SLIPS-LAB-A bioinspired bioanalysis system for metabolic evaluation of urinary stone disease.
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ABSTRACT:
SUBMITTER: Li H
PROVIDER: S-EPMC7244315 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description: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.
| S-EPMC10436313 | biostudies-literature
Project description:Urinary stone disease (USD) is associated with cardiovascular disease (CVD) in Western populations. However, the prevalence and relationship between USD and CVD risk have not been fully examined in the Chinese population.We performed a cross-sectional study of 10,281 participants in rural China. All subjects underwent renal ultrasound to detect USD, brachial-ankle pulsewave velocity (baPWV) measurement to estimate arterial stiffness, and ankle-brachial index (ABI) examination to detect peripheral arterial disease (PAD) (defined as ABI <0.9 on at least 1 side of the body).Mean age of the study population was 55.4 ± 10.0 years; 47.1% were men. Among all participants, 5.7% (n = 582) had USD, mean baPWV was 15.6 ± 3.2 m/s, and 4.0% had PAD. The prevalence of USD increased in parallel with mean arterial pressure, albuminuria, Framingham risk score, and baPWV. In multivariate analyses after adjustment for demographic characteristics, USD was significantly associated with an increased risk of hypertension (odds ratio [OR]: 1.32; 95% confidence interval [CI]: 1.08-1.62), albuminuria (OR: 2.17; 95% CI: 1.74-2.69), chronic kidney disease (OR: 2.11; 95% CI: 1.70-2.62), increased arterial stiffness (OR: 1.24; 95% CI: 1.01-1.52), and PAD (OR: 1.50; 95% CI: 1.04-2.16).In rural China, USD was associated with a high prevalence of traditional CVD risk factors, increased arterial stiffness, and PAD. The presence of USD should increase physician awareness of the concomitant presence of CVD risk factors.
| S-EPMC5733875 | biostudies-other
Project description:BackgroundKidney stones or nephrolithiasis is a chronic metabolic disease characterized by renal colic and hematuria. Currently, a pathogenetic mechanism resulting in kidney stone formation remains elusive. We performed a multi-omic study investigating urinary microbial compositions and metabolic alterations during nephrolithiasis.MethodUrine samples from healthy and individuals with nephrolithiasis were collected for 16S rRNA gene sequencing and liquid chromatography-mass spectroscopy. Microbiome and metabolome profiles were analyzed individually and combined to construct interactome networks by bioinformatic analysis.ResultsDistinct urinary microbiome profiles were determined in nephrolithiasis patients compared with controls. Thirty-nine differentially abundant taxa between controls and nephrolithiasis patients were identified, and Streptococcus showed the most significant enrichment in nephrolithiasis patients. We also observed significantly different microbial compositions between female and male nephrolithiasis patients. The metabolomic analysis identified 112 metabolites that were differentially expressed. Two significantly enriched metabolic pathways, including biosynthesis of unsaturated fatty acids and tryptophan metabolism, were also identified in nephrolithiasis patients. Four potentially diagnostic metabolites were also identified, including trans-3-hydroxycotinine, pyroglutamic acid, O-desmethylnaproxen, and FAHFA (16:0/18:2), and could function as biomarkers for the early diagnosis of nephrolithiasis. We also identified three metabolites that contributed to kidney stone size. Finally, our integrative analysis of the urinary tract microbiome and metabolome identified distinctly different network characteristics between the two groups.ConclusionsOur study has characterized important profiles and correlations among urinary tract microbiomes and metabolomes in nephrolithiasis patients for the first time. These results shed new light on the pathogenesis of nephrolithiasis and could provide early clinical biomarkers for diagnosing the disease.
| S-EPMC9484321 | biostudies-literature
Project description:IntroductionIn this study, a survey was prepared for urologists that asked about their primary choice of treatment for urolithiasis in daily practice and their answers were evaluated.MethodsThe survey was prepared on the Google Docs website and it was sent to 1,016 urologists via email with 752 confirmed deliveries. In addition to the demographic questions about each participant's age, gender, and institution, the survey presented case scenarios focusing on their preferred treatment modalities for distal ureteric, proximal ureteric, and renal calculi. The participating urologists were divided into two groups according to the frequency that they treat urolithiasis patients.ResultsOf the 752 surveys delivered, 211 urologists (28.05%) responded and 204 answered all questions. According to the results, there were no significant differences between the treatment approaches and the other localizations, but there was a statistically significant difference for treatment approaches to lower pole stones between two groups. In response to the question of which stone treatment method was used less frequently, 124 (60.7%) participants answered that they used shock wave lithotripsy less in the last 10 years.ConclusionThe present study has shown that while the management of renal and ureteric calculi by Turkish urologists is highly varied, the overall treatment patterns are in accordance with the European Association of Urology guidelines. However, similar to the global trend extracorporeal shock wave lithotripsy is less preferred by Turkish urologists.
| S-EPMC6074772 | biostudies-literature
Project description:IntroductionBecause of phenotypic overlap between monogenic urinary stone diseases (USD), gene-specific analyses can result in missed diagnoses. We used targeted next generation sequencing (tNGS), including known and candidate monogenic USD genes, to analyze suspected primary hyperoxaluria (PH) or Dent disease (DD) patients genetically unresolved (negative; N) after Sanger analysis of the known genes. Cohorts consisted of 285 PH (PHN) and 59 DD (DDN) families.MethodsVariants were assessed using disease-specific and population databases plus variant assessment tools and categorized using the American College of Medical Genetics (ACMG) guidelines. Prior Sanger analysis identified 47 novel PH or DD gene pathogenic variants.ResultsScreening by tNGS revealed pathogenic variants in 14 known monogenic USD genes, accounting for 45 families (13.1%), 27 biallelic and 18 monoallelic, including 1 family with a copy number variant (CNV). Recurrent genes included the following: SLC34A3 (n = 13), CLDN16 (n = 8), CYP24A1 (n = 4), SLC34A1 (n = 3), SLC4A1 (n = 3), APRT (n = 2), CLDN19 (n = 2), HNF4A1 (n = 2), and KCNJ1 (n = 2), whereas ATP6V1B1, CASR, and SLC12A1 and missed CNVs in the PH genes AGXT and GRHPR accounted for 1 pedigree each. Of the 48 defined pathogenic variants, 27.1% were truncating and 39.6% were novel. Most patients were diagnosed before 18 years of age (76.1%), and 70.3% of biallelic patients were homozygous, mainly from consanguineous families.ConclusionOverall, in patients suspected of DD or PH, 23.9% and 7.3% of cases, respectively, were caused by pathogenic variants in other genes. This study shows the value of a tNGS screening approach to increase the diagnosis of monogenic USD, which can optimize therapies and facilitate enrollment in clinical trials.
| S-EPMC8589729 | biostudies-literature
Project description:PurposeStone composition can provide valuable information for the diagnosis, treatment and recurrence prevention of urolithiasis. The aim of this study was to evaluate the distribution of urinary stone components and the impact of different crystal forms according to gender and age of patients in Germany.MethodsA total of 45,783 urinary stones submitted from 32,512 men and 13,271 women between January 2007 and December 2020 were analyzed by infrared spectroscopy. Only the first calculus obtained per patient was included in the analysis.ResultsThe most common main stone component was calcium oxalate (CaOx) (71.4%), followed by carbonate apatite (CA) (10.2%) and uric acid (UA) (8.3%). Struvite (2.1%), brushite (1.3%), protein (0.5%) and cystine (0.4%) stones were only rarely diagnosed. CaOx (75%) and UA stones (81%) were more frequently obtained from men than women (p < 0.001). Weddellite (COD) and uric acid dihydrate (UAD) were more common in younger ages than whewellite (COM) and anhydrous uric acid (UAA), respectively, in both men and women. The ratios of COM-to-COD and UAA-to-UAD calculi were approximately 4:1 and 8:1, respectively. The peak of stone occurrence was between the ages of 40 and 59 years.ConclusionStone composition is strongly associated with gender and age. The peak incidence of calculi in both women and men was in the most active phase of their working life. The distinction between different crystal forms could provide clues to the activity and mechanisms of lithogenesis. Further research is needed in understanding the causative factors and the process of stone formation.
| S-EPMC9236976 | biostudies-literature
Project description:PurposeWe determined the association between urology consultation and emergency department revisits for children with urinary stones.Materials and methodsThis retrospective cohort study included patients 18 years old or younger who presented to an emergency department in South Carolina with a urinary stone from 1997 to 2015. The primary exposure was urology consultation during the index emergency department visit. The primary outcome was a stone related emergency department revisit occurring within 180 days of discharge from an index emergency department visit. Secondary outcomes included computerized tomography use, inpatient admission and emergent surgery.ResultsOf 5,642 index emergency department visits for acute urinary stones 11% resulted in at least 1 stone related emergency department revisit within 180 days. Of revisits 59% occurred within 30 days of discharge and 39% were due to pain. The odds of emergency department revisit were highest within the first 48 hours of discharge home (OR 22.6, 95% CI 18.0 to 28.5) and rapidly decreased thereafter. Urology consultation was associated with a 37% lower adjusted odds of emergency department revisit (OR 0.63, 95% CI 0.44 to 0.90) and 68% lower odds of computerized tomography use across all emergency department visits (OR 0.32, 95% CI 0.15 to 0.69). Among patients who revisited the emergency department the frequency of pain complaints was 27% in those with a urological consultation at the index visit and 39% in those without.ConclusionsUrology consultation was associated with decreased emergency department revisits and computerized tomography use in pediatric patients with urinary stones. Future studies should identify patients who benefit most from urology consultation and ascertain processes of care that decrease emergency department revisits among high risk patients.
| S-EPMC6002942 | biostudies-literature
Project description:ObjectiveTo bridge the gap between evidence and clinical judgement, we defined scenarios appropriate for ureteral stent omission after uncomplicated ureteroscopy (URS) using the RAND/UCLA Appropriateness Method (RAM). We retrospectively assessed rates of appropriate stent omission, with the goal to implement these criteria in clinical practice.MethodsA panel of 15 urologists from the Michigan Urological Surgery Improvement Collaborative (MUSIC) met to define uncomplicated URS and the variables that influence stent omission decision-making. Over two rounds, they scored clinical scenarios for Appropriateness Criteria (AC) for stent omission based on a combination of variables. AC were defined by median scores: 1 to 3 (inappropriate), 4 to 6 (uncertain), and 7 to 9 (appropriate). Multivariable analysis determined the association of each variable with AC scores. Uncomplicated URS cases in the MUSIC registry were assigned AC scores and stenting rates assessed.ResultsSeven variables affecting stent decision-making were identified. Of the 144 scenarios, 26 (18%) were appropriate, 88 (61%) inappropriate, and 30 (21%) uncertain for stent omission. Most scenarios appropriate for omission were pre-stented (81%). Scenarios with ureteral access sheath or stones >10mm were only appropriate if pre-stented. Stenting rates of 5,181 URS cases correlated with AC scores. Stents were placed in 61% of cases appropriate for omission (practice range, 25% to 98%).ConclusionWe defined objective variables and AC for stent omission following uncomplicated URS. AC scores correlated with stenting rates but there was substantial practice variation. Our findings demonstrate that the appropriate use of stent omission is underutilized.
| S-EPMC9432824 | biostudies-literature
Project description:Finding early disease markers using non-invasive and widely available methods is essential to develop a successful therapy for Alzheimer's Disease. Few studies to date have examined urine, the most readily available biofluid. Here we report the largest study to date using comprehensive metabolic phenotyping platforms (NMR spectroscopy and UHPLC-MS) to probe the urinary metabolome in-depth in people with Alzheimer's Disease and Mild Cognitive Impairment. Feature reduction was performed using metabolomic Quantitative Trait Loci, resulting in the list of metabolites associated with the genetic variants. This approach helps accuracy in identification of disease states and provides a route to a plausible mechanistic link to pathological processes. Using these mQTLs we built a Random Forests model, which not only correctly discriminates between people with Alzheimer's Disease and age-matched controls, but also between individuals with Mild Cognitive Impairment who were later diagnosed with Alzheimer's Disease and those who were not. Further annotation of top-ranking metabolic features nominated by the trained model revealed the involvement of cholesterol-derived metabolites and small-molecules that were linked to Alzheimer's pathology in previous studies.
| S-EPMC7730184 | biostudies-literature
Project description:OBJECTIVE:To examine the recent epidemiology of pediatric urinary stone disease (USD) in the United States. METHODS:We utilized the 2004-2016 Optum© Clinformatics® Data Mart database, a de-identified adjudicated administrative health claims database that includes 15-18 million individuals covered annually by commercial insurance in all 50 US states. The analysis included 12,739,125 children aged 0-18 years. We calculated annual rates of USD, ambulatory visits, and procedures, and the prevalence of prescription fills. RESULTS:The 2005-2016 USD rate was 59.5 cases per 100,000 person-years. The annual rate rose gradually from 2005 to a peak of 65.2 cases per 100,000 person-years in 2011. The USD rate increased with increasing age, and was highest among females compared to males, non-Hispanic Whites compared to other race/ethnic groups, and those residing in the South compared to other geographic regions. The overall 2005-2016 rate in the 120 days following a USD episode was 1.9 for ambulatory visits, 0.24 for surgical procedures, and 1.1 for imaging procedures. Ureteroscopy was the most common surgical procedure and CT scan was the most common imaging procedures, although ultrasound utilization increased over time. Medications were filled in 46.9% of cases, and use was lowest among males (43.1%), Asians (34.8%), and in the Northeast (34.3%). Opiate agonists were the most prevalent prescription (39.9%). CONCLUSION:Our study provides one of the most comprehensive examinations of pediatric USD to date, demonstrating shifting rates and treatment patterns over time, as well as differences by age, gender, race/ethnicity, and geographic region.
| S-EPMC6988134 | biostudies-literature