Ces Urol 2022, 26(4):242-249

Profiling upper urinary tract microbiota: a feasibility study in patients with urinary stone disease

Jan Hrbáček¹, Vítězslav Hanáček¹, Vojtěch Tláskal^{2, 3}, Martina Saláková⁴, Pavel Čermák⁵, Ruth Tachezy⁴, Roman Zachoval¹

¹ Urologická klinika 3. lékařské fakulty Univerzity Karlovy a Fakultní Thomayerovy nemocnice, Praha

² Ústav půdní biologie a biogeochemie, Biologické centrum AV ČR, České Budějovice

³ Mikrobiologický ústav AV ČR, Praha

⁴ Katedra genetiky a mikrobiologie, Přírodovědecká fakulta Univerzity Karlovy, Praha

⁵ Oddělení klinické mikrobiologie Fakultní Thomayerovy nemocnice, Praha

Hrbáček J, Hanáček V, Tláskal V, Saláková M, Čermák P, Tachezy R, Zachoval R. Profiling upper urinary tract microbiota: a feasibility study in patients with urinary stone disease.

Aim: To investigate the putative existence of upper urinary tract microbiota and if present, to compare the microbial communities from the kidney with those in the urinary bladder.

Patients and Methods: Patients were undergoing endoscopic procedures under anesthesia for upper urinary tract stones. Bladder urine was obtained by aseptic catheterisation, renal urine samples were collected via ureteric catheter inserted into the renal pelvis under cystoscopic and radiographic guidance. Pairwise comparison of urine samples from the same individual were made with regard to their bacteriome and virome.

Results: A total of nine patients (8 males, 1 female) provided both samples for analysis. Next-generation sequencing of the V4 hypervariable region of the 16S rDNA using primers 515F and 806R was performed on eight of them and quantitative polymerase chain reaction for the presence of viral nucleic acids of seven common DNA viruses was performed on seven of them. There were no significant differences in alpha diversity measures (number of OTUs, iChao1, ACE, Shannon and Simpson indices) of samples from the kidney and bladder from the same individual. Likewise, microbial communities from the upper and lower urinary tract within the same individual were more similar to each other than samples within the respective group (e.g. all kidney samples). Viral nucleic acids were detected in the upper as well as lower urinary tract.

Conclusion: Upper urinary tracts seem to be inhabited by microbial communities whose composition resembles that of the lower urinary tract.

Keywords: Human microbiome, upper urinary tract, virome, kidney, urinary bladder.

Received: October 31, 2022; Revised: November 25, 2022; Accepted: November 25, 2022; Prepublished online: November 28, 2022; Published: December 8, 2022