Comparison of the microbiome of bladder urine, upper urinary tract urine, and kidney stones in patients with urolithiasis.

Introduction: It is believed that bacteria can be involved in the formation of all types of stones. The aim of study was to assess the urinary microbiome in patients with urolithiasis.

Material and methods: The study group included 50 patients qualified for endoscopic treatment of urinary tract stones using: ureteroscopic lithotripsy (URSL), retrograde intrarenal surgery (RIRS), percutaneous nephrolithotripsy (PCNL), endoscopic combined intrarenal surgery (ECIRS). Before the procedure, patients were asked to collect urine and stool for analysis. Urine from the upper urinary tract and stone fragments were collected intraoperatively. The research material was subjected to 16S rRNA sequencing. The chemical composition of stones was assessed using Raman spectroscopy.

Results: In the urinary bladder, upper urinary tract, and kidney stone microbiomes of patients with urolithiasis the predominant bacteria identified were: Acinetobacter, Bifidobacterium, Corynebacterium, Cutibacterium, Paracoccus, Pseudomonas, Staphylococcus and Streptococcus. Further analysis showed the relative similarity of the urinary bladder and upper urinary tract microbiomes and the dissimilarity of the kidney stone microbiome. A comparison of the upper urinary tract microbiome based on the method of urine collection and a comparison of urinary bladder and upper urinary tract microbiomes based on the presence of a DJ stent prior to the procedure showed no statistically significant differences.

Conclusions: The microbiome of stones differs from the microbiome of urine, which may play a role in the pathogenesis of urolithiasis. Bladder urine and upper urinary tract urine microbiomes do not differ. Therefore, bladder urine can replace upper urinary tract urine in microbiome studies.