Top

Published in:

Open Access 01-12-2023 | Urolithiasis | Research

The microbiome of kidney stones and urine of patients with nephrolithiasis

Authors: Ursula Lemberger, Petra Pjevac, Bela Hausmann, David Berry, Daniel Moser, Victoria Jahrreis, Mehmet Özsoy, Shahrokh F. Shariat, Julian Veser

Published in: Urolithiasis | Issue 1/2023

Abstract

The incidence of nephrolithiasis is rising worldwide. Although it is a multifactorial disease, lifestyle plays a major role in its etiology. Another considerable factor could be an aberrant microbiome. In our observational single-center study, we aimed to investigate the composition of bacteria in kidney stones and urine focusing on patients with features of metabolic syndrome. Catheterized urine and kidney stones were collected prospectively from 100 consecutive patients undergoing endoscopic nephrolithotomy between 2020 and 2021 at our clinic. Microbiome composition was analyzed via 16S rRNA gene amplicon sequencing. Detection of bacteria was successful in 24% of the analyzed kidney stones. These patients had a prolonged length of stay compared to patients without verifiable bacteria in their stones (2.9 vs 1.5 days). Patients with features of metabolic syndrome were characterized by kidney stones colonized with classical gastrointestinal bacteria and displayed a significant enrichment of Enterococcaceae and Enterobacteriaceae. Stones of patients without features of metabolic syndrome characterized by Ureaplasma and Staphylococcaceae. Patients with bacteria in their kidney stones exhibit a longer length of stay, possibly due to more complex care. Patients presenting with features of metabolic syndrome displayed a distinct stone microbiome compared to metabolically fit patients. Understanding the role of bacteria in stone formation could enable targeted therapy, prevention of post-operative complications and new therapeutic strategies.

Available only for authorised users

Chewcharat A, Curhan G (2021) Trends in the prevalence of kidney stones in the United States from 2007 to 2016. Urolithiasis 49(1):27–39. https://doi.org/10.1007/s00240-020-01210-wCrossRefPubMed

Wang K, Ge J, Han W, Wang D, Zhao Y, Shen Y et al (2022) Risk factors for kidney stone disease recurrence: a comprehensive meta-analysis. BMC Urol 22(1):62. https://doi.org/10.1186/s12894-022-01017-4CrossRefPubMedPubMedCentral

Shoag J, Tasian GE, Goldfarb DS, Eisner BH (2015) The new epidemiology of nephrolithiasis. Adv Chronic Kidney Dis 22(4):273–278. https://doi.org/10.1053/j.ackd.2015.04.004CrossRefPubMed

Scales CD Jr, Curtis LH, Norris RD, Springhart WP, Sur RL, Schulman KA et al (2007) Changing gender prevalence of stone disease. J Urol 177(3):979–982. https://doi.org/10.1016/j.juro.2006.10.069CrossRefPubMed

Romero V, Akpinar H, Assimos, DG (2010) Kidney stones: a global picture of prevalence, incidence, and associated risk factors. Rev Urol 12(2–3): e86–96. https://www.ncbi.nlm.nih.gov/pubmed/20811557

Batagello CA, Monga M, Miller AW (2018) Calcium oxalate urolithiasis: a case of missing microbes? J Endourol 32(11):995–1005. https://doi.org/10.1089/end.2018.0294CrossRefPubMed

Flannigan RK, Battison A, De S, Humphreys MR, Bader M, Lellig E et al (2018) Evaluating factors that dictate struvite stone composition: a multi-institutional clinical experience from the EDGE research consortium. Can Urol Assoc J 12(4):131–136. https://doi.org/10.5489/cuaj.4804CrossRefPubMed

Michel Daudon AD, Frochot V, Letavernier E, Haymann J-P, Jungers P, Bazin D (2016) Comprehensive morpho-constitutional analysis of urinary stones improves etiological diagnosis and therapeutic strategy of nephrolithiasis. C.R. Chimie 19(11–12):1470–1491. https://doi.org/10.1016/j.crci.2016.05.008CrossRef

Lippert K, Kedenko L, Antonielli L, Kedenko I, Gemeier C, Leitner M et al (2017) Gut microbiota dysbiosis associated with glucose metabolism disorders and the metabolic syndrome in older adults. Benef Microbes 8(4):545–556. https://doi.org/10.3920/BM2016.0184CrossRefPubMed

10.

Kachroo N, Lange D, Penniston KL, Stern J, Tasian G, Bajic P et al (2021) Standardization of microbiome studies for urolithiasis: an international consensus agreement. Nat Rev Urol 18(5):303–311. https://doi.org/10.1038/s41585-021-00450-8CrossRefPubMedPubMedCentral

11.

Pjevac P, Hausmann B, Schwarz J, Kohl G, Herbold CW, Loy A et al (2021) An Economical and flexible dual barcoding, two-step PCR approach for highly multiplexed amplicon sequencing. Front Microbiol 12:669776. https://doi.org/10.3389/fmicb.2021.669776CrossRefPubMedPubMedCentral

12.

Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP (2016) DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13(7):581–583. https://doi.org/10.1038/nmeth.3869CrossRefPubMedPubMedCentral

13.

Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP (2016) Bioconductor workflow for microbiome data analysis: from raw reads to community analyses. F1000Res 5:1492. https://doi.org/10.12688/f1000research.8986.2CrossRefPubMedPubMedCentral

14.

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P et al (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. https://doi.org/10.1093/nar/gks1219CrossRefPubMedPubMedCentral

15.

Huang R, Soneson C, Ernst FGM, Rue-Albrecht KC, Yu G, Hicks SC et al (2020) TreeSummarizedExperiment: a S4 class for data with hierarchical structure. F1000Res 9:1246. https://doi.org/10.12688/f1000research.26669.2CrossRefPubMed

16.

McMurdie PJ, Holmes S (2013) phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8(4):e61217. https://doi.org/10.1371/journal.pone.0061217CrossRefPubMedPubMedCentral

17.

Barnett DJM, Arts ICW, Penders J (2021) microViz: an R package for microbiome data visualization and statistics. J Open Sour Softw. https://doi.org/10.2115/joss.03201CrossRef

18.

Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15(12):550. https://doi.org/10.1186/s13059-014-0550-8CrossRefPubMedPubMedCentral

19.

Turk C, Petrik A, Sarica K, Seitz C, Skolarikos A, Straub M et al (2016) EAU guidelines on interventional treatment for urolithiasis. Eur Urol 69(3):475–482. https://doi.org/10.1016/j.eururo.2015.07.041CrossRefPubMed

20.

Magruder M, Sholi AN, Gong C, Zhang L, Edusei E, Huang J et al (2019) Gut uropathogen abundance is a risk factor for development of bacteriuria and urinary tract infection. Nat Commun 10(1):5521. https://doi.org/10.1038/s41467-019-13467-wCrossRefPubMedPubMedCentral

21.

Taylor EN, Stampfer MJ, Curhan GC (2005) Diabetes mellitus and the risk of nephrolithiasis. Kidney Int 68(3):1230–1235. https://doi.org/10.1111/j.1523-1755.2005.00516.xCrossRefPubMed

22.

Taylor EN, Stampfer MJ, Curhan GC (2005) Obesity, weight gain, and the risk of kidney stones. JAMA 293(4):455–462. https://doi.org/10.1001/jama.293.4.455CrossRefPubMed

23.

Zampini A, Nguyen AH, Rose E, Monga M, Miller AW (2019) Defining dysbiosis in patients with urolithiasis. Sci Rep 9(1):5425. https://doi.org/10.1038/s41598-019-41977-6CrossRefPubMedPubMedCentral

24.

Denburg MR, Koepsell K, Lee JJ, Gerber J, Bittinger K, Tasian GE (2020) Perturbations of the gut microbiome and metabolome in children with calcium oxalate kidney stone disease. J Am Soc Nephrol 31(6):1358–1369. https://doi.org/10.1681/ASN.2019101131CrossRefPubMedPubMedCentral

25.

Chen J, Zhao J, Cao Y, Zhang G, Chen Y, Zhong J et al (2019) Relationship between alterations of urinary microbiota and cultured negative lower urinary tract symptoms in female type 2 diabetes patients. BMC Urol 19(1):78. https://doi.org/10.1186/s12894-019-0506-0CrossRefPubMedPubMedCentral

26.

Barr-Beare E, Saxena V, Hilt EE, Thomas-White K, Schober M, Li B et al (2015) The interaction between enterobacteriaceae and calcium oxalate deposits. PLoS ONE 10(10):e0139575. https://doi.org/10.1371/journal.pone.0139575CrossRefPubMedPubMedCentral

27.

Wagenius M, Borglin J, Popiolek M, Forsvall A, Stranne J, Linder A (2020) Percutaneous nephrolithotomy and modern aspects of complications and antibiotic treatment. Scand J Urol 54(2):162–170. https://doi.org/10.1080/21681805.2020.1740316CrossRefPubMed

28.

Pohl HG, Groah SL, Perez-Losada M, Ljungberg I, Sprague BM, Chandal N et al (2020) The urine microbiome of healthy men and women differs by urine collection method. Int Neurourol J 24(1):41–51. https://doi.org/10.5213/inj.1938244.122CrossRefPubMedPubMedCentral

29.

Bajic P, Van Kuiken ME, Burge BK, Kirshenbaum EJ, Joyce CJ, Wolfe AJ et al (2020) Male bladder microbiome relates to lower urinary tract symptoms. Eur Urol Focus 6(2):376–382. https://doi.org/10.1016/j.euf.2018.08.001CrossRefPubMed

Title: The microbiome of kidney stones and urine of patients with nephrolithiasis
Authors: Ursula Lemberger
Petra Pjevac
Bela Hausmann
David Berry
Daniel Moser
Victoria Jahrreis
Mehmet Özsoy
Shahrokh F. Shariat
Julian Veser
Publication date: 01-12-2023
Publisher: Springer Berlin Heidelberg
Keyword: Urolithiasis
Published in: Urolithiasis / Issue 1/2023
Print ISSN: 2194-7228
Electronic ISSN: 2194-7236
DOI: https://doi.org/10.1007/s00240-022-01403-5

At a glance: The ONWARDS insulin icodec trials

Springer Medicine

The microbiome of kidney stones and urine of patients with nephrolithiasis

Abstract

At a glance: The ONWARDS insulin icodec trials

Springer Medicine

Abstract

Please log in to get access to this content

Other articles of this Issue 1/2023

Determining the safety and effectiveness of percutaneous nephrolithotomy and retrograde intrarenal surgery in treating nephrolithiasis in patients with solitary kidneys

The efficacy of intradermal sterile water application in severe renal colic: a randomised clinical trial

Quality of life after urinary stone surgery based on Japanese Wisconsin Stone Quality of Life questionnaire: multicenter analysis from SMART study group

Calculus anuria: a urological emergency with an excellent outcome

Stone-event-free survival after ureteroscopic lithotripsy by age: comparison between young and older patients