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Li Z, Zhang Z, Yu P, Ni Y. Microbial communities, antibiotic resistance genes, and virulence factors in urinary infectious stone-associated urinary tract infections. Urolithiasis 2024; 52:88. [PMID: 38874649 DOI: 10.1007/s00240-024-01588-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/03/2024] [Indexed: 06/15/2024]
Abstract
Urinary infectious stones are challenging due to bacterial involvement, necessitating a comprehensive understanding of these conditions. Antibiotic-resistant urease-producing bacteria further complicate clinical management. In this study, analysis of urine and stone samples from urinary tract infection (UTI) patients revealed microbial shifts, gene enrichment in stones, and metabolic pathway disparities; antibiotic resistance gene trends were phylum-specific, urease-producing bacteria are at risk of acquiring AMR carried by Enterobacteriaceae under antibiotic, emphasizing potential AMR dissemination between them; Correlations of key pathogenic species in kidney stone and urine microbial communities highlight the need for targeted therapeutic strategies to manage complexities in UTIs; Stones and urine contain a variety of deleterious genes even before antibiotic use, and piperacillin/tazobactam better reduced the abundance of antibiotic resistance genes in stones and urine. The presence of diverse antibiotic resistance and virulence genes underscores challenges in clinical management and emphasizes the need for effective treatment strategies to mitigate risks associated with UTIs and urinary infectious stone formation. Ongoing research is vital for advancing knowledge and developing innovative approaches to address these urological conditions.
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Affiliation(s)
- Ziyun Li
- Center for Translational Medicine Research, Shandong Provincial Third Hospital, Shandong University, Jinan, China
| | - Zhaocun Zhang
- Urology Department, Cheeloo College of Medicine, Qilu Hospital, Shandong University, Jinan, China
| | - Peng Yu
- Urology Department, Cheeloo College of Medicine, Qilu Hospital, Shandong University, Jinan, China
- Urology Department, Weihai Municipal Hospital, Shandong University, Weihai, China
| | - Yongliang Ni
- Urology Department, Shandong Provincial Third Hospital, Shandong University, Jinan, China.
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2
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Xie J, Zhang XQ, Guo JN, Yuan Q, Xiao KF, Yuan YQ. The urinary microbiota composition and functionality of calcium oxalate stone formers. Front Cell Infect Microbiol 2024; 14:1394955. [PMID: 38912208 PMCID: PMC11190077 DOI: 10.3389/fcimb.2024.1394955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 04/29/2024] [Indexed: 06/25/2024] Open
Abstract
Background Accumulated evidences indicate that dysbiosis of the urinary microbiota is associated with kidney stone formation. In the present study, we aimed to investigate the urinary microbiota composition and functionality of patients with calcium oxalate stones and compare it with those of healthy individuals. Method We collected bladder urine samples from 68 adult patients with calcium oxalate stones and 54 age-matched healthy controls by transurethral catheterization. 16S rRNA gene and shotgun sequencing were utilized to characterize the urinary microbiota and functionality associated with calcium oxalate stones. Results After further exclusion, a total of 100 subjects was finally included and analyzed. The diversity of the urinary microbiota in calcium oxalate stone patients was not significantly different from that of healthy controls. However, the urinary microbiota structure of calcium oxalate stone formers significantly differed from that of healthy controls (PERMANOVA, r = 0.026, P = 0.019). Differential representation of bacteria (e.g., Bifidobacterium) and several enriched functional pathways (e.g., threonine biosynthesis) were identified in the urine of calcium oxalate stone patients. Conclusion Our results showed significantly different urinary microbiota structure and several enriched functional pathways in calcium oxalate stone patients, which provide new insight into the pathogenesis of calcium oxalate stones.
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Affiliation(s)
- Jing Xie
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
- Shenzhen Engineering and Technology Center of Minimally Invasive Urology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Xue-qi Zhang
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
- Shenzhen Engineering and Technology Center of Minimally Invasive Urology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Ji-nan Guo
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
- Shenzhen Engineering and Technology Center of Minimally Invasive Urology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Qian Yuan
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
- Shenzhen Engineering and Technology Center of Minimally Invasive Urology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Ke-feng Xiao
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
- Shenzhen Engineering and Technology Center of Minimally Invasive Urology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Ye-qing Yuan
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
- Shenzhen Engineering and Technology Center of Minimally Invasive Urology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
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Wan W, Wu W, Amier Y, Li X, Yang J, Huang Y, Xun Y, Yu X. Engineered microorganisms: A new direction in kidney stone prevention and treatment. Synth Syst Biotechnol 2024; 9:294-303. [PMID: 38510204 PMCID: PMC10950756 DOI: 10.1016/j.synbio.2024.02.005] [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: 10/25/2023] [Revised: 01/31/2024] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Numerous studies have shown that intestinal and urinary tract flora are closely related to the formation of kidney stones. The removal of probiotics represented by lactic acid bacteria and the colonization of pathogenic bacteria can directly or indirectly promote the occurrence of kidney stones. However, currently existing natural probiotics have limitations. Synthetic biology is an emerging discipline in which cells or living organisms are genetically designed and modified to have biological functions that meet human needs, or even create new biological systems, and has now become a research hotspot in various fields. Using synthetic biology approaches of microbial engineering and biological redesign to enable probiotic bacteria to acquire new phenotypes or heterologous protein expression capabilities is an important part of synthetic biology research. Synthetic biology modification of microorganisms in the gut and urinary tract can effectively inhibit the development of kidney stones by a range of means, including direct degradation of metabolites that promote stone production or indirect regulation of flora homeostasis. This article reviews the research status of engineered microorganisms in the prevention and treatment of kidney stones, to provide a new and effective idea for the prevention and treatment of kidney stones.
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Affiliation(s)
- Wenlong Wan
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Weisong Wu
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yirixiatijiang Amier
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xianmiao Li
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Junyi Yang
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yisheng Huang
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yang Xun
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xiao Yu
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
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Joubran P, Roux FA, Serino M, Deschamps JY. Gut and Urinary Microbiota in Cats with Kidney Stones. Microorganisms 2024; 12:1098. [PMID: 38930480 PMCID: PMC11205531 DOI: 10.3390/microorganisms12061098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/10/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
Upper urinary tract urolithiasis is an emerging disease in cats, with 98% of kidney stones composed of calcium oxalate. In humans, disturbances in the intestinal and urinary microbiota are suspected to contribute to the formation of calcium oxalate stones. We hypothesized that similar mechanisms may be at play in cats. This study examines the intestinal and urinary microbiota of nine cats with kidney stones compared to nine healthy cats before, during, and after treatment with the antibiotic cefovecin, a cephalosporin. Initially, cats with kidney stones displayed a less diverse intestinal microbiota. Antibiotic treatment reduced microbiota diversity in both groups. The absence of specific intestinal bacteria could lead to a loss of the functions these bacteria perform, such as oxalate degradation, which may contribute to the formation of calcium oxalate stones. This study confirms the presence of a distinct urobiome in cats with kidney stones, characterized by greater richness and diversity compared to healthy cats. These findings highlight the potential of microbiota modulation as a strategy to prevent renal lithiasis in cats.
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Affiliation(s)
- Patrick Joubran
- Nutrition, PathoPhysiology and Pharmacology (NP3) Unit, Oniris VetAgro Bio, Nantes-Atlantic College of Veterinary Medicine, Food Science and Engineering, La Chantrerie, CEDEX 03, 44 307 Nantes, France; (P.J.); (F.A.R.)
| | - Françoise A. Roux
- Nutrition, PathoPhysiology and Pharmacology (NP3) Unit, Oniris VetAgro Bio, Nantes-Atlantic College of Veterinary Medicine, Food Science and Engineering, La Chantrerie, CEDEX 03, 44 307 Nantes, France; (P.J.); (F.A.R.)
- Emergency and Critical Care Unit, Oniris VetAgro Bio, Nantes-Atlantic College of Veterinary Medicine, Food Science and Engineering, La Chantrerie, CEDEX 03, 44 307 Nantes, France
| | - Matteo Serino
- IRSD, Institut de Recherche en Santé Digestive, Institut National de la Santé et de la Recherche Médicale (INSERM) U1220, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse III-Paul Sabatier (UPS), CS 60039, 31 024 Toulouse, France
| | - Jack-Yves Deschamps
- Nutrition, PathoPhysiology and Pharmacology (NP3) Unit, Oniris VetAgro Bio, Nantes-Atlantic College of Veterinary Medicine, Food Science and Engineering, La Chantrerie, CEDEX 03, 44 307 Nantes, France; (P.J.); (F.A.R.)
- Emergency and Critical Care Unit, Oniris VetAgro Bio, Nantes-Atlantic College of Veterinary Medicine, Food Science and Engineering, La Chantrerie, CEDEX 03, 44 307 Nantes, France
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5
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Noonin C, Thongboonkerd V. Beneficial roles of gastrointestinal and urinary microbiomes in kidney stone prevention via their oxalate-degrading ability and beyond. Microbiol Res 2024; 282:127663. [PMID: 38422861 DOI: 10.1016/j.micres.2024.127663] [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: 11/17/2023] [Revised: 02/11/2024] [Accepted: 02/19/2024] [Indexed: 03/02/2024]
Abstract
Formation of calcium oxalate (CaOx) crystal, the most common composition in kidney stones, occurs following supersaturation of calcium and oxalate ions in the urine. In addition to endogenous source, another main source of calcium and oxalate ions is dietary intake. In the intestinal lumen, calcium can bind with oxalate to form precipitates to be eliminated with feces. High intake of oxalate-rich foods, inappropriate amount of daily calcium intake, defective intestinal transporters for oxalate secretion and absorption, and gastrointestinal (GI) malabsorption (i.e., from gastric bypass surgery) can enhance intestinal oxalate absorption, thereby increasing urinary oxalate level and risk of kidney stone disease (KSD). The GI microbiome rich with oxalate-degrading bacteria can reduce intestinal oxalate absorption and urinary oxalate level. In addition to the oxalate-degrading ability, the GI microbiome also affects expression of oxalate transporters and net intestinal oxalate transport, cholesterol level, and short-chain fatty acids (SCFAs) production, leading to lower KSD risk. Recent evidence also shows beneficial effects of urinary microbiome in KSD prevention. This review summarizes the current knowledge on the aforementioned aspects. Potential benefits of the GI and urinary microbiomes as probiotics for KSD prevention are emphasized. Finally, challenges and future perspectives of probiotic treatment in KSD are discussed.
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Affiliation(s)
- Chadanat Noonin
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
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Ellison JS, Atkinson SN, Hayward M, Hokanson E, Sheridan KR, Salzman N. The intestinal microbiome of children with initial and recurrent nephrolithiasis: A pilot study and exploratory analysis. J Pediatr Urol 2024; 20:18-25. [PMID: 37802717 PMCID: PMC10922064 DOI: 10.1016/j.jpurol.2023.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/30/2023] [Accepted: 09/19/2023] [Indexed: 10/08/2023]
Abstract
INTRODUCTION Kidney stone disease in children is rising disproportionate to the general population, representing a disease population with a distinct biological mechanism as compared to adults. Factors influencing recurrent kidney stone disease in children are poorly characterized and the associations of the intestinal microbiome within sub-populations of kidney stone formers, however, are not well described. We evaluated a pilot cohort of children with nephrolithiasis comparing patients based on recurrent kidney stone episodes and abnormal 24-h urinary parameters, with dual aims to compare the microbiome signal in children with initial and recurrent nephrolithiasis and to explore additional associations in microbiome composition and diversity within this population. METHODS Children aged 6-18 with a history of nephrolithiasis, without an active ureteral calculus or antibiotic exposure within 30 days of study entry were eligible to participate. All participants had a 24-h urine study within 6 months of study entry and provided a fecal sample. Microbiome samples were analyzed using 16S ribosomal DNA sequencing techniques for alpha and beta diversity comparing initial and recurrent stone formers as well as microbiome multivariate association (MaAsLin2) to determine differentially abundant taxa. Shotgun sequencing reads were aligned to custom oxidase degradation and butyrate production gene databases (5 databases total). Comparisons for MaAsLin2 and shotgun metagenomics, normalized to sequencing depth, were based on stone recurrence, sex, hypercalcuria (≤4 mg/kg/day), hyperoxaluria (≥45 mg/1.73 m2), and hypocitraturia (<310 mg/1.73 m2 [females] or < 365 mg/1.73 m2 [males]). RESULTS A total of 16 enrolled children provided samples sufficient for analyses, including 9 girls and 7 boys, of whom 5 had experienced recurrent kidney stone events. Three participants had hypercalcuria, 2 had hyperoxaluria, and 4 had hypocitraturia. Comparisons of Formyl-CoA transferase between index and recurrent urinary stone disease revealed a trend towards higher mean abundance of the gene in initial stone formers (0.166% vs 0.0343%, p = 0.2847) (Summary Figure), while trends toward lower biodiversity were also noted in the recurrent stone cohort on both Faith (p = 0.06) and Shannon (p = 0.05) indices. Exploratory analyses found Eubacterium siraeum to be significantly greater in relative abundance in children with documented hypercalciuria (p = 0.001). DISCUSSION Our pilot study demonstrates possible signals in both microbial diversity and oxalate gene expression, both of which are lower in recurrent pediatric kidney stone patients. These findings warrant further investigation as a potential diagnostic marker for future kidney stone events.
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Affiliation(s)
- Jonathan S Ellison
- Division of Pediatric Urology & Department of Urology, Children's Wisconsin & Medical College of Wisconsin, Milwaukee WI, USA.
| | - Samantha N Atkinson
- Center for Microbiome Research, Medical College of Wisconsin, Milwaukee WI, USA
| | - Mike Hayward
- Center for Microbiome Research, Medical College of Wisconsin, Milwaukee WI, USA
| | - Elise Hokanson
- Division of Pediatric Urology & Department of Urology, Children's Wisconsin & Medical College of Wisconsin, Milwaukee WI, USA
| | - Katherine R Sheridan
- Division of Pediatric Urology & Department of Urology, Children's Wisconsin & Medical College of Wisconsin, Milwaukee WI, USA
| | - Nita Salzman
- Division of Pediatric Urology & Department of Urology, Children's Wisconsin & Medical College of Wisconsin, Milwaukee WI, USA; Center for Microbiome Research, Medical College of Wisconsin, Milwaukee WI, USA
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7
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He SK, Wang JH, Li T, Yin S, Cui JW, Xiao YF, Tang Y, Wang J, Bai YJ. Sleep and circadian rhythm disturbance in kidney stone disease: a narrative review. Front Endocrinol (Lausanne) 2023; 14:1293685. [PMID: 38089624 PMCID: PMC10711275 DOI: 10.3389/fendo.2023.1293685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023] Open
Abstract
The circadian rhythm generated by circadian clock genes functions as an internal timing system. Since the circadian rhythm controls abundant physiological processes, the circadian rhythm evolved in organisms is salient for adaptation to environmental change. A disturbed circadian rhythm is a trigger for numerous pathological events. Recently, accumulated data have indicated that kidney stone disease (KSD) is related to circadian rhythm disturbance. However, the mechanism between them has not been fully elucidated. In this narrative review, we summarized existing evidence to illustrate the possible association between circadian rhythm disturbance and KSD based on the epidemiological studies and risk factors that are linked to circadian rhythm disturbance and discuss some chronotherapies for KSD. In summary, KSD is associated with systemic disorders. Metabolic syndrome, inflammatory bowel disease, and microbiome dysbiosis are the major risk factors supported by sufficient data to cause KSD in patients with circadian rhythm disturbance, while others including hypertension, vitamin D deficiency, parathyroid gland dysfunction, and renal tubular damage/dysfunction need further investigation. Then, some chronotherapies for KSD were confirmed to be effective, but the molecular mechanism is still unclear.
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Affiliation(s)
- Si-Ke He
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Jia-Hao Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Li
- Department of Urology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Shan Yin
- Department of Urology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Jian-Wei Cui
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Yun-Fei Xiao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Yin Tang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Jia Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Yun-Jin Bai
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
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Kumar A, Estes Bright LM, Garren MRS, Manuel J, Shome A, Handa H. Chemical Modification of Tiopronin for Dual Management of Cystinuria and Associated Bacterial Infections. ACS APPLIED MATERIALS & INTERFACES 2023; 15:43332-43344. [PMID: 37671841 PMCID: PMC10520916 DOI: 10.1021/acsami.3c07160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/22/2023] [Indexed: 09/07/2023]
Abstract
Cystinuria is an inherited autosomal recessive disease of the kidneys of recurring nature that contributes to frequent urinary tract infections due to bacterial growth and biofilm formation surrounding the stone microenvironment. In the past, commonly used strategies for managing cystinuria involved the use of (a) cystine crystal growth inhibitors such as l-cystine dimethyl ester and lipoic acid, and (b) thiol-based small molecules such as N-(2-mercaptopropionyl) glycine, commonly known as tiopronin, that reduce the formation of cystine crystals by reacting with excess cystine and generating more soluble disulfide compounds. However, there is a dearth of simplistic chemical approaches that have focused on the dual treatment of cystinuria and the associated microbial infections. This work strategically exploited a single chemical approach to develop a nitric oxide (NO)-releasing therapeutic compound, S-nitroso-2-mercaptopropionyl glycine (tiopronin-NO), for the dual management of cystine stone formation and the related bacterial infections. The results successfully demonstrated that (a) the antibacterial activity of NO rendered tiopronin-NO effective against the stone microenvironment inhabitants, Escherichia coli and Pseudomonas aeruginosa, and (b) tiopronin-NO retained the ability to undergo disulfide exchange with cystine while being reported to be safe against canine kidney and mouse fibroblast cells. Thus, the synthesis of such a facile molecule aimed at the dual management of cystinuria and related infections is unprecedented in the literature.
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Affiliation(s)
- Anil Kumar
- School
of Chemical Materials and Biomedical Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Lori M. Estes Bright
- School
of Chemical Materials and Biomedical Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Mark Richard Stephen Garren
- School
of Chemical Materials and Biomedical Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - James Manuel
- School
of Chemical Materials and Biomedical Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Arpita Shome
- School
of Chemical Materials and Biomedical Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Hitesh Handa
- School
of Chemical Materials and Biomedical Engineering, University of Georgia, Athens, Georgia 30602, United States
- Pharmaceutical
and Biomedical Sciences Department, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
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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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Thongprayoon C, Vaughan LE, Barreto EF, Mehta RA, Koo K, Schulte PJ, Lieske JC, Rule AD. Outpatient Antibiotic Use is Not Associated with an Increased Risk of First-Time Symptomatic Kidney Stones. J Am Soc Nephrol 2023; 34:1399-1408. [PMID: 37184480 PMCID: PMC10400106 DOI: 10.1681/asn.0000000000000155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023] Open
Abstract
SIGNIFICANCE STATEMENT Antibiotics modify human microbiomes and may contribute to kidney stone risk. In a population-based case-control study using 1247 chart-validated first-time symptomatic kidney stone formers and 4024 age- and sex-matched controls, the risk of kidney stones was transiently higher during the first year after antibiotic use. However, this risk was no longer evident after adjustment for comorbidities and excluding participants with prior urinary symptoms. Findings were consistent across antibiotic classes and the number of antibiotic courses received. This suggests that antibiotics are not important risk factors of kidney stones. Rather, kidney stones when they initially cause urinary symptoms are under-recognized, resulting in antibiotic use before a formal diagnosis of kidney stones ( i.e. , reverse causality). BACKGROUND Antibiotics modify gastrointestinal and urinary microbiomes, which may contribute to kidney stone formation. This study examined whether an increased risk of a first-time symptomatic kidney stone episode follows antibiotic use. METHODS A population-based case-control study surveyed 1247 chart-validated first-time symptomatic kidney stone formers with a documented obstructing or passed stone (cases) in Olmsted County, Minnesota, from 2008 to 2013 and 4024 age- and sex-matched controls. All prescriptions for outpatient oral antibiotic use within 5 years before the onset of symptomatic stone for the cases and their matched controls were identified. Conditional logistic regression estimated the odds ratio (OR) of a first-time symptomatic kidney stone across time after antibiotic use. Analyses were also performed after excluding cases and controls with prior urinary tract infection or hematuria because urinary symptoms resulting in antibiotic prescription could have been warranted because of undiagnosed kidney stones. RESULTS The risk of a symptomatic kidney stone was only increased during the 1-year period after antibiotic use (unadjusted OR, 1.31; P = 0.001), and this risk was attenuated after adjustment for comorbidities (OR, 1.16; P = 0.08). After excluding cases and controls with prior urinary symptoms, there was no increased risk of a symptomatic kidney stone during the 1-year period after antibiotic use (unadjusted OR, 1.04; P = 0.70). Findings were consistent across antibiotic classes and the number of antibiotic courses received. CONCLUSIONS The increased risk of a first-time symptomatic kidney stone with antibiotic use seems largely due to both comorbidities and prescription of antibiotics for urinary symptoms. Under-recognition of kidney stones that initially cause urinary symptoms resulting in antibiotic use may explain much of the perceived stone risk with antibiotics ( i.e. , reverse causality).
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Affiliation(s)
| | - Lisa E. Vaughan
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, Minnesota
| | | | - Ramila A. Mehta
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, Minnesota
| | - Kevin Koo
- Department of Urology, Mayo Clinic, Rochester, Minnesota
| | - Phillip J. Schulte
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, Minnesota
| | - John C. Lieske
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Andrew D. Rule
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
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Lupu VV, Butnariu LI, Fotea S, Morariu ID, Badescu MC, Starcea IM, Salaru DL, Popp A, Dragan F, Lupu A, Mocanu A, Chisnoiu T, Pantazi AC, Jechel E. The Disease with a Thousand Faces and the Human Microbiome-A Physiopathogenic Intercorrelation in Pediatric Practice. Nutrients 2023; 15:3359. [PMID: 37571295 PMCID: PMC10420997 DOI: 10.3390/nu15153359] [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: 06/29/2023] [Revised: 07/18/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Numerous interrelationships are known in the literature that have the final effect of unmasking or influencing various pathologies. Among these, the present article aims to discuss the connection between systemic lupus erythematosus (SLE) and the human microbiome. The main purpose of this work is to popularize information about the impact of dysbiosis on the pathogenesis and evolutionary course of pediatric patients with SLE. Added to this is the interest in knowledge and awareness of adjunctive therapeutic means that has the ultimate goal of increasing the quality of life. The means by which this can be achieved can be briefly divided into prophylactic or curative, depending on the phase of the condition in which the patient is. We thus reiterate the importance of the clinician acquiring an overview of SLE and the human microbiome, doubled by in-depth knowledge of the physio-pathogenic interactions between the two (in part achieved through the much-studied gut-target organ axes-brain, heart, lung, skin), with the target objective being that of obtaining individualized, multimodal and efficient management for each individual patient.
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Affiliation(s)
- Vasile Valeriu Lupu
- Pediatrics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | | | - Silvia Fotea
- Clinical Medical Department, Faculty of Medicine and Pharmacy, “Dunarea de Jos” University of Galati, 800008 Galati, Romania
| | - Ionela Daniela Morariu
- Faculty of Pharmacy, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Minerva Codruta Badescu
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Iuliana Magdalena Starcea
- Pediatrics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Delia Lidia Salaru
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Alina Popp
- Pediatrics Department, Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Felicia Dragan
- Faculty of Medicine and Pharmacy, University of Oradea, 410087 Oradea, Romania
| | - Ancuta Lupu
- Pediatrics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Adriana Mocanu
- Pediatrics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Tatiana Chisnoiu
- Pediatrics Department, Faculty of Medicine, Ovidius University, 900470 Constanta, Romania
| | | | - Elena Jechel
- Pediatrics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
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Sodnom-Ish B, Eo MY, Cho YJ, Seo MH, Yang HC, Kim MK, Myoung H, Lee SK, Kim SM. Identification of biological components for sialolith formation organized in circular multi-layers. Sci Rep 2023; 13:12277. [PMID: 37507401 PMCID: PMC10382579 DOI: 10.1038/s41598-023-37462-w] [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: 12/31/2022] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
According to the previous studies of sialolithiasis reported so far, this study is aimed to identify the biological components of sialolith, which show different ultrastructures and chemical compositions from other stones, cholelith and urolith. Twenty-two specimens obtained from 20 patients were examined histologically, and analyzed with micro-CT, scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), and transmission electron microscopy (TEM). All sialoliths (n = 22) observed in this study showed a central nidus, which was filled with organoid matrix admixed with exosome vesicles, loose calcium apatite crystals, and many bacteria. The micro-CT and SEM observation clearly defined a single or multiple central nidus(es) encircled by highly calcified compact zone. The circular compact zone showed a band-like calcification, about 1-3 mm in thickness, and usually located between the central nidus and the peripheral multilayer zone. But some sialoliths (n = 5) showed severe erosion of compact zone by expanding multilayered zone depending on the level of calcification and inflammation in sialolith. By observing TEM images, many exosome vesicles and degraded cytoplasmic organelles were found in the central nidus, and some epithelial cells were also found in the calcified matrix of peripheral multilayer zone. Particularly, EDS analysis indicated the highest Ca/P ratio in the intermediate compact zone (1.77), and followed by the central nidus area (1.39) and the peripheral multilayer zone (0.87). Taken together, these data suggest that the central nidus containing many inflammatory exosomes and degraded cytoplasmic organelles has a potential to induce a band-like calcification of compact zone, and followed by the additional multilayer deposition of exfoliated salivary epithelial cells as well as salivary materials. Thereby, the calcium apatite-based sialolith is gradually growing in its volume size, and eventually obstructs the salivary flow and provides a site for the bacterial infection.
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Affiliation(s)
- Buyanbileg Sodnom-Ish
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Research Institute, Seoul National University, Seoul, Korea
| | - Mi Young Eo
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Research Institute, Seoul National University, Seoul, Korea
| | - Yun Ju Cho
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Research Institute, Seoul National University, Seoul, Korea
| | - Mi Hyun Seo
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Research Institute, Seoul National University, Seoul, Korea
| | - Hyeong-Cheol Yang
- Department of Dental Biomaterials Science, School of Dentistry, Dental Research Institute, Seoul National University, Seoul, Korea
| | - Min-Keun Kim
- Department of Oral and Maxillofacial Surgery, College of Dentistry, Gangneung-Wonju National University, Gangneung, Korea
| | - Hoon Myoung
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Research Institute, Seoul National University, Seoul, Korea
| | - Suk Keun Lee
- Department of Oral Pathology, College of Dentistry, Gangneung-Wonju National University, Gangneung, Korea.
| | - Soung Min Kim
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Dental Research Institute, Seoul National University, Seoul, Korea.
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Khan SR, Canales BK. Proposal for pathogenesis-based treatment options to reduce calcium oxalate stone recurrence. Asian J Urol 2023; 10:246-257. [PMID: 37538166 PMCID: PMC10394280 DOI: 10.1016/j.ajur.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/02/2022] [Accepted: 01/18/2023] [Indexed: 08/05/2023] Open
Abstract
Objective Prevalence of kidney stone disease continues to increase globally with recurrence rates between 30% and 50% despite technological and scientific advances. Reduction in recurrence would improve patient outcomes and reduce cost and stone morbidities. Our objective was to review results of experimental studies performed to determine the efficacy of readily available compounds that can be used to prevent recurrence. Methods All relevant literature up to October 2020, listed in PubMed is reviewed. Results Clinical guidelines endorse the use of evidence-based medications, such as alkaline agents and thiazides, to reduce urinary mineral supersaturation and recurrence. However, there may be additional steps during stone pathogenesis where medications could moderate stone risk. Idiopathic calcium oxalate stones grow attached to Randall's plaques or plugs. Results of clinical and experimental studies suggest involvement of reactive oxygen species and oxidative stress in the formation of both the plaques and plugs. The renin-angiotensin-aldosterone system (RAAS), nicotinamide adenine dinucleotide phosphate (NADPH) oxidase, mitochondria, and NOD-like receptor pyrin domain containing-3 (NLRP3) inflammasome have all been implicated at specific steps during stone pathogenesis in animal models. Conclusion In addition to supersaturation-reducing therapies, the use of anti-oxidants, free radical scavengers, and inhibitors of NADPH oxidase, NLRP3 inflammasome, and RAAS may prove beneficial for stone prevention. Compounds such as statins and angiotensin converting enzyme inhibitors are already in use as therapeutics for hypertension and cardio-vascular disease and have previously shown to reduce calcium oxalate nephrolithiasis in rats. Although clinical evidence for their use in stone prevention in humans is limited, experimental data support they be considered along with standard evidence-based medications and clinical expertise when patients are being counselled for stone prevention.
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Affiliation(s)
- Saeed R. Khan
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
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Reid G. Perspective: microbial interventions in the urinary tract. MICROBIOME RESEARCH REPORTS 2023; 2:3. [PMID: 38045610 PMCID: PMC10688806 DOI: 10.20517/mrr.2022.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/30/2023] [Accepted: 02/14/2023] [Indexed: 12/05/2023]
Abstract
Despite multiple advances in medicine, the management of urinary tract infections (UTIs) in women has remained stalled for decades. To prevent the development of symptomatic recurrences, low-dose antibiotics are the mainstay, while alternative approaches have been attempted with limited success. The use of probiotics was first considered forty years ago, and while some promising studies have been published, additional evidence in larger patient groups is needed to recommend specific strains as a primary preventive regimen. Overall, the role of beneficial microbes in reducing the risk of UTI and other urological diseases, such as urolithiasis, remains a target for researchers. The aim of this perspective is to offer a viewpoint on the status of this approach and recommendations for how to develop novel probiotic therapies.
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Affiliation(s)
- Gregor Reid
- Canadian R&D Centre for Human Microbiome and Probiotics, Lawson Health Research Institute, London, Ontario N6A 4V2, Canada
- Departments of Microbiology and Immunology, and Surgery, Western University, London, Ontario N6A 3K7, Canada
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Hong D, Zhang C, Wu W, Lu X, Zhang L. Modulation of the gut-brain axis via the gut microbiota: a new era in treatment of amyotrophic lateral sclerosis. Front Neurol 2023; 14:1133546. [PMID: 37153665 PMCID: PMC10157060 DOI: 10.3389/fneur.2023.1133546] [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: 12/29/2022] [Accepted: 03/17/2023] [Indexed: 05/10/2023] Open
Abstract
There are trillions of different microorganisms in the human digestive system. These gut microbes are involved in the digestion of food and its conversion into the nutrients required by the body. In addition, the gut microbiota communicates with other parts of the body to maintain overall health. The connection between the gut microbiota and the brain is known as the gut-brain axis (GBA), and involves connections via the central nervous system (CNS), the enteric nervous system (ENS), and endocrine and immune pathways. The gut microbiota regulates the central nervous system bottom-up through the GBA, which has prompted researchers to pay considerable attention to the potential pathways by which the gut microbiota might play a role in the prevention and treatment of amyotrophic lateral sclerosis (ALS). Studies with animal models of ALS have shown that dysregulation of the gut ecology leads to dysregulation of brain-gut signaling. This, in turn, induces changes in the intestinal barrier, endotoxemia, and systemic inflammation, which contribute to the development of ALS. Through the use of antibiotics, probiotic supplementation, phage therapy, and other methods of inducing changes in the intestinal microbiota that can inhibit inflammation and delay neuronal degeneration, the clinical symptoms of ALS can be alleviated, and the progression of the disease can be delayed. Therefore, the gut microbiota may be a key target for effective management and treatment of ALS.
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Affiliation(s)
- Du Hong
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Chi Zhang
- Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Wenshuo Wu
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaohui Lu
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Liping Zhang
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
- *Correspondence: Liping Zhang
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Taguchi K. Editorial Comment to Prospective randomized trial of 2 vs 12-weeks of postoperative antibiotics after percutaneous nephrolithotomy in complex patients with infection-related kidney stones. Int J Urol 2022; 29:1558-1559. [PMID: 36305755 DOI: 10.1111/iju.15084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kazumi Taguchi
- Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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