Decreased microbiota diversity associated with urinary tract infection in a trial of bacterial interference

3D-Bioprinted Urinary Catheters Enable Sustained Probiotic Recovery Under Flow and Improve Bladder Colonization In Vivo

Catheter-associated urinary tract infections (CAUTIs) account for a large proportion of healthcare-associated infections. CAUTIs, caused by colonization of the catheter surface by uropathogens, are challenging to treat, especially when compounded by antibiotic resistance. One prophylactic strategy that could reduce pathogen colonization is bacterial interference, whereby the catheter surface is coated with non-pathogenic bacteria. Current challenges include identifying appropriate bacterial interference strains that maintain stable association with the catheter and are viable, but not pathogenic, in the urinary tract environment. This study evaluated the stability of probiotic Lactobacillus rhamnosus in 3D bioprints mimicking urinary catheter tubing under urine flow and assessed viability and safety in an in vivo mouse model. Bioprints underwent hydraulic flow testing in vitro with artificial urine media (AUM), followed by evaluation of catheter structure, L. rhamnosus recovery, and biofilm formation. Mice were inoculated with free L. rhamnosus bacteria or implanted with L. rhamnosus-containing bioprints to measure urinary tract colonization and assess effects on the bladder tissue. Bioprinted segments exhibited minimal mass change while maintaining an intact shape and demonstrated viable L. rhamnosus recovery throughout 7 days. L. rhamnosus formed biofilms on the bioprint surface that were not disrupted by urinary flow conditions. Encouragingly, L. rhamnosus viability was maintained in bioprints in a mouse urinary tract catheterization model. Bioprints released L. rhamnosus in vivo and did not cause histological inflammation beyond that generated by standard silicone catheters. In summary, L. rhamnosus bioprints exhibited key desirable characteristics, including maintenance of probiotic viability, probiotic growth on the catheter surface, and enhanced probiotic colonization of the bladder. This study supports the development of bioprinted probiotic catheters as a new strategy to prevent CAUTI.

Engineered microorganisms: A new direction in kidney stone prevention and treatment

Numerous studies have shown that intestinal and urinary tract flora are closely related to the formation of kidney stones. The removal of probiotics represented by lactic acid bacteria and the colonization of pathogenic bacteria can directly or indirectly promote the occurrence of kidney stones. However, currently existing natural probiotics have limitations. Synthetic biology is an emerging discipline in which cells or living organisms are genetically designed and modified to have biological functions that meet human needs, or even create new biological systems, and has now become a research hotspot in various fields. Using synthetic biology approaches of microbial engineering and biological redesign to enable probiotic bacteria to acquire new phenotypes or heterologous protein expression capabilities is an important part of synthetic biology research. Synthetic biology modification of microorganisms in the gut and urinary tract can effectively inhibit the development of kidney stones by a range of means, including direct degradation of metabolites that promote stone production or indirect regulation of flora homeostasis. This article reviews the research status of engineered microorganisms in the prevention and treatment of kidney stones, to provide a new and effective idea for the prevention and treatment of kidney stones.

Etiology, presentation and management of urinary tract infections in multiple sclerosis patients: A review of the current literature

Urinary tract infections (UTIs) present a formidable challenge in the care of individuals affected by multiple sclerosis (MS). Lower urinary tract dysfunction is a prevalent issue among MS patients, predisposing them to an elevated risk of UTIs. When left untreated, UTIs can further exacerbate the already compromised quality of life in individuals with MS. The diagnosis and management of UTIs in MS patients necessitate a careful clinical evaluation. The objective of this review is to delineate preventive strategies and current and developing therapeutic approaches for preventing and treating UTIs associated with urinary dysfunction, catheterization, and upper urinary tract infections in patients with MS. Effectively addressing UTIs and urinary tract dysfunction in individuals with multiple sclerosis calls for a comprehensive, interdisciplinary approach.

Research progress on the microbiota in bladder cancer tumors

The microbiota, also referred to as the microbial community, is a crucial component of the human microenvironment. It is located predominantly in various organs, including the intestines, skin, oral cavity, respiratory tract, and reproductive tract. The microbiota maintains a symbiotic relationship with the human body, influencing physiological and pathological functions to a significant degree. There is increasing evidence linking the microbial flora to human cancers. In contrast to the traditional belief that the urethra and urine of normal individuals are sterile, recent advancements in high-throughput sequencing technology and bacterial cultivation methods have led to the discovery of specific microbial communities in the urethras of healthy individuals. Given the prevalence of bladder cancer (BCa) as a common malignancy of the urinary system, researchers have shifted their focus to exploring the connection between disease development and the unique microbial community within tumors. This shift has led to a deeper investigation into the role of microbiota in the onset, progression, metastasis, prognosis, and potential for early detection of BCa. This article reviews the existing research on the microbiota within BCa tumors and summarizes the findings regarding the roles of different microbes in various aspects of this disease.

A comprehensive status update on modification of foley catheter to combat catheter-associated urinary tract infections and microbial biofilms

Present-day healthcare employs several types of invasive devices, including urinary catheters, to improve medical wellness, the clinical outcome of disease, and the quality of patient life. Among urinary catheters, the Foley catheter is most commonly used in patients for bladder drainage and collection of urine. Although such devices are very useful for patients who cannot empty their bladder for various reasons, they also expose patients to catheter-associated urinary tract infections (CAUTIs). Catheter provides an ideal surface for bacterial colonization and biofilm formation, resulting in persistent bacterial infection and severe complications. Hence, rigorous efforts have been made to develop catheters that harbour antimicrobial and anti-fouling properties to resist colonization by bacterial pathogens. In this regard, catheter modification by surface functionalization, impregnation, blending, or coating with antibiotics, bioactive compounds, and nanoformulations have proved to be effective in controlling biofilm formation. This review attempts to illustrate the complications associated with indwelling Foley catheters, primarily focussing on challenges in fighting CAUTI, catheter colonization, and biofilm formation. In this review, we also collate scientific literature on catheter modification using antibiotics, plant bioactive components, bacteriophages, nanoparticles, and studies demonstrating their efficacy through in vitro and in vivo testing.

Virulence Factor Genes in Invasive Escherichia coli Are Associated with Clinical Outcomes and Disease Severity in Patients with Sepsis: A Prospective Observational Cohort Study

BACKGROUND

Escherichia coli harbours virulence factors that facilitate the development of bloodstream infections. Studies determining virulence factors in clinical isolates often have limited access to clinical data and lack associations with patient outcome. The goal of this study was to correlate sepsis outcome and virulence factors of clinical E. coli isolates in a large cohort.

METHODS

Patients presenting at the emergency department whose blood cultures were positive for E. coli were prospectively included. Clinical and laboratory parameters were collected at admission. SOFA-score was calculated to determine disease severity. Patient outcomes were in-hospital mortality and ICU admission. Whole genome sequencing was performed for E. coli isolates and virulence genes were detected using the VirulenceFinder database.

RESULTS

In total, 103 E. coli blood isolates were sequenced. Isolates had six to 41 virulence genes present. One virulence gene, kpsMII_K23, a K1 capsule group 2 of E. coli type K23, was significantly more present in isolates of patients who died. kpsMII_K23 and cvaC (Microcin C) were significantly more frequent in isolates of patients who were admitted to the ICU. Fourteen virulence genes (mchB, mchC, papA_fsiA_F16, sat, senB, iucC, iutA, iha, sfaD, cnf1, focG, vat, cldB, and mcmA) significantly differed between patients with and without sepsis.

CONCLUSIONS

Microcins, toxins, and fimbriae were associated with disease severity. Adhesins and iron uptake proteins seemed to be protective. Two genes were associated with worse clinical outcome. These findings contribute to a better understanding of host-pathogen interactions and could help identifying patients most at risk for a worse outcome.

Development and Characterization of Lactobacillus rhamnosus-Containing Bioprints for Application to Catheter-Associated Urinary Tract Infections

Catheter-associated urinary tract infections (CAUTI) are a significant healthcare burden affecting millions of patients annually. CAUTI are characterized by infection of the bladder and pathogen colonization of the catheter surface, making them especially difficult to treat. Various catheter modifications have been employed to reduce pathogen colonization, including infusion of antibiotics and antimicrobial compounds, altering the surface architecture of the catheter, or coating it with nonpathogenic bacteria. Lactobacilli probiotics offer promise for a "bacterial interference" approach because they not only compete for adhesion to the catheter surface but also produce and secrete antimicrobial compounds effective against uropathogens. Three-dimensional (3D) bioprinting has enabled fabrication of well-defined, cell-laden architectures with tailored release of active agents, thereby offering a novel means for sustained probiotic delivery. Silicone has shown to be a promising biomaterial for catheter applications due to mechanical strength, biocompatibility, and its ability to mitigate encrustation on the catheter. Additionally, silicone, as a bioink, provides an optimum matrix for bioprinting lactobacilli. This study formulates and characterizes novel 3D-bioprinted Lactobacillus rhamnosus (L. rhamnosus)-containing silicone scaffolds for future urinary tract catheterization applications. Weight-to-weight (w/w) ratio of silicone/L. rhamnosus was bioprinted and cured with relative catheter dimensions in diameter. Scaffolds were analyzed in vitro for mechanical integrity, recovery of L. rhamnosus, antimicrobial production, and antibacterial effect against uropathogenic Escherichia coli, the leading cause of CAUTI. The results show that L. rhamnosus-containing scaffolds are capable of sustained recovery of live bacteria over 14 days, with sustained production of lactic acid and hydrogen peroxide. Through the use of 3D bioprinting, this study presents a potential alternative strategy to incorporate probiotics into urinary catheters, with the ultimate goal of preventing and treating CAUTI.

Changes of microbiota level in urinary tract infections: A meta-analysis

No consensus has been reached on the dysbiosis signs of microbiota in patients with urinary tract infections (UTIs). This meta-analysis aimed to verify the relationship between microbiota levels and UTIs. PubMed, Web of Science, and Embase databases were retrieved for related articles published from inception until October 20, 2021. The standardized mean difference (SMD) and its related 95% confidence intervals (CIs) of the microbiota diversity and abundance were pooled under a random-effects model. Twelve studies were included in this meta-analysis. The pooled analysis revealed that the microbiota diversity was lower in patients with UTIs than in healthy individuals (SMD = -0.655, 95% CI = -1.290, -0.021, I ² = 81.0%, P = 0.043). The abundance of specific bacteria was higher in UTI subjects compared with healthy control individuals (SMD = 0.41, 95% CI = 0.07-0.74, P = 0.017), especially in North America patients with UTIs. Similar results were also found in studies with the total sample size being greater than 30. Importantly, Escherichia coli levels were increased in patients with UTI, whereas Lactobacillus levels decreased. E. coli and Lactobacilli have huge prospects as potential microbiota markers in the treatment of UTIs.

Building a nomogram plot based on the nanopore targeted sequencing for predicting urinary tract pathogens and differentiating from colonizing bacteria

Background

The identification of uropathogens (UPBs) and urinary tract colonizing bacteria (UCB) conduces to guide the antimicrobial therapy to reduce resistant bacterial strains and study urinary microbiota. This study established a nomogram based on the nanopore-targeted sequencing (NTS) and other infectious risk factors to distinguish UPB from UCB.

Methods

Basic information, medical history, and multiple urine test results were continuously collected and analyzed by least absolute shrinkage and selection operator (LASSO) regression, and multivariate logistic regression was used to determine the independent predictors and construct nomogram. Receiver operating characteristics, area under the curve, decision curve analysis, and calibration curves were used to evaluate the performance of the nomogram.

Results

In this study, the UPB detected by NTS accounted for 74.1% (401/541) of all urinary tract microorganisms. The distribution of ln(reads) between UPB and UCB groups showed significant difference (OR = 1.39; 95% CI, 1.246-1.551, p < 0.001); the reads number in NTS reports could be used for the preliminary determination of UPB (AUC=0.668) with corresponding cutoff values being 7.042. Regression analysis was performed to determine independent predictors and construct a nomogram, with variables ranked by importance as ln(reads) and the number of microbial species in the urinary tract of NTS, urine culture, age, urological neoplasms, nitrite, and glycosuria. The calibration curve showed an agreement between the predicted and observed probabilities of the nomogram. The decision curve analysis represented that the nomogram would benefit clinical interventions. The performance of nomogram with ln(reads) (AUC = 0.767; 95% CI, 0.726-0.807) was significantly better (Z = 2.304, p-value = 0.021) than that without ln(reads) (AUC = 0.727; 95% CI, 0.681-0.772). The rate of UPB identification of nomogram was significantly higher than that of ln(reads) only (χ^2 = 7.36, p-value = 0.009).

Conclusions

NTS is conducive to distinguish uropathogens from colonizing bacteria, and the nomogram based on NTS and multiple independent predictors has better prediction performance of uropathogens.

A Perspective of the Urinary Microbiome in Lower Urinary Tract Infections - A Review

PURPOSE OF REVIEW

Greater availability of sequencing methods has broadened the knowledge of the urinary microbiome in an environment previously believed to be sterile. This review discusses internal and external influences that promote either a balance or a dysbiosis of the urinary tract and the future perspectives in understanding lower urinary tract infections.

RECENT FINDINGS

Efforts have been made to identify a "core" urinary microbiome in which Firmicutes and Bacteroidetes account for most of the bacterial representations. A shift to a Proteobacteria-dominant representation shapes the fingerprint of the infectious urinary microbiome; furthermore, the virome and the mycobiome are important modulators of the urinary microbiome, which have been recently explored to determine their role in the health-disease process of the lower urinary tract. A disturbance of bacterial representation and diversity triggers a transition from health to disease; conversely, a functional cooperative interplay between the host and microbiome allows for basic metabolic and immune functions to take place.

How to Prevent Catheter-Associated Urinary Tract Infections: A Reappraisal of Vico's Theory-Is History Repeating Itself?

New, contextualized modern solutions must be found to solve the dilemma of catheter-associated urinary infection (CAUTI) in long-term care settings. In this paper, we describe the etiology, risk factors, and complications of CAUTI, explore different preventive strategies proposed in literature from the past to the present, and offer new insights on therapeutic opportunities. A care bundle to prevent CAUTI mainly consists of multiple interventions to improve clinical indications, identifying a timeline for catheter removal, or whether any alternatives may be offered in elderly and frail patients suffering from chronic urinary retention and/or untreatable urinary incontinence. Among the various approaches used to prevent CAUTI, specific urinary catheter coatings according to their antifouling and/or biocidal properties have been widely investigated. Nonetheless, an ideal catheter offering holistic antimicrobial effectiveness is still far from being available. After pioneering research in favor of bladder irrigations or endovesical instillations was initially published more than 50 years ago, only recently has it been made clear that evidence supporting their use to treat symptomatic CAUTI and prevent complications is needed.

Screening Biomarkers and Constructing a Predictive Model for Symptomatic Urinary Tract Infection and Asymptomatic Bacteriuria in Patients Undergoing Cutaneous Ureterostomy: A Metagenomic Next-Generation Sequencing Study

Objectives. To investigate the clinical diagnostic value of differential flora as biomarkers in patients with symptomatic urinary tract infection (UTI) and asymptomatic bacteriuria (ASB) undergoing cutaneous ureterostomy based on metagenomic next-generation sequencing and construct predictive models to provide a scientific reference for clinical diagnosis and treatment. Material and Methods. According to standard procedures, samples were taken from each patient for routine tests (urine, ureteral stent, and skin swab around the stoma). Cytokine levels in the blood were also detected. Urinary microflora were measured by mNGS, and potential biomarkers for distinguishing UTI and ASB were identified by differential flora. Finally, we generated the predictive models for ASB and UTI using the Lasso method and cytokine levels. Results. Urine culture was performed for 50 patients with cutaneous ureterostomy; 44 of these patients developed bacteriuria. The incidence of symptomatic bacteriuria was 54.55%. Biomarker analysis showed that Propionimicrobium lymphophilum, Staphylococcus haemolyticus, Stenotrophomonas maltophilia, Ralstonia insidiosa, and Aspergillus sydowii all had good predictive performance and were combined in a single model. The predictive model exhibited good prediction performance (area under the curve $\left(\text{AUC}\right)=0.8729$ , $\text{sensitivity}=80\%$ , $\text{specificity}=83.3\%$ , and $\text{cutoff}=1.855$ ). We also identified a significant negative correlation between the weight sum of the abundance for these five characteristic pathogens (Sum_weighted_Reads) and levels of the cytokine IL-6 and IL-1β ( $P<0.05$ ). Conclusion. mNGS had a higher positive detection rate for pathogens in urine samples. The selected differential bacteria can be used as biomarkers of ASB and UTI, and the prediction model has good predictive performance. Analysis also showed that the occurrence of symptoms was related to individual immunity. Combined with the Sum_weighted_Reads cutoff and cytokine levels (IL-6 and IL-1β) of differential flora, it was possible to judge the severity of symptoms in cutaneous ureterostomy patients with bacteriuria and provide new insights for the treatment and intervention of ASB and UTI.

Probiotics for the Management of Infectious Diseases: Reviewing the State of the Art

This review aims to provide insight into the potential of probiotics as a clinical modality targeted at infectious diseases by creating a comprehensive overview of the state of the art of research and development efforts as shown by patents and clinical trials of the past 20 years. Data were retrieved from patent and clinical trial databases to reflect the long- and short-term developments of probiotics research. The data were analyzed to extract information on the total number of patents and trials for each indication, application date and location, and applicant/sponsor type. A total of 80 infectious diseases were investigated, precipitating in 789 patents and 602 clinical trials for 67 indications studied as targets of probiotics. An increasing trend was seen for the number of patents and clinical trials that were applied for since 1999 with the highest number of patents and clinical trials targeted to digestive tract, respiratory, and urogenital indications. Overall, research demonstrated a substantial interest in probiotics targeting infectious diseases, which was in line with reported unmet needs and global probiotics sales estimates. However, the declining rate of translation from patents to clinical trials indicates that there are some barriers obstructing the research process.

Catheter-Associated Urinary Tract Infections: Current Challenges and Future Prospects

Catheter-associated urinary tract infection (CAUTI) is the most common healthcare-associated infection and cause of secondary bloodstream infections. Despite many advances in diagnosis, prevention and treatment, CAUTI remains a severe healthcare burden, and antibiotic resistance rates are alarmingly high. In this review, current CAUTI management paradigms and challenges are discussed, followed by future prospects as they relate to the diagnosis, prevention, and treatment. Clinical and translational evidence will be evaluated, as will key basic science studies that underlie preventive and therapeutic approaches. Novel diagnostic strategies and treatment decision aids under development will decrease the time to diagnosis and improve antibiotic accuracy and stewardship. These include several classes of biomarkers often coupled with artificial intelligence algorithms, cell-free DNA, and others. New preventive strategies including catheter coatings and materials, vaccination, and bacterial interference are being developed and investigated. The antibiotic pipeline remains insufficient, and new strategies for the identification of new classes of antibiotics, and rational design of small molecule inhibitor alternatives, are under development for CAUTI treatment.

Assessment of the Urinary Microbiota of MSM Using Urine Culturomics Reveals a Diverse Microbial Environment

BACKGROUND

The urinary tract is not sterile and is populated by microbial communities that influence urinary health. Men who have sex with men (MSM) are understudied yet have increased risk factors for genitourinary infections. Our objective was to interrogate the composition of MSM urinary microbiota.

METHODS

Midstream urine specimens (n = 129) were collected from MSM (n = 63) and men seen for routine care (clinical cohort, n = 30). Demographics and sexual/medical history were documented. Specimens underwent culture using standard-of-care and enhanced methods designed to isolate fastidious and anaerobic microorganisms. Isolates were identified by MALDI-TOF mass spectrometry or 16S rRNA gene sequencing.

RESULTS

The MSM cohort was younger (mean (SD), 35.4 (11.26) years) compared to the clinical cohort (62.7 (15.95) years). Organism recovery was significantly increased using enhanced vs standard culture for the MSM (mean of 9.1 vs 0.6 species/sample [P < 0.001]) and clinical (7.8 vs 0.9 species/sample [P < 0.001]) cohorts. The microbial composition of MSM urine specimens was dominated by Gram-positive and anaerobic microbes and clustered distinctly from that of clinical urine specimens. Composition of microbial species recovered within the same subject was dynamic between urine specimens but more similar relative to inter-individual comparisons. Principal coordinate analysis showed no correlation between urinary microbiota composition and age, recent antibiotic use, sexually transmitted infection/HIV status, or sexual practices.

CONCLUSIONS

Enhanced culture recovered a large diversity of microbial species from MSM urine specimens, especially taxa typically associated with mucosal surfaces. These findings may increase understanding of urologic disease in MSM and improve diagnostic methods for detection of genitourinary infections.

Asian guidelines for UTIs & STIs UTI section: Complicated UTIs with neurogenic bladder

EPIDEMIOLOGY AND PATHOGENESIS

Urinary tract infection (UTI) in patients with neurogenic bladder causes significant morbidity and mortality.

DIAGNOSIS

UTI in neurogenic bladder causes atypical symptomatology. Urine tests are pivotal in confirming or excluding UTI, and in guiding appropriate antibiotic treatment.

TREATMENT

1. Symptomatic UTI warrants appropriate antibiotic treatment with reference to culture results and local antibiotic resistance patterns. Asymptomatic bacteriuria should not be treated, and antibiotic prophylaxis is generally not recommended.2. Adequate bladder drainage is essential in reducing the occurrence of urinary tract infections.3. Recurrent UTI in neurogenic bladder may necessitate the treatment of neurogenic detrusor overactivity and the restoration of low bladder pressure during bladder storage and voiding by drugs or surgery.

Pathogenetic Role and Possibilities for Correction of Gut Microbiota Disorders in Urinary Tract Infections

The article presents current data on the role of gut microbiota in the development of urinary tract infections. The main pathogenetic mechanisms contributing to the chronic recurrent course of the disease, the spread of antimicrobial resistance, as well as their connection to the disorders of gut microbiota are shown. It is known that most pathogens of urinary infections originate from the gut microbiota, where they exist for a long time, forming reservoirs. The normal composition and functions of the microbiota prevent colonization of the intestine by pathogenic bacteria and reduce the risk of developing this disease. Ways of correction through diet, probiotics, as well as fecal microbiota transplantation are considered. Modulation of gut microbiota may be a promising approach in the treatment and prevention of urinary tract infections. Meanwhile, a qualitative evidence base on the effectiveness of this strategy has not been formed. Further research in this direction is required.

Changes in Conjunctival Microbiota Associated With HIV Infection and Antiretroviral Therapy

Purpose

HIV infection is associated with a variety of ocular surface diseases. Understanding the difference of the ocular microbiota between HIV-infected and healthy individuals as well as the influence of antiretroviral therapy will help to investigate the pathogenesis of these conditions.

Methods

A cross-sectional study was conducted on subjects including HIV-negative individuals, untreated HIV-infected individuals, and HIV-infected individuals with antiretroviral therapy. Conjunctival microbiota was assessed by bacterial 16S rRNA sequencing of the samples obtained from the conjunctival swab.

Results

The microbial richness in ocular surface was similar in HIV-negative, untreated HIV-positive, and highly active antiretroviral therapy (HAART) subjects. The bacterial compositions were similar in the two HIV infection groups but were significantly different from the HIV-negative group. HAART changed the beta diversity of bacterial community as determined by Shannon index. CD4+ T cell count had no significant influence on the diversity of ocular microbiota in HIV-infected individuals.

Conclusions

The data revealed the compositional and structural difference in conjunctival microbial community in subjects with and without HIV infection, indicating that HIV infection or its treatment, may contribute to ocular surface dysbiosis.

The microbiome and host mucosal interactions in urinary tract diseases

The urinary tract consists of the bladder, ureters, and kidneys, and is an essential organ system for filtration and excretion of waste products and maintaining systemic homeostasis. In this capacity, the urinary tract is impacted by its interactions with other mucosal sites, including the genitourinary and gastrointestinal systems. Each of these sites harbors diverse ecosystems of microbes termed the microbiota, that regulates complex interactions with the local and systemic immune system. It remains unclear whether changes in the microbiota and associated metabolites may be a consequence or a driver of urinary tract diseases. Here, we review the current literature, investigating the impact of the microbiota on the urinary tract in homeostasis and disease including urinary stones, acute kidney injury, chronic kidney disease, and urinary tract infection. We propose new avenues for exploration of the urinary microbiome using emerging technology and discuss the potential of microbiome-based medicine for urinary tract conditions.

Imprecision Medicine: Challenges in Diagnosis, Treatment, and Measuring Quality for Catheter-Associated Urinary Tract Infection

We question the reliability of the vague symptoms that most commonly define catheter-associated urinary tract infection (CAUTI) and encourage further examination of whether the current CAUTI definition reflects a true infection. While diagnosing CAUTI using the current surveillance definition, physicians may be missing a number of nonurinary etiologies for fever, prematurely diagnosing urinary tract infection, and prescribing unnecessary antibiotics. We believe it is time to reconsider the quality metric of CAUTI. By doing so, we can improve antibiotic use and quality of patient care.

Actinotignum schaalii: Relation to Concomitants and Connection to Patients' Conditions in Polymicrobial Biofilms of Urinary Tract Catheters and Urines

Actinotignum schaalii is an emerging, opportunistic pathogen and its connection to non-infectious diseases and conditions, such as prostate or bladder cancer, or chronic inflammation has been proposed. Here, we analyzed 297 urine, ureteral and urinary catheter samples from 128 patients by Polymerase Chain Reaction followed by Denaturing Gradient Gel Electrophoresis and Sequencing (PCR-DGGE-S), and culture, and 29 of these samples also by 16S rRNA Illumina sequencing, to establish A. schaalii’s prevalence in urinary tract-related samples, its relation to other bacteria, and its potential association with patients’ conditions and samples’ characteristics. A. schaalii-positive samples were significantly more diverse than A. schaalii negative and between-group diversity was higher than intra-group. Propionimicrobium lymphophilum, Fusobacterium nucleatum, Veillonella sp., Morganella sp., and Aerococcus sp. were significantly more often present in A. schaalii-positive samples; thus, we suggest these species are A. schaalii’s concomitants, while Enterobacter and Staphylococcaceae were more often identified in A. schaalii-negative samples; therefore, we propose A. schaalii and these species are mutually exclusive. Additionally, a significantly higher A. schaalii prevalence in patients with ureter stricture associated hydronephrosis (p = 0.020) was noted. We suggest that A. schaalii could be an early polybacterial biofilm colonizer, together with concomitant species, known for pro-inflammatory features.

Urinary Microbiome Characteristics in Female Patients with Acute Uncomplicated Cystitis and Recurrent Cystitis

Traditionally, the diagnostic mainstay of recurrent urinary tract infection has been urinary culture. However, the causative uropathogen of recurrent cystitis has not been well established. Urine DNA next-generation sequencing (NGS) can provide additional information on these infections. Herein, we compared urine NGS results and urine cultures in patients with acute uncomplicated cystitis (AUC) and recurrent cystitis (RC), and evaluated the difference in microbiome patterns in the NGS results. Patients who underwent urine culture and NGS due to AUC or RC were retrospectively reviewed. All urine samples were collected via a transurethral catheter and studied utilizing a type of NGS called 16S ribosomal RNA gene amplification and sequencing. The sensitivity of urine NGS was significantly higher than that of conventional urine culture (69.0% vs. 16.7%, p < 0.05). The detection rate of urine NGS was slightly lower in the RC group than in the AUC group (67.7% vs. 72.7%). Microbiome diversity was significantly higher in the RC group compared to the AUC group (p = 0.007), and the microbiome composition was significantly different between the AUC and RC groups. In the urine NGS results, Pseudomonas, Acinetobacter, and Enterobacteriaceae were found in the AUC group, and Sphingomonas, Staphylococcus, Streptococcus, and Rothia spp. were detected in the RC group. Urine NGS can significantly increase the diagnostic sensitivity compared to traditional urine culture methods, especially in RC patients. AUC and RC patients had significant differences in bacterial diversity and patterns. Therefore, recurrent cystitis might be approached from a different perspective.

The Roles of T cells in Bladder Pathologies

T lymphocytes play important roles in the skin and mucosal surfaces such as the gut and lung. Until recently the contributions of T cells to mammalian bladder immunity were largely unknown. With newer techniques, including single-cell RNA sequencing and reporter mice, an understanding is emerging of T cell roles in bladder diseases (bacterial infections, bladder cancer, chronic inflammation). In these pathologies, many bladder T cell responses can be harmful to the host through suboptimal clearance of bacteria or cancer cells, or by modulating autoinflammation. Recent findings suggest that T cell behavior might be influenced by resident T cell interactions with the bladder microbiota and other immunostimulants. Thus, regulating bladder T cell functions could emerge as a putative immunotherapy to treat some bladder diseases.

Perspectives from the Society for Pediatric Research: Probiotic use in urinary tract infections, atopic dermatitis, and antibiotic-associated diarrhea: an overview

Probiotics have received significant attention within both the scientific and lay communities for their potential health-promoting properties, including the treatment or prevention of various conditions in children. In this article, we review the published data on use of specific probiotic strains for three common pediatric conditions: the prevention of urinary tract infections and antibiotic-associated diarrhea and the treatment of atopic dermatitis. Research into the utility of specific probiotic strains is of varying quality, and data are often derived from small studies and case series. We discuss the scientific merit of these studies, their overall findings regarding the utility of probiotics for these indications, issues in reporting of methods, and results from these clinical trials, as well as future areas of investigation.

The Role of Gut, Vaginal, and Urinary Microbiome in Urinary Tract Infections: From Bench to Bedside

The current paradigm of urinary tract infection (UTI) pathogenesis takes into account the contamination of the periurethral space by specific uropathogens residing in the gut, which is followed by urethral colonization and pathogen ascension to the urinary bladder. Consequently, studying the relationship between gut microbiota and the subsequent development of bacteriuria and UTI represents an important field of research. However, the well-established diagnostic and therapeutic paradigm for urinary tract infections (UTIs) has come into question with the discovery of a multifaceted, symbiotic microbiome in the healthy urogenital tract. More specifically, emerging data suggest that vaginal dysbiosis may result in Escherichia coli colonization and prompt recurrent UTIs, while urinary microbiome perturbations may precede the development of UTIs and other pathologic conditions of the urinary system. The question is whether these findings can be exploited for risk reduction and treatment purposes. This review aimed to appraise the three aforementioned specific microbiomes regarding their potential influence on UTI development by focusing on the recent studies in the field and assessing the potential linkages between these different niches, as well as evaluating the state of translational research for novel therapeutic and preventative approaches.

Bacterial communities associated to the urethra of healthy gilts and pregnant sows undergoing different reproductive protocols

Nowadays, it is known that the urogenital microbiota plays a key role in the urinary health of mammalians. Despite the urinary infections affect the health and the welfare of breeding sows, the urethral microbiota of healthy sows remains unknown. Therefore, this work evaluates the urethral bacterial communities of healthy gilts and sows to determine the presence of Enterobacteriaceae populations, and the structure of this microbiota in gilts (G) and pregnant (P) sows. Samples were collected by scraping the urethral mucosa of G (n = 9) and P sows, which included natural mating (NM, n = 9) and artificial inseminated (AI, n = 7) sows. Samples were analyzed by culture-dependent techniques and 16S-rRNA gene high-throughput-sequencing. All females were positive for Enterobacteriaceae culture, without significant differences (Kruskal-Wallis) between G and P groups (median values: 2.78 and 3.09 log CFU/mL, respectively; P = 0.497). Also, the rate of Enterobacteriaceae/total mesophilic microorganisms was individually calculated, without significant differences between G and P sows (median values: 0.61 and 0.66, respectively; P = 0.497). When analyzing the bacterial communities, it was found similar richness in G, NM, and AI; however, diversity was lower in P sows than G (Mann Whitney/Kruskal-Wallis test, P < 0.01). The dominating phyla that constituted a "core microbiome" included Firmicutes, Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes, which were common for all the studied females. The relative abundance for phyla, families, and genera was estimated, and Firmicutes was significantly higher in NM than AI sows (P = 0.02, Mann-Whitney/Kruskal Wallis test for univariate statistical comparisons); Pseudomonadaceae and Enterobacteriaceae were higher in AI than in NM (Mann-Whitney/Kruskal-Wallis, P < 0.05). Lactobacillus and Pseudomonas were among the dominant genera; however, only Pseudomonas sp. was significantly higher in AI than NM (Mann-Whitney/Kruskal-Wallis, P = 0.006). The results represent the first evidence about the existence of a urethral microbiota that includes Enterobacteriaceae, as well as the patterns of this microbiota in G and P sows. The knowledge of this urethral microbiota might allow for future research to develop innovative protocols to restore and/or preserve the healthy ecology of the urinary microbiome to prevent diseases ensuring the welfare of breeding sows.

Relationship between intestinal microbiota, diet and biological systems: an integrated view

The health-disease process can be influenced by the intestinal microbiota. As this plays a fundamental role in protecting the organism, the importance of studying the composition and diversity of this community becomes increasingly evident. Changes in the composition of the intestinal bacterial community may result in dysbiosis, and this process may contribute to triggering various diseases in all biological systems. This imbalance of intestinal microbiota homeostasis may alter commensal bacteria and the host metabolism, as well as immune function. Dysbiosis also causes an increase in intestinal permeability due to exposure to molecular patterns associated with the pathogen and lipopolysaccharides, leading to a chronic inflammatory process that can result in diseases for all biological systems. In this context, dietary intervention through the use of probiotics, prebiotics and antioxidant foods can be considered a contribution to the modulation of intestinal microbiota. Probiotics have been used to provide up to 10 billion colony forming units, and probiotic foods, Kefir and fermented natural yogurt are also used. Prebiotics, in turn, are found in supplemental formulations of processed foods and in functional foods that are also sources of phenolic compounds, such as flavonoids, antioxidant and anti-inflammatory substances, polyunsaturated fatty acids, vitamins, and minerals. In this review, we will discuss the relationship between an imbalance in the intestinal microbiota with the development of diseases, besides indicating the need for future studies that can establish bacterial parameters for the gastrointestinal tract by modulating the intestinal microbiota, associated with the adoption of healthy habits during all life cycles.

A cross-sectional analysis of the urine microbiome of children with neuropathic bladders

BACKGROUND

Distinguishing a urinary tract infection (UTI) from asymptomatic bacteriuria (ASB) in children with neuropathic bladders is difficult. Currently used markers of infection, such as the routine urinalysis, lack specificity for UTI in this population. The urinary microbiome may help differentiate these states.

OBJECTIVE

The objective of this work was to describe the baseline microbiome in children with neuropathic bladders, and to determine if differences exist among the urine microbiomes of children with neuropathic bladders who have negative urine cultures, ASB, or UTI.

STUDY DESIGN

This is a cross-sectional study of children with neuropathic bladders who use clean intermittent catheterization for bladder management who had a urine culture sent as part of clinical management. Residual urine, initially collected via catheter for urine culture, was obtained for use in this work. Microbial DNA was isolated, and the V4 region of the 16SrRNA gene sequenced. The relative abundance of each bacteria was measured in each group. Alpha diversity, measured by Chao1 and the Shannon Diversity Index, was also measured in each group. PERMANOVA was used to compare the microbiota between groups.

RESULTS

36 children with neuropathic bladders were included in this study (UTI = 11, ASB = 19, negative cultures = 4). The most abundant bacteria were unspecified Enterobacteriaceae, Klebsiella, Staphylococcus, Streptococcus, and Enterococcus. Children who catheterize their urethra have a higher proportion of Staphylococcus, while the urine microbiome of those who catheterize through a Mitrofanoff consists predominantly of members of the family Enterobacteriaceae. Given the low numbers of patients with Mitrofanoffs and augmented bladders, we did not statistically compare the urine microbiomes between these patients. There was no difference in either alpha diversity or the overall microbiota between children with neuropathic bladders with UTI, ASB, and negative cultures.

DISCUSSION

In this pilot cohort of children with neuropathic bladders, bacteria that are members of the family Enterobacteriaceae are the most predominant bacteria in the urine microbiomes. There was no difference in the urine microbiome between those with UTI, ASB, and negative cultures. Route of catheterization may affect the composition of the urine microbiome, although due to limited sample size, this was not confirmed statistically.

CONCLUSION

There was no difference in the urine microbiome between patients with negative urine cultures, ASB, and UTI. Further work is needed to determine if the urine microbiome varies based on either the route of catheterization or the presence of augmented bladder.

The microbiome in urological diseases

Due to the rapid development of next-generation sequencing, it has become possible to obtain information on the sequences of all genes in a specific microbiome. The detection of bacteria in patients with no urinary tract infections indicated that the dogma that “urine is sterile” was false, leading to active research regarding the roles of the urinary microbiome in the human urinary tract. Here, we present a review of the current literature regarding the role of the microbiome in urology.

Recurrent UTIs in Girls: What Is the Role of the Microbiome?

Urinary tract infections (UTIs) are one of the most common childhood bacterial infections. Recurrent UTIs can lead to renal scarring. Compared to boys, girls are more likely to develop scars as a result of recurrent UTIs. Therefore, there is a need to identify girls at high risk for recurrent UTIs and develop interventions to decrease the risk of recurrent UTIs. In this commentary, we will review the hypothesized pathophysiology of recurrent UTIs, explore the literature on the role of the microbiome in recurrent UTIs, focusing on female pediatric patients when able, and highlight the need for future research in this area.

The urinary microbiome shows different bacterial genera in renal transplant recipients and non-transplant patients at time of acute kidney injury - a pilot study

Background

In the past urine was considered sterile. Through the introduction of next generation sequencing, it has become clear that a urinary microbiome exists. Acute kidney injury (AKI) represents a major threat to kidney transplant recipients. Remarkable changes in the urinary metabolome occur during AKI, which may influence the urinary microbiome. To our knowledge, this is the first study that examines the urinary microbiome in renal transplant recipients (RTX) and non-transplant recipients (nRTX) at time of AKI.

Methods

In this cross-sectional pilot-study the urinary microbiome of 21 RTX and 9 nRTX with AKI was examined. Clean catch morning urine samples were obtained from all patients on the first day of AKI diagnosis. AKI was defined according to KDIGO guidelines. Urinary microbiota and the urinary metabolome during AKI were assessed in one patient. 16S rRNA sequencing was performed. Sequences were processed using UPARSE-pipeline for operational taxonomic units (OTU) and taxon finding.

Results

We successfully extracted and sequenced bacterial DNA from 100% of the urine samples. All 30 patients revealed at least 106,138 reads. 319 OTU and 211 different genera were identified. The microbiotic diversity richness in the RTX group was no different from the nRTX group. Eighteen genera were solely present in nRTX and 7 in RTX.

Conclusions

The urinary microbiome at time of AKI showed different bacterial genera in RTX compared to nRTX. The nRTX group exhibited no different diversity to the RTX group. Irrespective of the status of a previous renal transplantation, the urinary microbiome comprised > 210 different genera. An intraindividual change in microbiota diversity and richness was observed in one study patient during recovery from AKI.

Defining a Molecular Signature for Uropathogenic versus Urocolonizing Escherichia coli: The Status of the Field and New Clinical Opportunities

Urinary tract infections (UTIs) represent a major burden across the population, although key facets of their pathophysiology and host interaction remain unclear. Escherichia coli epitomizes these obstacles: this gram-negative bacterial species is the most prevalent agent of UTIs worldwide and can also colonize the urogenital tract in a phenomenon known as asymptomatic bacteriuria (ASB). Unfortunately, at the level of the individual E. coli strains, the relationship between UTI and ASB is poorly defined, confounding our understanding of microbial pathogenesis and strategies for clinical management. Unlike diarrheagenic pathotypes of E. coli, the definition of uropathogenic E. coli (UPEC) remains phenomenologic, without conserved phenotypes and known genetic determinants that rigorously distinguish UTI- and ASB-associated strains. This article provides a cross-disciplinary review of the current issues from interrelated mechanistic and diagnostic perspectives and describes new opportunities by which clinical resources can be leveraged to overcome molecular challenges. Specifically, we present our work harnessing a large collection of patient-derived isolates to identify features that do (and do not) distinguish UTI- from ASB-associated E. coli strains. Analyses of biofilm formation, previously reported to be higher in ASB strains, revealed extensive phenotypic heterogeneity that did not correlate with symptomatology. However, metabolomic experiments revealed distinct signatures between ASB and cystitis isolates, including in the purine pathway (previously shown to be critical for intracellular survival during acute infection). Together, these studies demonstrate how large-scale, wild-type approaches can help dissect the physiology of colonization versus infection, suggesting that the molecular definition of UPEC may rest at the level of global bacterial metabolism.

Diagnosis of Urinary Tract Infection in the Neuropathic Bladder: Changing the Paradigm to Include the Microbiome

Bacteriuria, a non-specific term that refers to the presence of bacteria in the urine, is common in people with neuropathic bladders. However, accurately determining when bacteriuria represents a urinary tract infection (UTI) as opposed to asymptomatic bacteriuria is difficult. There is currently no widely accepted definition of what constitutes a UTI in people with neuropathic bladders. As a result, there is significant variation in care, which likely leads to unnecessary use of antibiotics for bacteriuria. To improve the clinical management of people with neuropathic bladders, it is important to be able to accurately diagnose and treat UTIs. In this article, we review the difficulties associated with accurately diagnosing UTIs and then review proposed definitions. Finally, we discuss the emerging literature of the urinary microbiome and how this may assist in accurately diagnosing UTIs in people with neuropathic bladders.

Urinary Catheter Coating Modifications: The Race against Catheter-Associated Infections

Urinary catheters are common medical devices, whose main function is to drain the bladder. Although they improve patients’ quality of life, catheter placement predisposes the patient to develop a catheter-associated urinary tract infection (CAUTI). The catheter is used by pathogens as a platform for colonization and biofilm formation, leading to bacteriuria and increasing the risk of developing secondary bloodstream infections. In an effort to prevent microbial colonization, several catheter modifications have been made ranging from introduction of antimicrobial compounds to antifouling coatings. In this review, we discuss the effectiveness of different coatings in preventing catheter colonization in vitro and in vivo, the challenges in fighting CAUTIs, and novel approaches targeting host–catheter–microbe interactions.

Optimizing bacterial DNA extraction in urine

Urine is an acceptable, non-invasive sample for investigating the human urogenital microbiota and for the diagnosis of sexually transmitted infections. However, low quantities of bacterial DNA and PCR inhibitors in urine may prevent efficient PCR amplification for molecular detection of bacteria. Furthermore, cold temperatures used to preserve DNA and bacteria in urine can promote precipitation of crystals that interfere with DNA extraction. Saline, Dulbecco’s Phosphate Buffered Saline, or Tris-EDTA buffer were added to urine from adult men to determine if crystal precipitation could be reversed without heating samples beyond ambient temperature. Total bacterial DNA concentrations and PCR inhibition were measured using quantitative PCR assays to compare DNA yields with and without buffer addition. Dissolution of crystals with Tris-EDTA prior to urine centrifugation was most effective in increasing bacterial DNA recovery and reducing PCR inhibition. DNA recovery using Tris-EDTA was further tested by spiking urine with DNA from bacterial isolates and median concentrations of Lactobacillus jensenii and Escherichia coli 16S rRNA gene copies were found to be higher in urine processed with Tris-EDTA. Maximizing bacterial DNA yield from urine may facilitate more accurate assessment of bacterial populations and increase detection of specific bacteria in the genital tract.

Urinary tract infections in patients with neurogenic bladder

Urinary tract infections (UTIs) in patients with neurogenic bladder are a major public health issue due to their high incidence and major consequences. Despite their frequency and potential severity, their physiopathology and management are poorly known. We provide a narrative literature review on the epidemiology, physiopathology, diagnostic criteria, microbiology, antimicrobial management, and prevention. UTIs among patients with neurogenic bladder are associated with high morbidity and healthcare utilization. Risk factors for UTI among this population are: indwelling catheter, urinary stasis, high bladder pressure, and bladder stones. Their diagnosis is a major challenge as clinical signs are often non-specific and rare. A urinary sample should be analyzed in appropriate conditions before any antibiotic prescription. According to most guidelines, a bacterial threshold≥103CFU/ml associated with symptoms is acceptable to define UTI in patients with neurogenic bladder. The management of acute symptomatic UTI is not evidence-based. A management with a single agent and a short antibiotic treatment of 10 days or less seems effective. Antibiotic selection should be based on the patient's resistance patterns. Asymptomatic bacteriuria should not be treated to avoid the emergence of bacterial resistance. Regarding preventive measures, use of clean intermittent catheterization, intravesical botulinum toxin injection, and prevention using antibiotic cycling are effective. Bacterial interference is promising but randomized controlled trials are needed. Large ongoing cohorts and randomized controlled trials should soon provide more evidence-based data.

Human Bacterial Repertoire of the Urinary Tract: a Potential Paradigm Shift

The aim of this article is to review the human repertoire of bacteria in urine already described by culture and metagenomic techniques and published in the literature. Our study led us to compare this repertoire with other available human repertoires. We followed automatic and manual bibliographical methods and found 562 bacterial species reported in the literature as part of the human urinary microbiota. Of the 562 species, 322 were described only by culture, 101 by both culture and metagenomics, and 139 only by metagenomics. A total of 352 species (62.6%) have been associated with at least one case report of human infection, of which 225 (40.0%) have been described as causative agents of urinary tract infection. The urinary tract bacterial repertoire contains 21.4% of the known prokaryotic diversity associated with human beings (464 species in common), and it shares 23.6% species with the human gut microbiota (350 species in common, 62.3% of the urine species). The urinary repertoire shares a significant difference in aerointolerant species compared with those of the gut microbiota (100/562 [17.8%] and 505/1,484 [34.0%], respectively; P < 0.001; odds ratio [OR] = 9.0 [7.0 to 11.4]). Studies using high-throughput sequencing show a higher proportion of aerointolerant bacteria in urine (74/240 [30.8%]) than studies using culture techniques (40/423 [9.5%]). Most pathogenic bacteria are part of the commensal human urinary tract bacteria, and their pathogenicity may occur following any imbalance of this microbiota. The restoration of urinary tract health can occur following a fecal transplantation. The potential gut origin of the human bacterial microbiota has to be explored.

Antimicrobial strategies for urinary catheters

Over 75% of hospital-acquired or nosocomial urinary tract infections are initiated by urinary catheters, which are used during the treatment of 16% of hospitalized patients. Taking the United States as an example, the costs of catheter-associated urinary tract infections (CAUTI) are in excess of $451 million dollars/year. The biofilm formation by pathogenic microbes that protects pathogens from host immune defense and antimicrobial agents is the leading cause for CAUTI. Thus, tremendous efforts have been devoted to antimicrobial coating for urinary catheters in the past few decades, and it has been demonstrated to be one of the most direct and efficient strategies to reduce infections. In this article, we briefly summarize the current methods for preparation of antimicrobial coatings based on different stages in the biofilm formation, highlight recent progress in the urinary catheter coating material design and selection, discuss approaches to improving their long-term antimicrobial efficacy, biocompatibility, multidrug resistance and recurrent infections, and finally outline future requirements and prospects in antimicrobial coating material design. The scope of the works surveyed is confined to antimicrobial urinary catheters. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 445-467, 2019.

Enterococcus faecalis persistence in pediatric patients treated with antibiotic prophylaxis for recurrent urinary tract infections

Aim: Enterococcus faecalis is one of the most common causes of recurrent urinary tract infection (RUTI), yet enterococcal pathogenesis is poorly understood. Our aims were to identify the prevalence of enterococci in RUTI patients and characterize the enterococcal response to nitrofurantoin and trimethoprim-sulfamethoxazole. Materials & methods: We studied pediatric patients receiving antibiotic prophylaxis and those only under clinical observation for 12 months (n = 39). We then assessed the response of uropathogenic E. faecalis to nitrofurantoin and trimethoprim–sulfamethoxazole. Results: Enterococci were isolated from almost half of patients and exposure of Enterococcus to nitrofurantoin increased virulence properties; this did not correlate with increased expression of virulence factors. Conclusion: Our results demonstrate that antibiotic prophylaxis may not be suitable for treatment of enterococcal RUTI (NCT02357758).

The iron hand of uropathogenic Escherichia coli: the role of transition metal control in virulence

The role of iron as a critical nutrient in pathogenic bacteria is widely regarded as having driven selection for iron acquisition systems among uropathogenic Escherichia coli (UPEC) isolates. Carriage of multiple transition metal acquisition systems in UPEC suggests that the human urinary tract manipulates metal-ion availability in many ways to resist infection. For siderophore systems in particular, recent studies have identified new roles for siderophore copper binding as well as production of siderophore-like inhibitors of iron uptake by other, competing bacterial species. Among these is a process of nutritional passivation of metal ions, in which uropathogens access these vital nutrients while simultaneously protecting themselves from their toxic potential. Here, we review these new findings within the current understanding of UPEC transition metal acquisition.

Urinary Tract Infection and Asymptomatic Bacteriuria in Older Adults

Urinary tract infections (UTIs) are a significant cause of morbidity among older adults. However, antibiotic prescriptions for clinically suspected UTIs are often inappropriate. Health care providers frequently struggle to differentiate UTI from asymptomatic bacteriuria, particularly in patients presenting with nonspecific symptoms. Patients with baseline cognitive impairments that limit history-taking can be particularly challenging. This article reviews the epidemiology and pathogenesis of UTI in older adults. It discusses an approach to diagnosis and treatment focused on recognizing patients who would likely benefit from antibiotic treatment and on identifying patients for whom empiric antibiotic therapy should not be given.

The Role of the Genitourinary Microbiome in Pediatric Urology: a Review

PURPOSE OF REVIEW

In this review, we highlight the effects of the microbiome on urologic diseases that affect the pediatric patient.

RECENT FINDINGS

Perturbations in the urinary microbiome have been shown to be associated with a number of urologic diseases affecting children, namely urinary tract infection, overactive bladder/urge urinary incontinence, and urolithiasis. Recently, improved cultivation and sequencing technologies have allowed for the discovery of a significant and diverse microbiome in the bladder, previously assumed to be sterile. Early studies aimed to identify the resident bacterial species and demonstrate the efficacy of sequencing and enhanced quantitative urine culture. More recently, research has sought to elucidate the association between the microbiome and urologic disease, as well as to demonstrate effects of manipulation of the microbiome on various urologic pathologies. With an improved appreciation for the impact of the urinary microbiome on urologic disease, researchers have begun to explore the impact of these resident bacteria in pediatric urology.

Coating of silicone with mannoside-PAMAM dendrimers to enhance formation of non-pathogenic Escherichia coli biofilms against colonization of uropathogens

Bacterial interference using non-pathogenic Escherichia coli 83972 is a novel strategy for preventing catheter-associated urinary tract infection (CAUTI). Crucial to the success of this strategy is to establish a high coverage and stable biofilm of the non-pathogenic bacteria on the catheter surface. However, this non-pathogenic strain is sluggish to form biofilms on silicone as the most widely used material for urinary catheters. We have addressed this issue by modifying the silicone catheter surfaces with mannosides that promote the biofilm formation, but the stability of the non-pathogenic biofilms challenged by uropathogens over long-term remains a concern. Herein, we report our study on the stability of the non-pathogenic biofilms grown on propynylphenyl mannoside-modified silicone. The result shows that 94% non-pathogenic bacteria were retained on the modified silicone under >0.5 Pa shear stress. After being challenged by three multidrug-resistant uropathogenic isolates in artificial urine for 11 days, large amounts (>4 × 10⁶ CFU cm^-2) of the non-pathogenic bacteria remained on the surfaces. These non-pathogenic biofilms reduced the colonization of the uropathogens by >3.2-log.

STATEMENT OF SIGNIFICANCE

In bacterial interference, the non-pathogenic Escherichia coli strains are sluggish to form biofilms on the catheter surfaces, due to rapid removal by urine flow. We have demonstrated a solution to this bottleneck by pre-functionalization of mannosides on the silicone surfaces to promote E. coli biofilm formation. A pre-conjugated high affinity propynylphenyl mannoside ligand tethered to the nanometric amino-terminated poly(amido amine) (PAMAM) dendrimer is used for binding to a major E. coli adhesin FimH. It greatly improves the efficiency for the catheter modification, the non-pathogenic biofilm coverage, as well as the (long-term) stability for prevention of uropathogen infections.

The inflammatory microenvironment and microbiome in prostate cancer development

Chronic inflammation promotes the development of several types of solid cancers and might contribute to prostate carcinogenesis. This hypothesis partly originates in the frequent observation of inflammatory cells in the prostate microenvironment of adult men. Inflammation is associated with putative prostate cancer precursor lesions, termed proliferative inflammatory atrophy. Inflammation might drive prostate carcinogenesis via oxidative stress and generation of reactive oxygen species that induce mutagenesis. Additionally, inflammatory stress might cause epigenetic alterations that promote neoplastic transformation. Proliferative inflammatory atrophy is enriched for proliferative luminal epithelial cells of intermediate phenotype that might be prone to genomic alterations leading to prostatic intraepithelial neoplasia and prostate cancer. Studies in animals suggest that inflammatory changes in the prostate microenvironment contribute to reprogramming of prostate epithelial cells, a possible step in tumour initiation. Prostatic infection, concurrent with epithelial barrier disruption, might be a key driver of an inflammatory microenvironment; the discovery of a urinary microbiome indicates a potential source of frequent exposure of the prostate to a diverse number of microorganisms. Hence, current evidence suggests that inflammation and atrophy are involved in prostate carcinogenesis and suggests a role for the microbiome in establishing an inflammatory prostate microenvironment that might promote prostate cancer development and progression.

Enterobacteria secrete an inhibitor of Pseudomonas virulence during clinical bacteriuria

Escherichia coli and other Enterobacteriaceae are among the most common pathogens of the human urinary tract. Among the genetic gains of function associated with urinary E. coli isolates is the Yersinia high pathogenicity island (HPI), which directs the biosynthesis of yersiniabactin (Ybt), a virulence-associated metallophore. Using a metabolomics approach, we found that E. coli and other Enterobacteriaceae expressing the Yersinia HPI also secrete escherichelin, a second metallophore whose chemical structure matches a known synthetic inhibitor of the virulence-associated pyochelin siderophore system in Pseudomonas aeruginosa. We detected escherichelin during clinical E. coli urinary tract infection (UTI) and experimental human colonization with a commensal, potentially probiotic E. coli bacteriuria strain. Escherichelin production by colonizing enterobacteria may help human hosts resist opportunistic infections by Pseudomonas and other pyochelin-expressing bacteria. This siderophore-based mechanism of microbial antagonism may be one of many elements contributing to the protective effects of the human microbiome. Future UTI-preventive probiotic strains may benefit by retaining the escherichelin biosynthetic capacity of the Yersinia HPI while eliminating the Ybt biosynthetic capacity.

Impact of the Microbiota on Bacterial Infections during Cancer Treatment

Patients being treated for cancer are at high risk for infectious complications, generally due to colonizing organisms that gain access to sterile sites via disrupted epithelial barriers. There is an emerging understanding that the ability of bacterial pathogens, including multidrug-resistant organisms, to colonize and subsequently infect humans is largely dependent on protective bacterial species present in the microbiome. Thus, herein we review recent studies demonstrating strong correlations between the microbiome of the oncology patient and infections occurring during chemotherapy. An increased knowledge of the interplay between potential pathogens, protective commensals, and the host immune system may facilitate the development of novel biomarkers or therapeutics that could help ameliorate the toll that infections take during the treatment of cancer.

Management of urinary tract infections in patients with neurogenic bladder: challenges and solutions

INTRODUCTION

Urinary tract infections (UTIs) are one of the most common morbidities in persons with neurogenic lower urinary tract dysfunction (NLUTD). They are associated with a significant morbidity and mortality, and they affect the quality of life of the affected patients. Diagnosis and treatment of UTI in this group of patients are challenging. In this review, the current strategies regarding diagnosis, treatment, and prevention are summarized.

DIAGNOSTICS

it is important to correctly diagnose a UTI, as treatment of bacteriuria should strictly be avoided. A UTI is defined as a combination of laboratory findings (leukocyturia and bacteriuria) and symptoms. Laboratory findings without symptoms are classified as asymptomatic bacteriuria. Routine urine screening is not advised.

TREATMENT

Only UTI should be treated; treatment of asymptomatic bacteriuria is not indicated. Prior to treatment, urine for a urine culture should be obtained. Antibiotic treatment for ~7 days is advised.

PREVENTION

In recurrent UTI, bladder management should be optimized and morphologic causes for UTI should be excluded. If UTIs persist, medical prophylaxis should be considered. Currently, no prophylactic measure with evidence-based efficacy exists. Long-term antibiotic prophylaxis should be used merely as an ultimate measure. Among the various mentioned innovative approaches for UTI prevention, bacteriophages, intravesical instillations, complementary and alternative medicine techniques, and probiotics seem to be most promising.

CONCLUSION

Recently, several promising innovative options for UTI prophylaxis have been developed which may help overcome the current therapeutic dilemma. However, further well designed studies are necessary to evaluate the safety and efficacy of these approaches.

Gram-Positive Uropathogens, Polymicrobial Urinary Tract Infection, and the Emerging Microbiota of the Urinary Tract

Gram-positive bacteria are a common cause of urinary-tract infection (UTI), particularly among individuals who are elderly, pregnant, or who have other risk factors for UTI. Here we review the epidemiology, virulence mechanisms, and host response to the most frequently isolated Gram-positive uropathogens: Staphylococcus saprophyticus, Enterococcus faecalis, and Streptococcus agalactiae. We also review several emerging, rare, misclassified, and otherwise underreported Gram-positive pathogens of the urinary tract including Aerococcus, Corynebacterium, Actinobaculum, and Gardnerella. The literature strongly suggests that urologic diseases involving Gram-positive bacteria may be easily overlooked due to limited culture-based assays typically utilized for urine in hospital microbiology laboratories. Some UTIs are polymicrobial in nature, often involving one or more Gram-positive bacteria. We herein review the risk factors and recent evidence for mechanisms of bacterial synergy in experimental models of polymicrobial UTI. Recent experimental data has demonstrated that, despite being cleared quickly from the bladder, some Gram-positive bacteria can impact pathogenic outcomes of co-infecting organisms. When taken together, the available evidence argues that Gram-positive bacteria are important uropathogens in their own right, but that some can be easily overlooked because they are missed by routine diagnostic methods. Finally, a growing body of evidence demonstrates that a surprising variety of fastidious Gram-positive bacteria may either reside in or be regularly exposed to the urinary tract and further suggests that their presence is widespread among women, as well as men. Experimental studies in this area are needed; however, there is a growing appreciation that the composition of bacteria found in the bladder could be a potentially important determinant in urologic disease, including susceptibility to UTI.

Microbiome in the urinary system-a review

Urine was considered sterile in healthy individuals for many years, and the presence of bacteria signified urinary tract infection. With the development of Expanded Quantitative Urine Culture (EQUC) and utilization of molecular techniques, the previous clinical dogma is no longer valid. Instead, healthy people harbor a considerable microbial community, or microbiota, in their urinary systems. Similar to other physiological niches where microbiota contribute to the health status of their hosts, recent studies demonstrated different microbial populations also play a crucial role in urinary health of individuals. Understanding urinary microbiome thus allows a more holistic approach in the diagnosis, treatment, and prevention of diseases and disorders in urinary system. This review article provides an overview of current findings in urinary microbiome and discusses some of the gaps for future research.