting were included in the study [1]. After sterile removal of stents they were analysed by five different methods, i.e., cultivation, scanning electron microscopy (SEM), X-ray diffraction (XRD), quantitative polymerase chain reaction (qPCR) and next generation sequencing (NGS). After cutting small pieces from stents for SEM, mechanical abrasion was applied for extraction of encrustations. The encrustations were applied for cultivation and XRD analysis. For molecular analysis, the DNA was isolated by using the MolYsis™ Complete5 kit (Molzym, Germany), including the degradation of the host and extracellular DNA from microorganisms. NGS was based upon paired-end reads of the V3/V4 region of the 16S rRNA gene on an Illumina® MiSeq and qPCR was accomplished by calibration with dilutions of known copies of plasmid DNA carrying the 16S rRNA gene [1].

Microbiome profiling of samples from the urinary tract is complicated due to the low bacterial load in the samples and the influence of contaminations and inhibitors. Only in 20% of the samples bacterial DNA was detectable by qPCR at loads of 2x10⁵ bacteria per stent which correlated with microscopy. SEM showed only few samples with structures like bacteria. Among positive samples in NGS analysis, 81% of the sequences could be assigned to the species level with a median of 3.8x10⁵ bacteria per stent, which was concordant with qPCR results. Microbiome profiles were dominated by Lactobacillus (for female patients) and Corynebacterium (for male patients).

All in all, a substantial proportion of microorganisms found in the encrustations from urinary stents were associated with bladder microbiota as deposit over the weeks of indwelling. The microbiome profiles showed different urotypes correlating with male and female patients, albeit at low numbers of bacteria, including potentially pathogenic species [1].