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Razi A, Ghiaei A, Dolatabadi FK, Haghighi R. Unraveling the association of bacteria and urinary stones in patients with urolithiasis: an update review article. Front Med (Lausanne) 2024; 11:1401808. [PMID: 39281813 PMCID: PMC11392849 DOI: 10.3389/fmed.2024.1401808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 08/14/2024] [Indexed: 09/18/2024] Open
Abstract
Urinary stone disease (USD) is a prevalent urological condition, ranking as one of the most common urinary tract disorders globally. Various risk factors influence the formation of kidney stones, and recent research indicates a rising prevalence of urolithiasis worldwide, particularly in developing countries. While the morbidity associated with urinary stones has decreased in recent years, long-term complications such as stone recurrence, kidney failure, and uremia continue to burden patients. Understanding the etiologies of urolithiasis, including the role of bacteria, is crucial as they can contribute to stone recurrence. The incidence of urinary tract infection (UTI) stones can be attributed to specific infectious risk factors, socio-demographic factors, and comorbid metabolic disorders. This review article explores the emerging evidence suggesting the involvement of bacteria in USD. It discusses the potential role of microorganisms in non-infection stones and highlights the association between UTIs and urolithiasis. Furthermore, it surveys the relationship between kidney stones and recurrent UTIs and the formation of bacterial biofilms in UTIs. Considering various risk factors, including biochemical stone analysis and the presence of bacteria, is essential for treating patients with infectious stones optimally. This review aims to provide an updated understanding of the association between bacteria and urinary stones in patients with urolithiasis, shedding light on the pathophysiology of urinary stone formation, urinary stone characteristics, and the urinary microbiome in urinary stones.
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Affiliation(s)
- Abdolah Razi
- Department of Urology, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Azita Ghiaei
- Department of Microbiology, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
| | - Fahimeh Kamali Dolatabadi
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Ramin Haghighi
- Department of Urology, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
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Suarez Arbelaez MC, Monshine J, Porto JG, Shah K, Singh PK, Roy S, Amin K, Marcovich R, Herrmann TRW, Shah HN. The emerging role of the urinary microbiome in benign noninfectious urological conditions: an up-to-date systematic review. World J Urol 2023; 41:2933-2948. [PMID: 37737900 DOI: 10.1007/s00345-023-04588-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/21/2023] [Indexed: 09/23/2023] Open
Abstract
PURPOSE The goal of this systematic review was to examine the current literature on the urinary microbiome and its associations with noninfectious, nonmalignant, urologic diseases. Secondarily, we aimed to describe the most common bioinformatics used to analyze the urinary microbiome. METHODS A comprehensive literature search of Ovid MEDLINE using the keywords "microbiota" AND "prostatic hyperplasia," "microbiota" AND "urinary bladder, overactive," "microbiota" AND "pelvic pain," and "microbiota" AND "urolithiasis" OR "nephrolithiasis" OR "urinary calculi" AND "calcium oxalate" was performed to identify relevant clinical microbiome studies associated with noninfectious benign urological conditions published from 2010 to 2022. We included human studies that evaluated the urinary, stone, or semen microbiota, or any combination of the above-mentioned locations. RESULTS A total of 25 human studies met the inclusion criteria: 4 on benign prostatic hyperplasia (BPH), 9 on overactive bladder (OAB), 8 on calcium oxalate stones, and 4 on chronic pelvic pain syndrome (CPPS). Specific taxonomic profiles in the urine microbiome were associated with each pathology, and evaluation of alpha- and beta-diversity and relative abundance was accounted for most of the studies. Symptom prevalence and severity were also analyzed and showed associations with specific microbes. CONCLUSION The study of the urogenital microbiome is rapidly expanding in urology. Noninfectious benign urogenital diseases, such as BPH, calcium oxalate stones, CPPS, and OAB were found to be associated with specific microbial taxonomies. Further research with larger study populations is necessary to solidify the knowledge of the urine microbiome in these conditions and to facilitate the creation of microbiome-based diagnostic and therapeutic approaches.
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Affiliation(s)
| | - Joshua Monshine
- Desai Sethi Urology Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Joao G Porto
- Desai Sethi Urology Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Khushi Shah
- Desai Sethi Urology Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Praveen K Singh
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sabita Roy
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Katherine Amin
- Desai Sethi Urology Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Robert Marcovich
- Desai Sethi Urology Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Hemendra N Shah
- Desai Sethi Urology Institute, University of Miami Miller School of Medicine, Miami, FL, USA.
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Suryavanshi M, Agudelo J, Miller A. Rare phylotypes in stone, stool, and urine microbiomes are associated with urinary stone disease. Front Mol Biosci 2023; 10:1210225. [PMID: 37602324 PMCID: PMC10436313 DOI: 10.3389/fmolb.2023.1210225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction: In complex microbial communities, the importance of microbial species at very low abundance levels and their prevalence for overall community structure and function is increasingly being recognized. Clinical microbiome studies on urinary stone disease (USD) have indicated that both the gut and urinary tract microbiota are associated with the onset of the disease and that kidney stones them-selves harbor a complex, yet consistent and viable, microbiome. However, how rare phylotypes contribute to this association remains unclear. Delineating the contribution of rare and common phylotypes to urinary stone disease is important for the development of bacteriotherapies to promote urologic health. Methods: The objectives of the current report were to conduct a metaanalysis of 16S rRNA datasets derived from the kidney stone, stool, and urine samples of participants with or without urinary stone disease. To delineate the impact of rare and common phylotypes, metaanalyses were conducted by first separating rare and common taxa determined by both the frequency and abundance of amplicon sequence variants. Results: Consistent with previous analyses, we found that gut, upper urinary, and lower urinary tract microbiomes were all unique. Rare phylotypes comprised the majority of species observed in all sample types, with kidney stones exhibiting the greatest bias toward rarity, followed by urine and stool. Both rare and common fractions contributed significantly to the differences observed between sample types and health disparity. Furthermore, the rare and common fractions were taxonomically unique across all sample types. A total of 222 and 320 unique rare phylotypes from urine and stool samples were found to be significantly associated with USD. A co-occurrence correlation analysis revealed that rare phylotypes are most important for microbiome structure in stones, followed by urine and stool. Discussion: Collectively, the results indicate that rare phylotypes may be important for the pathophysiology of USD, particularly in the kidney stone matrix, which is inherently a very low microbial biomass niche that can have implications for the diagnosis and treatment of kidney stones. Further studies are needed to investigate the functional significance of rare phylotypes in kidney stone pathogenesis.
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Affiliation(s)
- Mangesh Suryavanshi
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, United States
| | - Jose Agudelo
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, United States
| | - Aaron Miller
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, United States
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, United States
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Miller AW, Penniston KL, Fitzpatrick K, Agudelo J, Tasian G, Lange D. Mechanisms of the intestinal and urinary microbiome in kidney stone disease. Nat Rev Urol 2022; 19:695-707. [PMID: 36127409 PMCID: PMC11234243 DOI: 10.1038/s41585-022-00647-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2022] [Indexed: 02/08/2023]
Abstract
Kidney stone disease affects ~10% of the global population and the incidence continues to rise owing to the associated global increase in the incidence of medical conditions associated with kidney stone disease including, for example, those comprising the metabolic syndrome. Considering that the intestinal microbiome has a substantial influence on host metabolism, that evidence has suggested that the intestinal microbiome might have a role in maintaining oxalate homeostasis and kidney stone disease is unsurprising. In addition, the discovery that urine is not sterile but, like other sites of the human body, harbours commensal bacterial species that collectively form a urinary microbiome, is an additional factor that might influence the induction of crystal formation and stone growth directly in the kidney. Collectively, the microbiomes of the host could influence kidney stone disease at multiple levels, including intestinal oxalate absorption and direct crystal formation in the kidneys.
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Affiliation(s)
- Aaron W Miller
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Kristina L Penniston
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Kate Fitzpatrick
- Division of Urology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - José Agudelo
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Gregory Tasian
- Division of Urology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dirk Lange
- The Stone Centre at Vancouver General Hospital, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
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Todorov LG, Sivaguru M, Krambeck AE, Lee MS, Lieske JC, Fouke BW. GeoBioMed perspectives on kidney stone recurrence from the reactive surface area of SWL-derived particles. Sci Rep 2022; 12:18371. [PMID: 36319741 PMCID: PMC9626463 DOI: 10.1038/s41598-022-23331-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/29/2022] [Indexed: 11/18/2022] Open
Abstract
Shock wave lithotripsy (SWL) is an effective and commonly applied clinical treatment for human kidney stones. Yet the success of SWL is counterbalanced by the risk of retained fragments causing recurrent stone formation, which may require retreatment. This study has applied GeoBioMed experimental and analytical approaches to determine the size frequency distribution, fracture patterns, and reactive surface area of SWL-derived particles within the context of their original crystal growth structure (crystalline architecture) as revealed by confocal autofluorescence (CAF) and super-resolution autofluorescence (SRAF) microscopy. Multiple calcium oxalate (CaOx) stones were removed from a Mayo Clinic patient using standard percutaneous nephrolithotomy (PCNL) and shock pulse lithotripsy (SPL). This produced approximately 4-12 mm-diameter PCNL-derived fragments that were experimentally treated ex vivo with SWL to form hundreds of smaller particles. Fractures propagated through the crystalline architecture of PCNL-derived fragments in a variety of geometric orientations to form rectangular, pointed, concentrically spalled, and irregular SWL-derived particles. Size frequency distributions ranged from fine silt (4-8 μm) to very fine pebbles (2-4 mm), according to the Wentworth grain size scale, with a mean size of fine sand (125-250 μm). Importantly, these SWL-derived particles are smaller than the 3-4 mm-diameter detection limit of clinical computed tomography (CT) techniques and can be retained on internal kidney membrane surfaces. This creates clinically undetectable crystallization seed points with extremely high reactive surface areas, which dramatically enhance the multiple events of crystallization and dissolution (diagenetic phase transitions) that may lead to the high rates of CaOx kidney stone recurrence after SWL treatment.
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Affiliation(s)
- Lauren G. Todorov
- grid.35403.310000 0004 1936 9991Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Mayandi Sivaguru
- grid.35403.310000 0004 1936 9991Cytometry and Microscopy to Omics Facility, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Amy E. Krambeck
- grid.66875.3a0000 0004 0459 167XDepartment of Urology, Mayo Clinic, Rochester, MN USA ,grid.16753.360000 0001 2299 3507Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Matthew S. Lee
- grid.16753.360000 0001 2299 3507Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - John C. Lieske
- grid.66875.3a0000 0004 0459 167XDivision of Nephrology and Hypertension, Mayo Clinic, Rochester, MN USA ,grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Bruce W. Fouke
- grid.35403.310000 0004 1936 9991Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Department of Evolution, Ecology and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL USA
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6
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Agudelo J, Miller AW. A Perspective on the Metabolic Potential for Microbial Contributions to Urolithiasis. KIDNEY360 2021; 2:1170-1173. [PMID: 35368346 PMCID: PMC8786102 DOI: 10.34067/kid.0000492021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/21/2021] [Indexed: 02/04/2023]
Affiliation(s)
- Jose Agudelo
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, Ohio
| | - Aaron W. Miller
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, Ohio
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio
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Sivaguru M, Saw JJ, Wilson EM, Lieske JC, Krambeck AE, Williams JC, Romero MF, Fouke KW, Curtis MW, Kear-Scott JL, Chia N, Fouke BW. Human kidney stones: a natural record of universal biomineralization. Nat Rev Urol 2021; 18:404-432. [PMID: 34031587 DOI: 10.1038/s41585-021-00469-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2021] [Indexed: 02/04/2023]
Abstract
GeoBioMed - a new transdisciplinary approach that integrates the fields of geology, biology and medicine - reveals that kidney stones composed of calcium-rich minerals precipitate from a continuum of repeated events of crystallization, dissolution and recrystallization that result from the same fundamental natural processes that have governed billions of years of biomineralization on Earth. This contextual change in our understanding of renal stone formation opens fundamentally new avenues of human kidney stone investigation that include analyses of crystalline structure and stratigraphy, diagenetic phase transitions, and paragenetic sequences across broad length scales from hundreds of nanometres to centimetres (five Powers of 10). This paradigm shift has also enabled the development of a new kidney stone classification scheme according to thermodynamic energetics and crystalline architecture. Evidence suggests that ≥50% of the total volume of individual stones have undergone repeated in vivo dissolution and recrystallization. Amorphous calcium phosphate and hydroxyapatite spherules coalesce to form planar concentric zoning and sector zones that indicate disequilibrium precipitation. In addition, calcium oxalate dihydrate and calcium oxalate monohydrate crystal aggregates exhibit high-frequency organic-matter-rich and mineral-rich nanolayering that is orders of magnitude higher than layering observed in analogous coral reef, Roman aqueduct, cave, deep subsurface and hot-spring deposits. This higher frequency nanolayering represents the unique microenvironment of the kidney in which potent crystallization promoters and inhibitors are working in opposition. These GeoBioMed insights identify previously unexplored strategies for development and testing of new clinical therapies for the prevention and treatment of kidney stones.
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Affiliation(s)
- Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Carl Zeiss Labs@Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Jessica J Saw
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Mayo Clinic School of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Elena M Wilson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - John C Lieske
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Amy E Krambeck
- Department of Urology, Mayo Clinic, Rochester, MN, USA.,Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - James C Williams
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michael F Romero
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.,Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Kyle W Fouke
- Jackson School of Geosciences, University of Texas at Austin, Austin, TX, USA
| | - Matthew W Curtis
- Carl Zeiss Microscopy LLC, One North Broadway, White Plains, NY, USA
| | | | - Nicholas Chia
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Bruce W Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Carl Zeiss Labs@Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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