Profiling upper urinary tract microbiota: a feasibility study in patients with urinary stone disease
Authors:
Jan Hrbáček 1; Vítězslav Hanáček 1; Vojtěch Tláskal 2,3; Martina Saláková 4; Pavel Čermák 5; Ruth Tachezy 4; Roman Zachoval 1
Authors‘ workplace:
Urologická klinika 3. lékařské fakulty Univerzity Karlovy a Fakultní Thomayerovy nemocnice, Praha
1; Ústav půdní biologie a biogeochemie, Biologické centrum AV ČR, České Budějovice
2; Mikrobiologický ústav AV ČR, Praha
3; Katedra genetiky a mikrobiologie, Přírodovědecká fakulta Univerzity Karlovy, Praha
4; Oddělení klinické mikrobiologie Fakultní Thomayerovy nemocnice, Praha
5
Published in:
Ces Urol 2022; 26(4): 242-249
Category:
Original Articles
Overview
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. Nextgeneration 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.
Major statement: Upper urinary tract seems to harbour microbial communities, similar to the lower urinary tract.
Keywords:
kidney – urinary bladder – upper urinary tract – human microbiome – virome
Sources
1. Siddiqui H, Nederbragt AJ, Lagesen K, Jeansson SL, Jakobsen KS. Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons. BMC Microbiol. 2011; (11): 1–12.
2. Price TK, Dune T, Hilt EE, et al. The Clinical Urine Culture: Enhanced Techniques Improve Detection of Clinically Relevant Microorganisms. J Clin Microbiol. 2016; 54(5): 1216–22.
3. Pearce MM, Hilt EE, Rosenfeld AB, et al. The female urinary microbiome: a comparison of women with and without urgency urinary incontinence. MBio. 2014; 5(4).
4. Siddiqui H, Lagesen K, Nederbragt AJ, Jeansson SL, Jakobsen KS. Alterations of microbiota in urine from women with interstitial cystitis. BMC Microbiol [Internet]. 2012; 12: 205. Available from: http://www.biomedcentral.com/1471-2180/12/205.
5. Bajic P, Kuiken ME van, Burge BK, et al. Male Bladder Microbiome Relates to Lower Urinary Tract Symptoms. Eur Urol Focus [Internet]. 2020; 15(6): 376–82. Available from: https://doi.org/10.1016/j.euf.2018. 08. 001.
6. Wu P, Zhang G, Zhao J, et al. Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China. Front Cell Infect Microbiol. 2018; 8: 167.
7. Novotná E, Viklický O. BK virová infekce po transplantaci ledvin. Vnitř Lék. 2008; 54(9): 835–41.
8. Miller‑Ensminger T, Garretto A, Brenner J, Thomas‑white K, Zambom A, Wolfe AJ. Bacteriophages of the Urinary Microbiome. J Bacteriol. 2018; 200(7): e00738-17.
9. Sigdel TK, Mercer N, Nandoe S, Nicora CD. Urinary Virome Perturbations in Kidney Transplantation. Front Med. 2018; 5(April): 72.
10. Garretto A, Thomas‑White K, Wolfe AJ, Putonti C. Detecting viral genomes in the female urinary microbiome. J Gen Virol. 2018; 99: 1141–6.
11. Hrbacek J, Morais D, Cermak P, Hanacek V, Zachoval R. Alpha‑diversity and microbial community structure of the male urinary microbiota depend on urine sampling method. Sci Rep [Internet]. 2021; 11(1). Available from: https://doi.org/10.1038/s41598-021-03292-x.
12. Hrbacek J, Tlaskal V, Cermak P, Hanacek V, Zachoval R. Bladder Microbiota Are Associated with Clinical Conditions That Extend beyond the Urinary Tract. Microorganisms. 2022; 10(5): 1–14.
13. Hrbáček J, Tláskal V, Čermák P, Hanáček V, Zachoval R. Bladder cancer is associated with decreased urinary microbiota diversity and alterations in microbial community composition. Urol Oncol Semin Orig Investig. 2022; přijato k publikaci.
14. R Core Team. R: A language and environment for statistical computing. [Internet]. 2022 [cited 2021 Sep 22]. Available from: http://www.r‑project.org/.
15. Oksanen AJ, Blanchet FG, Friendly M, et al. vegan: Community Ecology Package. R package version 2.6-2. Vol. 5, Community Ecology Package. 2022.
16. Chiu CH, Wang YT, Walther BA, Chao A. An improved nonparametric lower bound of species richness via a modified good‑turing frequency formula. Biometrics. 2014; 70(3): 671–82.
17. O’Hara RB. Species richness estimators: How many species can dance on the head of a pin? J Anim Ecol. 2005; 74(2): 375–86.
18. Tachezy R, Smahelova J, Kaspirkova J, Salakova M. Human papillomavirus type‑specific prevalence in the cervical cancer screening population of Czech women. PLoS One. 2013; 8(11): 2–9.
19. Dornbier RA, Bajic P, Van Kuiken M, et al. The microbiome of calcium‑based urinary stones. Urolithiasis [Internet]. 2020; 48(3): 191–9. Available from: https://doi.org/10.1007/s00240-019-01146-w.
20. Xie J, Huang JS, Huang XJ, et al. Profiling the urinary microbiome in men with calcium‑based kidney stones. BMC Microbiol. 2020; 20(1): 1–10.
21. Zhong S, Zheng HY, Suzuki M, et al. Age‑related urinary excretion of BK polyomavirus by nonimmunocompromised individuals. J Clin Microbiol. 2007; 45(1): 193–8.
22. Maggi F, Pistello M, Vatteroni M, et al. Dynamics of persistent TT virus infection, as determined in patients treated with alpha interferon for concomitant hepatitis C virus infection. J Virol. 2001; 75(24): 11999–2004.
23. Frye BC, Bierbaum S, Falcone V, et al. Kinetics of Torque Teno Virus‑DNA Plasma Load Predict Rejection in Lung Transplant Recipients. Transplantation. 2019; 103(4): 815–22.
24. Saláková M, Nemecek V, König J, Tachezy R. Age‑specific prevalence, transmission and phylogeny of TT virus in the Czech Republic. BMC Infect, DiS. 2004; 4(1): 56.
25. Giovannelli I, Ciccone N, Vaggelli G, et al. Utility of droplet digital PCR for the quantitative detection of polyomavirus JC in clinical samples. J Clin Virol. 2016; 82: 70–5.
Labels
Paediatric urologist Nephrology UrologyArticle was published in
Czech Urology
2022 Issue 4
Most read in this issue
- Robotic-assisted reimplantation of the ureter
- The effect of covid-19 on male fertility
- Throwback to the 68th Annual Conference of Czech Urological Society
- Inferior vena cava reconstruction in a patient with locally advanced and recurrent renal cancer