Secondarily infected nonstruvite urolithiasis: a prospective evaluation

Association between urinary lithiasis, other than struvite by crystallography and non-ureolytic bacteria

The relationship between urinary tract infection caused by urease-producing bacteria and lithiasis due to struvite stones is well established in the literature. However, there is limited knowledge on whether non-urease producing bacteria can also promote crystallization. In our study, we analyzed the association between urinary lithiasis, other than struvite by crystallography and non-ureolytic bacteria, in 153 patients who underwent surgery for urinary stone. The collected samples were sent for crystallographic analysis and culture. Additionally, preoperatory urine culture was collected for combined evaluation with the previous data. Percutaneous nephrolithotomy was the most commonly performed approach (45.8%). Struvite stones were more frequently identified in women (90.3%). Among stones with positive cultures, except struvite, 45.5% were composed of calcium oxalate monohydrate. The difference between urine culture and stone culture was different in 24.8% of the cases. Among stones with positive cultures that did not contain struvite, 86.4% showed non-urease bacteria in their cultures and 47.1% of struvite stones also did not have urease-producing bacteria in their cultures (p < 0.021). Our findings suggest that there is an association between non-ureolytic bacteria and stones that are not composed of struvite.

Identifying Two Novel Clusters in Calcium Oxalate Stones With Urinary Tract Infection Using 16S rDNA Sequencing

Urinary stones and urinary tract infection (UTI) are the most common diseases in urology and they are characterized by high incidence and high recurrence rate in China. Previous studies have shown that urinary stones are closely associated with gut or urine microbiota. Calcium oxalate stones are the most common type of urinary stones. However, the profile of urinary tract microorganisms of calcium oxalate stones with UTI is not clear. In this research, we firstly found two novel clusters in patients with calcium oxalate stones (OA) that were associated with the WBC/HP (white blood cells per high-power field) level in urine. Two clusters in the OA group (OA1 and OA2) were distinguished by the key microbiota Firmicutes and Enterobacteriaceae. We found that Enterobacteriaceae enriched in OA1 cluster was positively correlated with several infection-related pathways and negatively correlated with a few antibiotics-related pathways. Meantime, some probiotics with higher abundance in OA2 cluster such as Bifidobacterium were positively correlated with antibiotics-related pathways, and some common pathogens with higher abundance in OA2 cluster such as Enterococcus were positively correlated with infection-related pathways. Therefore, we speculated that as a sub-type of OA disease, OA1 was caused by Enterobacteriaceae and the lack of probiotics compared with OA2 cluster. Moreover, we also sequenced urine samples of healthy individuals (CK), patients with UTI (I), patients with uric acid stones (UA), and patients with infection stones (IS). We identified the differentially abundant taxa among all groups. We hope the findings will be helpful for clinical treatment and diagnosis of urinary stones.

Gender differences in the microbial spectrum and antibiotic sensitivity of uropathogens isolated from patients with urinary stones

Purpose

The characteristics and resistance patterns of urine bacteriology urolithiasis patients between male and female have not been extensively studied. This study aims to investigate the gender differences in microbial spectrum and antibiotic susceptibility of uropathogens isolated from urolithiasis patients and provide insights for appropriate antimicrobial therapies.

Materials and Methods

We retrospectively collected clinical microbiology data from urine culture in urolithiasis patients between March 2014 and December 2018 in Xiangya Hospital. Then the patients were divided into male and female groups. The microbial spectrum and frequency of susceptibility to antibiotics were compared.

Results

A total of 359 uropathogen isolates were collected from 335 patients, including 144 males (43.0%) and 191 females (57.0%). E. coli dominated in both groups, indicating higher frequency in females (53.2%) than in males (26.6%, p < 0.001), followed by E. faecalis, with higher frequency in males (15.6%) than in females (2.9%, p < 0.001). Major Gram‐negative (E. coli and K. pneumoniae) bacteria showed high sensitivity to cefoperazone/sulbactam, cefotetan, piperacillin/ tazobactam, and amikacin. In contrast, the resistance level was high to penicillin, tetracycline, and vancomycin in both groups. Gram‐positive (E. faecalis and E. faecium) isolates demonstrated high sensitivity to gentamicin and vancomycin in both groups. Furthermore, uropathogens isolated from female urolithiasis patients were more susceptible to antimicrobials than males.

Conclusions

Uropathogen microbial spectrum in female urolithiasis patients is different from males. High susceptibility antibiotics should be used empirically according to gender to avoid multidrug‐resistant bacteria increase.

Human kidney stones: a natural record of universal biomineralization

GeoBioMed - a new transdisciplinary approach that integrates the fields of geology, biology and medicine - reveals that kidney stones composed of calcium-rich minerals precipitate from a continuum of repeated events of crystallization, dissolution and recrystallization that result from the same fundamental natural processes that have governed billions of years of biomineralization on Earth. This contextual change in our understanding of renal stone formation opens fundamentally new avenues of human kidney stone investigation that include analyses of crystalline structure and stratigraphy, diagenetic phase transitions, and paragenetic sequences across broad length scales from hundreds of nanometres to centimetres (five Powers of 10). This paradigm shift has also enabled the development of a new kidney stone classification scheme according to thermodynamic energetics and crystalline architecture. Evidence suggests that ≥50% of the total volume of individual stones have undergone repeated in vivo dissolution and recrystallization. Amorphous calcium phosphate and hydroxyapatite spherules coalesce to form planar concentric zoning and sector zones that indicate disequilibrium precipitation. In addition, calcium oxalate dihydrate and calcium oxalate monohydrate crystal aggregates exhibit high-frequency organic-matter-rich and mineral-rich nanolayering that is orders of magnitude higher than layering observed in analogous coral reef, Roman aqueduct, cave, deep subsurface and hot-spring deposits. This higher frequency nanolayering represents the unique microenvironment of the kidney in which potent crystallization promoters and inhibitors are working in opposition. These GeoBioMed insights identify previously unexplored strategies for development and testing of new clinical therapies for the prevention and treatment of kidney stones.

Recent advances on the mechanisms of kidney stone formation (Review)

Kidney stone disease is one of the oldest diseases known to medicine; however, the mechanisms of stone formation and development remain largely unclear. Over the past decades, a variety of theories and strategies have been developed and utilized in the surgical management of kidney stones, as a result of recent technological advances. Observations from the authors and other research groups suggest that there are five entirely different main mechanisms for kidney stone formation. Urinary supersaturation and crystallization are the driving force for intrarenal crystal precipitation. Randall's plaques are recognized as the origin of calcium oxalate stone formation. Sex hormones may be key players in the development of nephrolithiasis and may thus be potential targets for new drugs to suppress kidney stone formation. The microbiome, including urease-producing bacteria, nanobacteria and intestinal microbiota, is likely to have a profound effect on urological health, both positive and negative, owing to its metabolic output and other contributions. Lastly, the immune response, and particularly macrophage differentiation, play crucial roles in renal calcium oxalate crystal formation. In the present study, the current knowledge for each of these five aspects of kidney stone formation is reviewed. This knowledge may be used to explore novel research opportunities and improve the understanding of the initiation and development of kidney stones for urologists, nephrologists and primary care.

In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis

Background

Human kidney stones form via repeated events of mineral precipitation, partial dissolution, and reprecipitation, which are directly analogous to similar processes in other natural and manmade environments, where resident microbiomes strongly influence biomineralization. High-resolution microscopy and high-fidelity metagenomic (microscopy-to-omics) analyses, applicable to all forms of biomineralization, have been applied to assemble definitive evidence of in vivo microbiome entombment during urolithiasis.

Methods

Stone fragments were collected from a randomly chosen cohort of 20 patients using standard percutaneous nephrolithotomy (PCNL). Fourier transform infrared (FTIR) spectroscopy indicated that 18 of these patients were calcium oxalate (CaOx) stone formers, whereas one patient formed each formed brushite and struvite stones. This apportionment is consistent with global stone mineralogy distributions. Stone fragments from seven of these 20 patients (five CaOx, one brushite, and one struvite) were thin sectioned and analyzed using brightfield (BF), polarization (POL), confocal, super-resolution autofluorescence (SRAF), and Raman techniques. DNA from remaining fragments, grouped according to each of the 20 patients, were analyzed with amplicon sequencing of 16S rRNA gene sequences (V1-V3, V3-V5) and internal transcribed spacer (ITS1, ITS2) regions.

Results

Bulk-entombed DNA was sequenced from stone fragments in 11 of the 18 patients who formed CaOx stones, and the patients who formed brushite and struvite stones. These analyses confirmed the presence of an entombed low-diversity community of bacteria and fungi, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Aspergillus niger. Bacterial cells approximately 1 μm in diameter were also optically observed to be entombed and well preserved in amorphous hydroxyapatite spherules and fans of needle-like crystals of brushite and struvite.

Conclusions

These results indicate a microbiome is entombed during in vivo CaOx stone formation. Similar processes are implied for brushite and struvite stones. This evidence lays the groundwork for future in vitro and in vivo experimentation to determine how the microbiome may actively and/or passively influence kidney stone biomineralization.

Bacteriological Profile of Urine in Patients with Different Types of Kidney Stones in a Tertiary Care Hospital: A Descriptive Cross-sectional Study

Introduction:

The association of bacteriology in the pathogenesis of urolithiasis is a known and fact. The urinary tract stones being the most common problem that brings the patient to the surgical outpatient department; it is important to know the relation between the types of stone and the organism isolated from the urine for better management of the patient. The aim of this study was to find out the urine bacteriological profile of patients with kidney stones.

Methods:

This is a descriptive cross-sectional study done over 18 months in a tertiary care hospital in Nepal. Ethical clearance was taken from the Institutional Review Committee (No: 03/16). Preoperative urine cultures were done routinely in all the patients who agreed to take participate in the study. The biochemical stone analysis was done. Urinary microbial floras and stone composition were noted. Data entry and analysis was done using Statistical Package for the Social Sciences version 25.0.

Results:

Among 107 patients, kidney stones were more common in males and most of the patients were in their 2^nd to 4^th decade. Female patients 45 (42.05%) had more predilections towards the urinary tract infection. Among 15 (14.01%) positive cultures, Escherichia coli 10 (67%) was the most common organism isolated followed by Klebsiella; 4 (27%), and Pseudomonas; 1 (6%).

Conclusions:

Thus, we would like to state that Escherichia coli, though being a non-urease producing organism, is a major organism isolated in the preoperative culture of urine in a patient with kidney stones.

Urinary Calculi: A Microbiological and Biochemical Analysis at a Tertiary Care Hospital in Eastern Nepal

Background

The occurrence of urinary tract infection in presence of urolithiasis is frequently noted; however, microbial agents of urolithiasis and their antimicrobial susceptibility patterns remain underinvestigated. This study aimed to identify the microorganisms isolated from urine and stone matrices to determine their antimicrobial susceptibility, to find the association between the pathogens of urine and stone matrices, and to perform the biochemical analysis of stones.

Methods

A total of 88 cases of urolithiasis admitted for elective stone removal at Department of surgery, B.P. Koirala Institute of Health Sciences (BPKIHS), were enrolled. Preoperative urine culture and postoperative stone culture were performed. Isolation, identification, and AST were done by the standard microbiological technique. Further qualitative biochemical analysis of stones was also attempted.

Result

Among 88 stone formers recruited, culture of urine, whole stone, and nidus yielded the growth of bacteria 44, 32, and 30, respectively. Bacteria isolated from urine culture correlated with those from stone matrices with a sensitivity of 90%, specificity of 79.69%, PPV of 63.64%, and NPV of 95.45%. Escherichia coli (46.7%) was the most common bacteria followed by Klebsiella pneumoniae (16.7%) and Proteus mirabilis (13.3%) from urine and stone cultures. Almost all the uropathogens isolated were susceptible to commonly used antibiotics. Calcium oxalate (84.1%) was common biochemical constituent found in stone formers followed by calcium oxalate + phosphate (8%).

Conclusions

The association of microorganism isolated from urine and nidus culture was significant that can predict the source of infective stone; however, in some cases, microorganisms and the antimicrobial susceptibility pattern from urine and nidus were different. This study emphasizes the use of appropriate antimicrobial agents to prevent the regrowth of residual stones and minimize the risk of infectious complications after surgical removal of stones.

Urolithiasis and cystitis associated with Staphylococcus delphini group A and mortality in post-weaning mink kits (Neovison vison)

Mortality of mink kits represents a significant loss to production. However, causes of post-weaning mortality in mink kits in modern Danish mink production systems are still relatively poorly documented. We performed a cross-sectional mortality study on eight Danish mink farms including 1893 post mortem examinations of mink kits found dead or euthanized. We assessed the prevalence of cystitis and urolithiasis leading to mortality. Gross pathological findings as well as animal characteristics were recorded and associations with post mortem microbiology (using culture and MaldiTof-MS Vitek MS system) were investigated. Cystitis and/or urolithiasis were associated with death in 33 % (n = 476) and 37 % (n = 166) of the examined mink kits in 2015 and 2017. On farm level, the prevalence of cystitis and/or urolithiasis leading to mortality varied from 0.25 % to 1.27 % with a low overall mortality of 0.9-4.5 %. The bacterial agent most frequently isolated in post mortem bladder swabs from mink with a post mortem diagnosis of urolithiasis and cystitis was Staphylococcus delphini group A (51/283) with a significant (p < 0.0001, CI = [19.5;4745.7]) association to gross pathological findings in the urinary tract. Staphylococcus delphini group A was cultured from 70 % of the skin swabs obtained from apparently healthy mink euthanized at pelting (n = 222). In conclusion urinary tract disease (cystitis and urolithiasis) was the most prevalent post mortem diagnosis during the growth period and was associated with Staphylococcus delphini group A.

Treatment of non-obstructive, non-struvite urolithiasis is effective in treatment of recurrent urinary tract infections

PURPOSE

To determine if treatment of non-obstructing urolithiasis is effective in management of recurrent UTI.

MATERIALS AND METHODS

A retrospective review was performed of patients undergoing elective management of non-struvite upper tract urinary calculi with recurrent UTI from 2009 to 2016. Recurrent UTI was defined at ≥ 3 UTI in 12 months, with symptoms and documented urine culture. Preoperative CT was performed in all patients to determine stone burden. All patients had postoperative imaging and ≥ 12 months of follow-up. Pre- and postoperative variables were between patients who had recurrent UTI after treatment versus those who did not.

RESULTS

46 patients met inclusion criteria. 42 (91.3%) were female. Median age was 63.7 years (IQR 49.1, 73.4) and median total stone burden was 20 mm (IQR 14-35). Within the cohort, 20 (43.5%) underwent ureteroscopy only, 26 (56.5%) underwent PCNL ± URS, and none underwent ESWL. Median postoperative follow-up was 2.9 years (IQR 2.0, 4.3). Only five patients (10.9%) had recurrent UTI after treatment. 80% were with the preoperative pathogen. The presence of residual stone was an independent risk factor for recurrent UTI after treatment (p < 0.046). Diabetes, hypertension, immunosuppression and chronic kidney disease were not.

CONCLUSIONS

Stone removal for patients with recurrent UTIs was associated with a high rate of success (89.1%) in elimination of further recurrent UTIs. Residual fragments are independently associated with persistent recurrent UTIs and thus, complete stone removal is of paramount importance in treatment of this patient population.

Bacterial Effect on the Crystallization of Mineral Phases in a Solution Simulating Human Urine

The effect of bacteria that present in the human urine (Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Staphylococcus aureus) was studied under the conditions of biomimetic synthesis. It was shown that the addition of bacteria significantly affects both the phase composition of the synthesized material and the position of crystallization boundaries of the resulting phosphate phases, which can shift toward more acidic (struvite, apatite) or toward more alkaline (brushite) conditions. Under conditions of oxalate mineralization, bacteria accelerate the nucleation of calcium oxalates by almost two times and also increase the amount of oxalate precipitates along with phosphates and stabilize the calcium oxalate dihydrate (weddellite). The multidirectional changes in the pH values of the solutions, which are the result of the interaction of all system components and the crystallization process, were analyzed. The obtained results are the scientific basis for understanding the mechanisms of bacterial involvement in stone formation within the human body and the creation of biotechnological methods that inhibit this process.