Prevalence of virulent Candida spp. in complicated urinary tract infection of nephrolithiatic patients from surgical units of tertiary care hospitals Islamabad.

Candida species are the commensal organisms of human mucosa and opportunistically cause the diseases in susceptible persons. This study aimed to determine the prevalence and virulence of different Candida spp. among nephrolithiatic patients and their association with complicated UTI (cUTI). A total of 164 urine samples were collected from surgical units of two tertiary care hospitals (Poly Clinic and Pakistan Institute of Medical Sciences Hospital, Islamabad). From 74 kidney stone patients, 77 isolates of Candida spp. were confirmed through standard microbiological and molecular characterization. C. albicans was the predominant species with 51 isolates (66.2%) followed by 26 (33.8%) of C. non-albicans. The nephrolithiatic patients suffering from cUTI were more prone to be infected with Candida (P=0.047). Among all isolates, 83% (64) of the Candida isolates were biofilm formers, 80% (60) showed the esterase production and 64.9% (50) showed phospholipase production. Candida isolates positive for various virulence factors were more prevalently isolated from both catheterized and recurrent UTI patients. Among Candida spp., 16.9% (13) isolates showed resistance to fluconazole and 19.5% (15) against voriconazole and 11 isolates were resistant for both tested antifungals. Candida isolated from cUTI cases showed comparatively enhanced virulence attributes and antifungal resistance, suggesting that these factors might have role in development of cUTI in nephrolithiatic patients. Hence, this work highlights the high prevalence of both C. albicans and non albicans spp. in nephrolithiatic patients. So, there is need to administer evidence based antifungal therapy rather than empirical therapy to reduce the cUTI in nephrolithiatic patients.

The relationship between gut microbiota and short chain fatty acids in the renal calcium oxalate stones disease.

The relationship of gut microbiota and calcium oxalate stone has been limited investigated, especially with no study of gut microbiota and short chain fatty acids (SCFAs) in nephrolithiasis. We provided Sprague Dawley rats of renal calcium oxalate stones with antibiotics and examined the renal crystals deposition. We also performed a case-control study by analyzing 16S rRNA microbial profiling, shotgun metagenomics and SCFAs in 153 fecal samples from non-kidney stone (NS) controls, patients with occasional renal calcium oxalate stones (OS) and patients with recurrent stones (RS). Antibiotics reduced bacterial load in feces and could promote the formation of renal calcium crystals in model rats. In addition, both OS and RS patients exhibited higher fecal microbial diversity than NS controls. Several SCFAs-producing gut bacteria, as well as metabolic pathways associated with SCFAs production, were considerably lower in the gut microbiota among the kidney stone patients compared with the NS controls. Representation of genes involved in oxalate degradation showed no significance difference among groups. However, fecal acetic acid concentration was the highest in RS patients with high level of urinary oxalate, which was positively correlated with genes involvement in oxalate synthesis. Administration of SCFAs reduced renal crystals. These results shed new light on bacteria and SCFAs, which may promote the development of treatment strategy in nephrolithiasis.

Perturbations of the Gut Microbiome and Metabolome in Children with Calcium Oxalate Kidney Stone Disease.

BACKGROUND: The relationship between the composition and function of gut microbial communities and early-onset calcium oxalate kidney stone disease is unknown. METHODS: We conducted a case-control study of 88 individuals aged 4-18 years, which included 44 individuals with kidney stones containing ≥50% calcium oxalate and 44 controls matched for age, sex, and race. Shotgun metagenomic sequencing and untargeted metabolomics were performed on stool samples. RESULTS: Participants who were kidney stone formers had a significantly less diverse gut microbiome compared with controls. Among bacterial taxa with a prevalence >0.1%, 31 taxa were less abundant among individuals with nephrolithiasis. These included seven taxa that produce butyrate and three taxa that degrade oxalate. The lower abundance of these bacteria was reflected in decreased abundance of the gene encoding butyryl-coA dehydrogenase (P=0.02). The relative abundance of these bacteria was correlated with the levels of 18 fecal metabolites, and levels of these metabolites differed in individuals with kidney stones compared with controls. The oxalate-degrading bacterial taxa identified as decreased in those who were kidney stone formers were components of a larger abundance correlation network that included Eggerthella lenta and several Lactobacillus species. The microbial (α) diversity was associated with age of stone onset, first decreasing and then increasing with age. For the individuals who were stone formers, we found the lowest α diversity among individuals who first formed stones at age 9-14 years, whereas controls displayed no age-related differences in diversity. CONCLUSIONS: Loss of gut bacteria, particularly loss of those that produce butyrate and degrade oxalate, associates with perturbations of the metabolome that may be upstream determinants of early-onset calcium oxalate kidney stone disease.

Application of whole-genome sequencing in a case study of renal tuberculosis in a child.

BACKGROUND: Urogenital tuberculosis (TB) is rare in children and usually develops due to reactivation of the foci in the genitourinary tract after the latency period following initial infection. Urogenital TB in children has no pathognomonic clinical features that can result in overlooking or misdiagnosing this clinical entity. Here, we report important findings regarding the pathogenesis and transmission of TB by using genotyping and whole-genome sequencing (WGS) in a study of renal TB case in a child. CASE PRESENTATION: A 13-year-old boy was admitted to the hospital because of high fever, severe dry cough, flank pain and painful urination. Abdominal ultrasonography and CT revealed an 8 mm calculus in the kidney, and clinical findings were initially interpreted as nephrolithiasis. Nevertheless, due to the atypical clinical presentation of kidney stone disease, additional investigations for possible TB were performed. The QuantiFERON®-TB Gold Plus test was positive, and the Mantoux test resulted in 15 mm of induration, confirming infection with Mycobacterium tuberculosis (Mtb). Chest X-ray was normal. Chest CT revealed calcified intrathoracic lymph nodes. The urine sample tested positive for acid-fast bacilli, and Mtb cultures were obtained from urine and bronchial aspirate samples, resulting in a final diagnosis of intrathoracic lymph node and renal TB. Contact investigation revealed that the child's father was diagnosed with TB when the child was 1 year old. Genotyping and WGS analysis of Mtb isolates of the child and his father confirmed the epidemiological link and pointed to the latency of infection in the child. CONCLUSIONS: This case report confirmed the development of active TB from calcified lesions in adolescent after 12 years of exposure, demonstrated the absence of microevolutionary changes in the Mtb genome during the period of latency, and proved the importance of appropriate evaluation and management to prevent the progression of TB infection to active TB disease. The use of WGS provided the ultimate resolution for the detection of TB transmission and reactivation events.

Calcium Oxalate Nephrolithiasis and Gut Microbiota: Not just a Gut-Kidney Axis. A Nutritional Perspective.

Recent studies have shown that patients with kidney stone disease, and particularly calcium oxalate nephrolithiasis, exhibit dysbiosis in their fecal and urinary microbiota compared with controls. The alterations of microbiota go far beyond the simple presence and representation of Oxalobacter formigenes, a well-known symbiont exhibiting a marked capacity of degrading dietary oxalate and stimulating oxalate secretion by the gut mucosa. Thus, alterations of the intestinal microbiota may be involved in the pathophysiology of calcium kidney stones. However, the role of nutrition in this gut-kidney axis is still unknown, even if nutritional imbalances, such as poor hydration, high salt, and animal protein intake and reduced fruit and vegetable intake, are well-known risk factors for kidney stones. In this narrative review, we provide an overview of the gut-kidney axis in nephrolithiasis from a nutritional perspective, summarizing the evidence supporting the role of nutrition in the modulation of microbiota composition, and their relevance for the modulation of lithogenic risk.

Understanding the gut-kidney axis in nephrolithiasis: an analysis of the gut microbiota composition and functionality of stone formers.

OBJECTIVES: The involvement of the gut microbiota in the pathogenesis of calcium nephrolithiasis has been hypothesised since the discovery of the oxalate-degrading activity of Oxalobacter formigenes, but never comprehensively studied with metagenomics. The aim of this case-control study was to compare the faecal microbiota composition and functionality between recurrent idiopathic calcium stone formers (SFs) and controls. DESIGN: Faecal samples were collected from 52 SFs and 48 controls (mean age 48±11). The microbiota composition was analysed through 16S rRNA microbial profiling approach. Ten samples (five SFs, five controls) were also analysed with deep shotgun metagenomics sequencing, with focus on oxalate-degrading microbial metabolic pathways. Dietary habits, assessed through a food-frequency questionnaire, and 24-hour urinary excretion of prolithogenic and antilithogenic factors, including calcium and oxalate, were compared between SFs and controls, and considered as covariates in the comparison of microbiota profiles. RESULTS: SFs exhibited lower faecal microbial diversity than controls (Chao1 index 1460±363vs 1658±297, fully adjusted p=0.02 with stepwise backward regression analysis). At multivariate analyses, three taxa (Faecalibacterium, Enterobacter, Dorea) were significantly less represented in faecal samples of SFs. The Oxalobacter abundance was not different between groups. Faecal samples from SFs exhibited a significantly lower bacterial representation of genes involved in oxalate degradation, with inverse correlation with 24-hour oxalate excretion (r=-0.87, p=0.002). The oxalate-degrading genes were represented in several bacterial species, whose cumulative abundance was inversely correlated with oxaluria (r=-0.85, p=0.02). CONCLUSIONS: Idiopathic calcium SFs exhibited altered gut microbiota composition and functionality that could contribute to nephrolithiasis physiopathology.

Urologic Emergencies.

Urologic emergencies can involve the kidneys, ureters, bladder, urethra, penis, scrotum, or testicles. History and physical examination are essential to diagnosis, whereas imaging is increasingly used to confirm diagnoses. Acute urinary retention should be relieved with Foley placement. Penile emergencies include paraphimosis, which can be treated by foreskin reduction, whereas penile fracture and priapism require urologic intervention. Fournier gangrene and testicular torsion are scrotal emergencies requiring emergent surgery. Nephrolithiasis, although painful, is not an emergency unless there is concern for concomitant urinary tract infection, both ureters are obstructed by stones, or there is an obstructing stone in a solitary kidney.

[The role of urinary tract infection in the development of recurrent nephrolithiasis].

This is a literature review on the role of microbial flora in the development of recurrent urolithiasis. The authors outline pathogenetic aspects of recurrent stone formation associated bacterial flora. A number of studies reported that standard urine culture has limited sensitivity in detecting urinary tract infection.

Oxalobacter formigenes-associated host features and microbial community structures examined using the American Gut Project.

BACKGROUND: Increasing evidence shows the importance of the commensal microbe Oxalobacter formigenes in regulating host oxalate homeostasis, with effects against calcium oxalate kidney stone formation, and other oxalate-associated pathological conditions. However, limited understanding of O. formigenes in humans poses difficulties for designing targeted experiments to assess its definitive effects and sustainable interventions in clinical settings. We exploited the large-scale dataset from the American Gut Project (AGP) to study O. formigenes colonization in the human gastrointestinal (GI) tract and to explore O. formigenes-associated ecology and the underlying host-microbe relationships. RESULTS: In >8000 AGP samples, we detected two dominant, co-colonizing O. formigenes operational taxonomic units (OTUs) in fecal specimens. Multivariate analysis suggested that O. formigenes abundance was associated with particular host demographic and clinical features, including age, sex, race, geographical location, BMI, and antibiotic history. Furthermore, we found that O. formigenes presence was an indicator of altered host gut microbiota structure, including higher community diversity, global network connectivity, and stronger resilience to simulated disturbances. CONCLUSIONS: Through this study, we identified O. formigenes colonizing patterns in the human GI tract, potential underlying host-microbe relationships, and associated microbial community structures. These insights suggest hypotheses to be tested in future experiments. Additionally, we proposed a systematic framework to study any bacterial taxa of interest to computational biologists, using large-scale public data to yield novel biological insights.

Xanthogranulomatous pyelonephritis presenting as acute pleuritic chest pain: a case report.

BACKGROUND: Xanthogranulomatous pyelonephritis is a rare and serious manifestation of chronic kidney inflammation that can be life-threatening if not recognized and treated appropriately, often with antibiotics and surgery. Affected patients are most commonly females in their fifth or sixth decade of life with a background of obstructive uropathy, nephrolithiasis, or recurrent urinary tract infections who present with vague nonspecific symptoms. CASE PRESENTATION: A 43-year-old woman of Russian ethnicity with a history of nephrolithiasis presented to our emergency department with new left-sided pleuritic chest pain amid a 6-week history of constitutional symptoms including fevers, night sweats, and 7 kg of weight loss. Workup for acute coronary syndrome and pulmonary embolism in our emergency department was negative. Given that she was clinically unwell, she was admitted to internal medicine to expedite workup for the cause of her symptoms. A broad differential diagnosis for various infectious, inflammatory/autoimmune, and neoplastic processes was considered. Based on classic radiographic and histopathologic findings, she was ultimately diagnosed with xanthogranulomatous pyelonephritis of her left kidney, which was a direct consequence of chronic inflammation. This inflammation exhibited spread to local tissues and across her left hemidiaphragm, resulting in a unilateral pleural effusion which explained her chest discomfort. She was treated with antibiotics administered intravenously and urgent total nephrectomy with a good functional outcome. CONCLUSIONS: Our case illustrates an uncommon but clinically important do-not-miss diagnosis that underlies a common clinical presentation of pleuritic chest pain. The case underscores the importance of maintaining a broad differential diagnosis and organized approach when treating patients with undifferentiated clinical presentations.

Nephrolithiasis by Corynebacterium urealyticum infection: literature review and case report.

INTRODUCTION: Alkaline-encrusted cystitis or pyelonephritis is a chronic inflammatory condition due to deposition of crystals usually caused by urea-splitting bacteria. Corynebacterium urealyticum (CU) is a gram-positive, urea-splitting and multi-antibiotic resistant bacillus with special tropism for the urinary tract and it is often associated with encrusted pyelocystitis. METHODS AND RESULTS: Here we report the case of a 75-year-old Caucasian man with a prolonged history of renal stones who was admitted for gross hematuria associated with renal failure. A diagnosis of encrusted pyelocystitis due to CU infection was made and the patient was appropriately treated. CONCLUSIONS: At 6-month follow-up the patient was in good general conditions and asymptomatic. Signs of urinary tract infection or of renal calculosis were still detectable.

[The value of PCR method in the species-level identification of a mucoid Salmonella sp. strain isolated from the urine culture of a case with asymptomatic nephrolithiasis]. / Nefrolitiazisli asemptomatik bir olgunun idrar kültüründen izole edilen mukoid Salmonella sp. susunun tür düzeyinde tanimlanmasinda PCR yönteminin degeri.

Colonies of the Salmonella strains usually show a smooth (S) character. Therefore, Salmonella strains producing mucoid colony are very rarely encountered in the literature. Identification of the mucoid Salmonella strains to the species level is difficult via conventional methods, since the mucus layer does not allow the bacterium to respond to the antigenic reactions. In this study we aimed to emphasize the identification of Salmonella serotypes by the polymerase chain reaction (PCR) when rough (R) or mucoid (M) Salmonella isolates are encountered in the laboratory. The urine culture of a 17-year-old female patient revealed growth of 100.000 cfu/mL gram-negative bacilli in mucoid colony morphology. The isolate was identified as Salmonella sp. by biochemical tests and Vitek 2 (bioMérieux, France) automated identification system. Agglutination tests showed negative reaction with the known antiserums. Absence of agglutination was attributed to the mucoid character of the isolate. Identification of the Salmonella sp. was confirmed by Vitek MS MALDI-TOF (bioMérieux, France) analysis method, however, the serotype of the strain could not be identified. In order to verify that the mucoid colony was Salmonella spp., species-specific PCR was performed using invA primers, and Salmonella sp. identification was verified by observing a 284 base-pair (bp) PCR amplicon. Subsequently, serogrouping was done by multiplex-PCR (mPCR), which could identify the O:B (O:4), O:C1 (O:7), O:C2-C3 (O:8), O:D (O:9, O:9,46, O:9,46,27), and O:E (O:3,10, O:3,19) somatic antigens. It was detected that the mucoid Salmonella sp. formed a band of approximately 615 bp in size and took place in group D. Another mPCR directed towards O:D1(O:9) and O:E1(3,10) somatic antigens to detect subgroups of group D mucoid Salmonella spp., revealed that the isolate formed a DNA band of approximately 624 bp in size and took place in group D1 which is usually isolated from human. Modified version of another mPCR was used to determine phase-1 flagellar antigen of common Salmonella serovars, as well as to determine the phase-1 flagellar antigen of mucoid Salmonella spp. in group D1. Thus, the isolate was serotyped as Salmonella Enteritidis (1.9,12:g,m:-). Antibiotic susceptibility test performed by disc diffusion method in line with the recommendations of CLSI, revealed that the isolate was susceptible to ampicillin, ciprofloxacin, ceftriaxone, trimethoprim-sulfamethoxazole and chloramphenicol. In conclusion, PCR is a reliable and rapid alternative method that contributes to the conventional serotyping of Salmonella when rough or mucoid strains that lack somatic and flagellar antigens, are isolated.

The genetic composition of Oxalobacter formigenes and its relationship to colonization and calcium oxalate stone disease.

Oxalobacter formigenes is a unique intestinal organism that relies on oxalate degradation to meet most of its energy and carbon needs. A lack of colonization is a risk factor for calcium oxalate stone disease. Protection against calcium oxalate stone disease appears to be due to the oxalate degradation that occurs in the gut on low calcium diets with a possible further contribution from intestinal oxalate secretion. Much remains to be learned about how the organism establishes and maintains gut colonization and the precise mechanisms by which it modifies stone risk. The sequencing and annotation of the genomes of a Group 1 and a Group 2 strain of O. formigenes should provide the informatic tools required for the identification of the genes and pathways associated with colonization and survival. In this review we have identified genes that may be involved and where appropriate suggested how they may be important in calcium oxalate stone disease. Elaborating the functional roles of these genes should accelerate our understanding of the organism and clarify its role in preventing stone formation.

[Oxalobacter formigenes--characteristics and role in development of calcium oxalate urolithiasis]. / Oxalobacter formigenes--charakterystyka i rola w rozwoju kamicy szczawianowo-wapniowej.

Microorganisms are one of the important factors for urinary calculi formation. While urease-positive bacteria and nanobacteria contribute to stone formation, Oxalobacter formigenes rods play a protective role against the development of urolithiasis. Proteus mirabilis alkaline environment of the urinary tract and cause crystallization mainly of struvite (magnesium ammonium phosphate). However, nanobacteria, due to the possibility of apatite deposition on the surface of their cells, have long been considered as an etiological factor of urinary calculi consisting of calcium phosphates. O. formigenes is an anaerobe using oxalate as the main source of carbon and energy and occurs as natural gastrointestinal microflora of humans and animals. These bacteria control the amount of oxalate excretion degrading oxalates and regulating their transport by intestinal epithelium. Lower colonization of the human colon by O. formigenes can cause increased oxalate excretion and lead to the development of oxalate urolithiasis. Due to the positive influence of O. formigenes, there is ongoing research into the use of this microorganism as a probiotic in the prophylaxis or treatment of hyperoxaluria, both secondary and primary. The results of these studies are very promising, but they still require continuation. Future studies focus on the exact characteristics of O. formigenes including their metabolism and the development of methods for applying as a therapeutic agent the bacteria or their enzymes degrading the oxalate.

Extensive characterizations of bacteria isolated from catheterized urine and stone matrices in patients with nephrolithiasis.

BACKGROUND: Urinary tract infections are generally known to be associated with nephrolithiasis, particularly struvite stone, in which the most common microbe found is urea-splitting bacterium, i.e. Proteus mirabilis. However, our observation indicated that it might not be the case of stone formers in Thailand. We therefore extensively characterized microorganisms associated with all types of kidney stones. METHODS: A total of 100 kidney stone formers (59 males and 41 females) admitted for elective percutaneous nephrolithotomy were recruited and microorganisms isolated from catheterized urine and cortex and nidus of their stones were analyzed. RESULTS: From 100 stone formers recruited, 36 cases had a total of 45 bacterial isolates cultivated from their catheterized urine and/or stone matrices. Among these 36 cases, chemical analysis by Fourier-transformed infrared spectroscopy revealed that 8 had the previously classified 'infection-induced stones', whereas the other 28 cases had the previously classified 'metabolic stones'. Calcium oxalate (in either pure or mixed form) was the most common and found in 64 and 75% of the stone formers with and without bacterial isolates, respectively. Escherichia coli was the most common bacterium (approximately one-third of all bacterial isolates) found in urine and stone matrices (both nidus and periphery). Linear regression analysis showed significant correlation (r = 0.860, P < 0.001) between bacterial types in urine and stone matrices. Multidrug resistance was frequently found in these isolated bacteria. Moreover, urea test revealed that only 31% were urea-splitting bacteria, whereas the majority (69%) had negative urea test. CONCLUSIONS: Our data indicate that microorganisms are associated with almost all chemical types of kidney stones and urea-splitting bacteria are not the major causative microorganisms found in urine and stone matrices of the stone formers in Thailand. These data may lead to rethinking and a new roadmap for future research regarding the role of microorganisms in kidney stone formation.

Urosepsis caused by Globicatella sanguinis and Corynebacterium riegelii in an adult: case report and literature review.

We report an extremely rare case of urosepsis caused by Globicatella sanguinis and Corynebacterium riegelii coinfection in a 94-year-old Japanese man with nephrolithiasis. Prompt identification of this coinfection is important so that effective antimicrobial coverage can be initiated.

Effects of Lactobacillus casei and Bifidobacterium breve on urinary oxalate excretion in nephrolithiasis patients.

It had been suggested that lactic acid bacteria (LAB) may degrade oxalate in the intestinal lumen, reducing urinary oxalate excretion. We aimed to evaluate the effect of a LAB mixture containing Lactobacillus casei (LC) and Bifidobacterium breve (BB) (LC + BB) upon urinary oxalate reduction in stone-forming (SF) patients without hyperoxaluria under conditions of an oxalate-rich diet. After an oxalate restriction period (7 days washout), 14 SF patients consumed an oxalate-rich diet during 4 weeks (200 mg/day) and a lyophilized LC + BB preparation was given t.i.d. after meals during the last 2 weeks. Twenty-four-hour urine samples were collected for determination of oxalate, calcium, magnesium, citrate, sodium, potassium and creatinine at baseline, after 2 weeks (DIET) and 4 weeks (DIET + LC + BB). The mean urinary oxalate excretion was significantly higher after DIET versus baseline (27 +/- 8 vs. 35 +/- 11 mg/24 h), but the mean decrease was not significant between DIET + LC + BB and DIET periods (35 +/- 11 vs. 33 +/- 10 mg/24 h). Seven out of 14 patients presented a reduction in oxaluria after LC + BB versus DIET, being the reduction higher than 25% in 4, and up to 50% in 2 of them. The latter two patients were those who had presented the greatest increase in oxaluria in response to dietary oxalate. In conclusion, this mixture of L. casei and B. breve was shown to possess a variable lowering effect upon urinary oxalate excretion that may be dependent on dietary oxalate intake.