Indwelling urological device biofilm composition and characteristics in the presence and absence of infection.

OBJECTIVE: To characterize microbial biofilms associated with different device types used in the urological field including ureteral stents, sacral neuromodulation (SNM) devices, penile prostheses, and artificial urinary sphincters (AUS). MATERIALS AND METHODS: Data from four studies, each reporting biofilm composition of a particular device type, were pooled and included for inter-device analysis. Studies recruited adults scheduled for ureteral stent, SNM, IPP, or AUS removal/revision. Device (n=115) biofilms and controls were analyzed with multi-omics approaches, and compositions were compared across device types and clinical factors. RESULTS: Microbiota present on each device type was distinct from that of perineal, rectal, or urine flora (p<0.01). Biofilm microbial counts (p<0.001) and diversity (p=0.024) differed by device type. Ureteral stents had greater microbial counts than other device types (p<0.001). Staphylococcus, Pseudomonas, Lactobacillus, Ureaplasma were commonly detected across devices. Device biofilms harbored a greater proportion of Proteobacteria phylum, and the rectal, perineal, and urine flora harbored a greater proportion of Firmicutes. Unique microbe-metabolite interaction networks were identified in presence and absence of infection. Antibiotic resistance genes including sul2 (sulfonamide resistance) and rpoB (rifampin resistance) were detected in biofilms across device types. Biofilm reconstitution in vitro differed by device type from which strains were isolated. CONCLUSIONS: Ureteral stents, sacral neuromodulation devices, penile prostheses, and artificial urinary sphincters harbored unique microbial and metabolite profiles that differed from those of skin, urine, and rectal flora. The findings of this study set the groundwork for investigation of novel strategies to reduce device-associated infection risk within and outside urology. DATA AVAILABILITY STATEMENT: Data are available from corresponding author upon reasonable request.

Association of Aggression with Lower Urinary Tract Symptoms and Overactive Bladder in Men: Observations from a Large Population-representative Study.

Background and objective: Lower urinary tract symptoms (LUTS) and overactive bladder (OAB) intimately affect the psychological wellbeing and mental health of men. However, to date, the association of aggression with LUTS and OAB has not been investigated. To address this knowledge gap, we evaluated the association of aggression with LUTS and OAB in a large representative cohort of men at the population level. Methods: We used computer-assisted web interviews that included reliable questionnaires for assessment of LUTS, OAB, and aggression. A population-representative group of men was based on the most recent census. For data analysis, we developed univariate and multivariate regression models. Key findings and limitations: We analyzed data for a cohort of 3001 men that was representative for age and place of residence. Aggression was more prevalent among respondents with LUTS and OAB in comparison to men without these conditions (p < 0.001). The scores for aggression were directly proportional to the scores for LUTS and OAB (Spearman's rank correlation coefficients of 0.261 for LUTS and 0.284 for OAB). Univariate linear regression models revealed an association between aggression and LUTS or OAB in all age groups. Finally, multivariable linear regression models confirmed that correlations of aggression with LUTS and OAB were independent of age, sociodemographic parameters, comorbidities, and lifestyle habits (regression coefficients of 0.013 for LUTS and 0.024 for OAB). Conclusions and clinical implications: Our study is the first to show that aggression among men is consistently associated with LUTS and OAB. Our results open a new research area on the effect of LUTS and OAB or their causes on psychological wellbeing and mental health, and may even support screening for hostile behavior in the clinical setting for individuals who report LUTS and OAB. Patient summary: We performed the first study to investigate whether aggression is linked to lower urinary tract symptoms (LUTS) and overactive bladder (OAB). Results from our survey in a representative group of men in Poland show that aggression is linked to LUTS and OAB. More research is needed to confirm these results.

External Validation Demonstrates Machine Learning Models Outperform Human Experts in Prediction of Objective and Patient-Reported Overactive Bladder Treatment Outcomes.

OBJECTIVE: To predict treatment response for overactive bladder (OAB) for a specific patient remains elusive. We sought to develop accurate models using machine learning for prediction of objective and patient-reported treatment response to intravesical botulinum toxin (OBTX-A) injection. We sought to validate the models in a challenging setting using an external dataset of a markedly different patient cohort and dosing regimen. We hypothesized the model would outperform human experts and top available algorithms. METHODS: Algorithms using "operator splitting" designed for accuracy and efficiency even in small training datasets with variable completeness, were trained to predict objective response and patient-reported symptomatic improvement using the ROSETTA trial cohort and validated using the ABC trial cohort of patients who underwent OBTX-A. Areas under the curve (AUC) of algorithms were compared to the top publicly-available machine-learning classifier XGBoost, logistic regression with cross validation, and human expert predictions in the external validation set. RESULTS: In the validation set, the operator splitting neural network had AUC of 0.66 and outperformed XGBoost with DART (top available machine-learning classifier, AUC: 0.58), logistic regression (AUC 0.55), and human experts (AUC 0.47-0.53) for prediction of clinical responder status. It was similarly accurate in prediction of patient subjective improvement in symptoms following OBTX-A (AUC: 0.64), again outperforming other algorithms and human experts (AUC 0.41-0.62). CONCLUSION: The neural network outperformed human experts and other machine-learning approaches in prediction of objective and patient-reported OBTX-A outcomes for OAB in a challenging independent validation cohort. Clinical implementation could improve counseling and treatment selection.

Towards a Reference Standard Definition of Urinary Tract Infection for Research.

Urinary tract infection (UTI) is among the most common human bacterial infections. In the context of increasing antibiotic resistance, there are many research efforts to improve the pathophysiological understanding, diagnosis, and treatment of UTI. Despite the high clinical relevance of UTI, there is high variability in definitions in the literature, making interpretation and comparison of research studies difficult, and even impossible in some cases. A recent Delphi consensus study generated a new reference standard definition for UTI that incorporates symptoms, pyuria, and urine culture results. This definition allows for designation of systemic involvement, and no longer categorizes UTIs as complicated or uncomplicated. The definition aligns with guidance from regulatory bodies for approval of UTI drugs. Implementation of a reference standard definition in the design and reporting of future investigations will allow better research design and interpretability within and outside the urology field. The new reference standard resolves some issues and offers a suitable way to unify methodology, and hence increase the potential strength of research in this area. There are some limitations and challenges for implementation, such as difficulties in establishing sensitivity and specificity values for the various settings in which the definition will be used. The inclusion of "probable" and "possible" UTI categories could be a problem in studies that require dichotomous outcomes. Nonetheless, the reference standard should be recommended until new developments become available, notably a more specific UTI biomarker than pyuria. Approaches to standardized diagnosis of catheter-associated UTIs remain unresolved. PATIENT SUMMARY: A new research definition for urinary tract infection (UTI) has been developed. Use of a single standardized definition in research will help in better design of research studies and comparison of results. Although the new definition will help in reducing the variability in UTI research reports, it has some limitations and there may be challenges to overcome before it is widely used.

Clinical Microbiome Testing for Urology.

The urine culture is imperfect, and a series of alternative approaches are in development to assist in diagnosis, treatment, and prevention of urinary tract infection (UTI). Culture-independent approaches typically do not distinguish between viable and nonviable bacteria, and are generally not included in current clinical guidance. Next-generation sequencing may play an important future role in precise targeting of antibiotic treatment of asymptomatic bacteriuria prior to endourologic surgery or in pregnancy. Future studies are needed to determine whether microbiota modulation could prevent UTI. Possible modulation mechanisms may include fecal microbiota transplant, application of topical vaginal estrogen or probiotics, and bacteriophage therapy.

Urinary Microbiome Research Has Not Established a Conclusive Influence: Revisiting Koch's Postulates.

In order to establish a causal relationship between urinary microbiota and a urological disease or condition, a series of rigorous scientific criteria must be met. Demonstration of an association between microbiota and a condition does not necessarily imply causality, importance, or clinical relevance.

Urinalysis is predictive for absence of urinary tract infection in men with and without catheters.

OBJECTIVES: To determine accuracy of negative urinalysis (UA) for predicting negative urine culture and the absence of urinary tract infection (UTI), and optimal urine culture growth cutoff for UTI diagnosis in men with and without urinary catheters. SUBJECTS AND METHODS: UAs with urine cultures within 1 week from adult men were identified and evaluated. Predictive values for the absence of UTI (absence of ≥1 of the following criteria: documentation of UTI diagnosis, antibiotic prescription, uropathogen presence on culture) were calculated. RESULTS: In total, 22 883 UAs were included. Negative UA had a high predictive value for negative urine culture (0.95, 95% confidence interval [CI]: 0.94-0.95) and absence of UTI (0.99, CI: 0.99-0.995) in the overall cohort. Negative UA also had a high predictive value for negative urine culture (0.93, CI: 0.90-0.95) and absence of UTI (0.99, CI: 0.98-0.999) in those with indwelling urinary catheters. The traditional threshold of culture growth of 100 000 colony-forming units (CFU)/mL did not capture 22% of UTIs. CONCLUSION: UA exhibits high predictive value for negative urine culture and absence of UTI in men, supporting a protocol wherein culture is only performed in the context of abnormal UA. The traditional 100 000 CFU/mL cut-off may have not captured a subset of UTI in the male population, and warrants further investigation.

Sexually transmitted infections and the vaginal microbiome after vaginoplasty.

PURPOSE OF REVIEW: Transgender and gender-diverse individuals (TGD) are at risk for sexually transmitted infections. Gender affirmation surgery is a cornerstone of care for many TGD individuals. For genital gender affirmation, the surgical creation of a vagina may be performed through a number of techniques. Those who have undergone vaginoplasty have unique anatomical and biopsychosocial considerations, which we discuss. RECENT FINDINGS: While sexually-transmitted infections including HPV, HSV, HIV, gonorrhea, and chlamydia, have been described in TGD individuals after vaginoplasty, the reports are very rare, and the provider should maintain an index of suspicion and maintain a broad differential for symptoms including neovaginal discharge. We discuss the association of the neovaginal microbiota composition with bacterial vaginosis, and how its modulation could potentially reduce bacterial vaginosis and sexually transmitted infection risk. SUMMARY: We examine the literature regarding sexually-transmitted infections following vaginoplasty, and the neovaginal microbiome and its similarities and differences relative to the natal vaginal microbiome.

Sacral neuromodulation device biofilm differs in the absence and presence of infection, harbors antibiotic resistance genes, and is reproducible in vitro.

INTRODUCTION/PURPOSE: Sacral neuromodulation (SNM) is effective therapy for overactive bladder refractory to oral therapies, and non-obstructive urinary retention. A subset of SNM devices is associated with infection requiring surgical removal. We sought to compare microbial compositions of explanted devices in the presence and absence of infection, by testing phase, and other clinical factors, and to investigate antibiotic resistance genes present in the biofilms. We analyzed resistance genes to antibiotics used in commercially-available anti-infective device coating/pouch formulations. We further sought to assess biofilm reconstitution by material type and microbial strain in vitro using a continuous-flow stir tank bioreactor, which mimics human tissue with an indwelling device. We hypothesized that SNM device biofilms would differ in composition by infection status, and genes encoding resistance to rifampin and minocycline would be frequently detected. MATERIALS/METHODS: Patients scheduled to undergo removal or revision of SNM devices were consented per IRB-approved protocol (IRB 20-415). Devices were swabbed intraoperatively upon exposure, with controls and precautions to reduce contamination of the surrounding field. Samples and controls were analyzed with next-generation sequencing and RT-PCR, metabolomics, and culture-based approaches. Associations between microbial diversity or microbial abundance, and clinical variables were then analyzed using t-tests and ANOVA. Reconstituted biofilm deposition in vitro using the bioreactor was compared by microbial strain and material type using plate-based assays and scanning electron microscopy. RESULTS: Thirty seven devices were analyzed, all of which harbored detectable microbiota. Proteobacteria, Firmicutes and Actinobacteriota were the most common phyla present overall. Beta-diversity differed in the presence versus absence of infection (p = 0.014). Total abundance, based on normalized microbial counts, differed by testing phase (p < 0.001), indication for placement (p = 0.02), diabetes mellitus (p < 0.001), cardiac disease (p = 0.008) and history of UTI (p = 0.008). Significant microbe-metabolite interaction networks were identified overall and in the absence of infection. 24% of biofilms harbored the tetA tetracycline/minocycline resistance gene and 53% harbored the rpoB rifampin resistance gene. Biofilm was reconstituted across tested strains and material types. Ceramic and titanium did not differ in biofilm deposition for any tested strain. CONCLUSIONS: All analyzed SNM devices harbored microbiota. Device biofilm composition differed in the presence and absence of infection and by testing phase. Antibiotic resistance genes including to rifampin and tetracycline/minocycline, which are used in commercially-available anti-infective pouches, were frequently detected. Isolated organisms from SNM devices demonstrated the ability to reconstitute biofilm formation in vitro. Biofilm deposition was similar between ceramic and titanium, materials used in commercially-available SNM device casings. The findings and techniques used in this study together provide the basis for the investigation of the next generation of device materials and coatings, which may employ novel alternatives to traditional antibiotics. Such alternatives might include bacterial competition, quorum-sensing modulation, or antiseptic application, which could reduce infection risk without significantly selecting for antibiotic resistance.

An exploratory study investigating the impact of the bladder tumor microbiome on Bacillus Calmette Guerin (BCG) response in non-muscle invasive bladder cancer.

PURPOSE: Intravesical Bacillus Calmette-Guerin (BCG) is standard of care for intermediate- and high-risk non-muscle invasive bladder cancer (NMIBC). The effect of the bladder microbiome on response to BCG is unclear. We sought to characterize the microbiome of bladder tumors in BCG-responders and non-responders and identify potential mechanisms that drive treatment response. MATERIALS AND METHODS: Patients with archival pre-treatment biopsy samples (2012-2018) were identified retrospectively. Prospectively, urine and fresh tumor samples were collected from individuals with high-risk NMIBC (2020-2023). BCG response was defined as tumor-free 2 years from induction therapy. Extracted DNA was sequenced for 16S rRNA and shotgun metagenomics. Primary outcomes were species richness (α-diversity) and microbial composition (ß-diversity). Paired t-tests were performed for α-diversity (Observed species/Margalef). Statistical analysis for ß-diversity (weighted and unweighted UniFrac distances, weighted Bray-Curtis dissimilarity) were conducted through Permanova, with 999 permutations. RESULTS: Microbial species richness (P < 0.001) and composition (P = 0.001) differed between BCG responders and non-responders. Lactobacillus spp. were significantly enriched in BCG-responders. Shotgun metagenomics identified possible mechanistic pathways such as assimilatory sulfate reduction. CONCLUSION: A compositional difference exists in the tumor microbiome of BCG responders and non-responders with Lactobacillus having increased abundance in BCG responders.

Bladder Compliance: How We Define It and Why It Is Important.

Bladder compliance is the relationship between detrusor pressure and bladder storage volume. We discuss the definition of compliance, how it may be accurately measured, and its clinical relevance. Specifically, we discuss the association between low compliance and upper urinary tract deterioration. We discuss medical and surgical therapies that have been demonstrated to improve compliance and reduce upper tract risk. Finally, we propose a model, which not only considers compliance but also differential pressure between the bladder and ureters, and how this may also be an accurate predictor of upper tract deterioration. We call for further investigation to test this model.

Surgical Management and Oncologic Outcomes of Renal Cell Carcinoma and Inferior Vena Caval Thrombi With Aggressive Histologic Variants.

OBJECTIVE: To characterize the surgical management, perioperative, and cancer-specific outcomes, and the influence of aggressive histologic variants (AHV) on operative management among patients with renal cell carcinoma (RCC) and inferior vena cava (IVC) thrombus. RCC with rhabdoid and/or sarcomatoid differentiation, which we defined as AHV, portends a worse prognosis. AHV can be associated with a desmoplastic reaction which may complicate resection. METHODS: We reviewed patients undergoing radical nephrectomy and IVC thrombectomy between 1990 and 2020. Comparative statistics were employed as appropriate. Survival analysis was performed according to the Kaplan-Meier method, and intergroup analysis performed with log-rank statistics. Multivariable cox proportional hazards regression was used to assess the effect of AHV, age, thrombus level, vena cavectomy, metastases, and medical comorbidities on recurrence and overall survival (OS). RESULTS: Ninety-four of 403 (23.3%) patients had AHV, including 43 (46%) rhabdoid, 39 (41%) sarcomatoid, and 12 (13%) with both. AHV were more likely to present with advanced disease; however, increased perioperative complications or decreased OS were not observed. Median (IQR) survival was 16.7 (4.8-47) months without AHV and 12.6 (4-29) months with AHV (P = .157). Sarcomatoid differentiation was independently associated with worse OS (HR = 2.016, CI 1.38-2.95, P <.001), whereas rhabdoid alone or with sarcomatoid demonstrated similar OS (P = 0.063). CONCLUSION: RCC and IVC thrombus with AHV are more likely to present with metastatic disease, and sarcomatoid differentiation is associated with a worse OS. Resection of tumors with and without AHV have similar perioperative complications, suggesting that surgery can be safely accomplished in patients with RCC and IVC thrombus with AHV.

Penile prostheses harbor biofilms driven by individual variability and manufacturer even in the absence of clinical infection.

BACKGROUND: Culture-based studies have shown that penile prostheses harbor biofilms in the presence and absence of infection, but these findings have not been adequately validated using contemporary microbiome analytic techniques. AIM: The study sought to characterize microbial biofilms of indwelling penile prosthesis devices according to patient factors, device components, manufacturer, and infection status. METHODS: Upon penile prostheses surgical explantation, device biofilms were extracted, sonicated, and characterized using shotgun metagenomics and culture-based approaches. Device components were also analyzed using scanning electron microscopy. OUTCOMES: Outcomes included the presence or absence of biofilms, alpha and beta diversity, specific microbes identified and the presence of biofilm, and antibiotic resistance genes on each prosthesis component. RESULTS: The average age of participants from whom devices were explanted was 61 ± 11 years, and 9 (45%) of 20 had a diagnosis of diabetes mellitus. Seventeen devices were noninfected, and 3 were associated with clinical infection. Mean device indwelling time prior to explant was 5.1 ± 5.1 years. All analyzed components from 20 devices had detectable microbial biofilms, both in the presence and absence of infection. Scanning electron microscopy corroborated the presence of biofilms across device components. Significant differences between viruses, prokaryotes, and metabolic pathways were identified between individual patients, device manufacturers, and infection status. Mobiluncus curtisii was enriched in manufacturer A device biofilms relative to manufacturer B device biofilms. Bordetella bronchialis, Methylomicrobium alcaliphilum, Pseudoxanthomonas suwonensis, and Porphyrobacter sp. were enriched in manufacturer B devices relative to manufacturer A devices. The most abundant bacterial phyla were the Proteobacteria, Actinobacteria, and Firmicutes. Glycogenesis, the process of glycogen synthesis, was among the predominant metabolic pathways detected across device components. Beta diversity of bacteria, viruses, protozoa, and pathways did not differ among device components. CLINICAL IMPLICATIONS: All components of all penile prostheses removed from infected and noninfected patients have biofilms. The significance of biofilms on noninfected devices remains unknown and merits further investigation. STRENGTHS AND LIMITATIONS: Strengths include the multipronged approach to characterize biofilms and being the first study to include all components of penile prostheses in tandem. Limitations include the relatively few number of infected devices in the series, a relatively small subset of devices included in shotgun metagenomics analysis, and the lack of anaerobic and other expanded conditions for culture. CONCLUSION: Penile prosthesis biofilms are apparent in the presence and absence of infection, and the composition of biofilms was driven primarily by device manufacturer, individual variability, and infection, while being less impacted by device component.

Microbe-metabolite interaction networks, antibiotic resistance, and in vitro reconstitution of the penile prosthesis biofilm support a paradigm shift from infection to colonization.

To understand differences between asymptomatic colonized and infected states of indwelling medical devices, we sought to determine penile prosthesis biofilm composition, microbe-metabolite interaction networks, and association with clinical factors. Patients scheduled for penile prosthesis removal/revision were included. Samples from swabbed devices and controls underwent next-generation sequencing, metabolomics, and culture-based assessments. Biofilm formation from device isolates was reconstituted in a continuous-flow stir tank bioreactor. 93% of 27 analyzed devices harbored demonstrable biofilm. Seven genera including Faecalibaculum and Jeotgalicoccus were more abundant in infected than uninfected device biofilms (p < 0.001). Smokers and those with diabetes mellitus or cardiac disease had lower total normalized microbial counts than those without the conditions (p < 0.001). We identified microbe-metabolite interaction networks enriched in devices explanted for infection and pain. Biofilm formation was recapitulated on medical device materials including silicone, PTFE, polyurethane, and titanium in vitro to facilitate further mechanistic studies. Nearly all penile prosthesis devices harbor biofilms. Staphylococcus and Escherichia, the most common causative organisms of prosthesis infection, had similar abundance irrespective of infection status. A series of other uncommon genera and metabolites were differentially abundant, suggesting a complex microbe-metabolite pattern-rather than a single organism-is responsible for the transition from asymptomatic to infected or painful states.

Urinalysis Exhibits Excellent Predictive Capacity for the Absence of Urinary Tract Infection.

OBJECTIVE: To assess predictive value of urinalysis for negative urine culture and absence of urinary tract infection, re-evaluate the microbial growth threshold for positive urine culture result, and describe antimicrobial resistance features. Urine culture is associated with 27% of U.S. hospitalizations, and unnecessary antibiotic prescription is a main antibiotic resistance contributor. METHODS: Urinalyses with urine culture from women ages 18-49 from 2013 to 2020 were studied. Clinically diagnosed urinary tract infection (CUTI) was defined as (1) uropathogen growth, (2) documented diagnosis of urinary tract infection, and (3) antibiotic prescription. Sensitivity, specificity, and diagnostic predictive values were used to assess urinalysis performance in predicting isolation of a uropathogen by culture and in detection of CUTI. RESULTS: Total 12,252 urinalyses were included. Forty-one percent of urinalyses were associated with positive urine culture and 1287 (10.5%) with CUTI. Negative urinalysis exhibited high predictive accuracy for negative urine culture (specificity 90.3%, PPV 87.3%) and absence of CUTI (specificity 92.2%, PPV 97.4%). Twenty-four percent of patients not meeting the CUTI definition were still prescribed antibiotics. Twenty-two percent of cultures associated with CUTI exhibited growth less than 100,000 CFU/mL. Escherichia coli was implemented as causing 70% of CUTIs, and 4.2% of these produced an extended spectrum beta-lactamase. CONCLUSION: Negative urinalysis exhibits high predictive accuracy for absence of CUTI. A reporting threshold of 10,000 CFU/mL is more clinically appropriate than a 100,000 CFU/mL cutpoint. Reflex culture based on urinalysis results could complement clinical judgement and improve laboratory and antibiotic stewardship in premenopausal women.

Ureteral Stents Harbor Complex Biofilms With Rich Microbiome-Metabolite Interactions.

PURPOSE: We sought to determine microbe-metabolite composition and interactions within indwelling ureteral stent biofilms, determine their association with patient factors including infection, and reconstitute biofilm formation on relevant surface materials in vitro. MATERIALS AND METHODS: Upon ureteral stent removal from patients, proximal and distal ends were swabbed. Samples were analyzed by 16S next-generation sequencing and metabolomics. A continuous-flow stir-tank bioreactor was used to reconstitute and quantify in vitro biofilm formation from stent-isolated bacteria on stent-related materials including silicone, polytetrafluoroethylene, polyurethane, polycarbonate, and titanium. Diversity, relative abundance, and association with clinical factors were analyzed with ANOVA and Bonferroni t-tests or PERMANOVA. Biofilm deposition by microbial strain and device material type were analyzed using plate counts and scanning electron microscopy following bioreactor incubation. RESULTS: All 73 samples from 37 ureteral stents harbored microbiota. Specific genera were more abundant in samples from stents wherein there was antibiotic exposure during indwelling time (Escherichia/Shigella, Pseudomonas, Staphylococcus, Ureaplasma) and in those associated with infection (Escherichia/Shigella, Ureaplasma). The enriched interaction subnetwork in stent-associated infection included Ureaplasma and metabolite 9-methyl-7-bromoeudistomin. Strains identified as clinically relevant and central to interaction networks all reconstituted biofilm in vitro, with differential formation by strain (Enterococcus faecalis most) and material type (titanium least). CONCLUSIONS: Ureteral stent biofilms exhibit patterns unique to stent-associated infection and antibiotic exposure during indwelling time. Microbes isolated from stents reconstituted biofilm formation in vitro. This work provides a platform to test novel materials, evaluate new coatings for anti-biofilm properties, and explore commensal strain use for bacterial interference against pathogens.