Utility of DNA Next-Generation Sequencing and Expanded Quantitative Urine Culture in Diagnosis and Management of Chronic or Persistent Lower Urinary Tract Symptoms

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.

ColiSeq: a multiplex amplicon assay that provides strain level resolution of Escherichia coli directly from clinical specimens

Escherichia coli is a diverse pathogen, causing a range of disease in humans, from self-limiting diarrhea to urinary tract infections (UTIs). Uropathogenic E. coli (UPEC) is the most frequently observed uropathogen in UTIs, a common disease in high-income countries, incurring billions of dollars yearly in treatment costs. Although E. coli is easily grown and identified in the clinical laboratory, genotyping the pathogen is more complicated, yet critical for reducing the incidence of disease. These goals can be achieved through whole-genome sequencing of E. coli isolates, but this approach is relatively slow and typically requires culturing the pathogen in the laboratory. To genotype E. coli rapidly and inexpensively directly from clinical samples, including but not limited to urine, we developed and validated a multiplex amplicon sequencing assay, called ColiSeq. The assay consists of targets designed for E. coli species confirmation, high resolution genotyping, and mixture deconvolution. To demonstrate its utility, we screened the ColiSeq assay against 230 clinical urine samples collected from a hospital system in Flagstaff, Arizona, USA. A limit of detection analysis demonstrated the ability of ColiSeq to identify E. coli at a concentration of ~2 genomic equivalent (GEs)/mL and to generate high-resolution genotyping at a concentration of 1 × 105 GEs/mL. The results of this study suggest that ColiSeq could be a valuable method to understand the source of UPEC strains and guide infection mitigation efforts. As sequence-based diagnostics become accepted in the clinical laboratory, workflows such as ColiSeq will provide actionable information to improve patient outcomes.IMPORTANCEUrinary tract infections (UTIs), caused primarily by Escherichia coli, create an enormous health care burden in the United States and other high-income countries. The early detection of E. coli from clinical samples, including urine, is important to target therapy and prevent further patient complications. Additionally, understanding the source of E. coli exposure will help with future mitigation efforts. In this study, we developed, tested, and validated an amplicon sequencing assay focused on direct detection of E. coli from urine. The resulting sequence data were demonstrated to provide strain level resolution of the pathogen, not only confirming the presence of E. coli, which can focus treatment efforts, but also providing data needed for source attribution and contact tracing. This assay will generate inexpensive, rapid, and reproducible data that can be deployed by public health agencies to track, diagnose, and potentially mitigate future UTIs caused by E. coli.

Comparison of polymerase chain reaction and next-generation sequencing with conventional urine culture for the diagnosis of urinary tract infections: A meta-analysis

The limitations of conventional urine culture methods can be avoided by using culture-independent approaches like polymerase chain reaction (PCR) and next-generation sequencing (NGS). However, the efficacy of these approaches in this setting is still subject to contention. PRISMA-compliant searches were performed on MEDLINE/PubMed, EMBASE, Web of Sciences, and the Cochrane Database until March 2023. The included articles compared PCR or NGS to conventional urine culture for the detection of urinary tract infections (UTIs). RevMan performed meta-analysis, and the Cochrane Risk of Bias Assessment Tool assessed study quality. A total of 10 selected studies that involved 1,291 individuals were included in this meta-analysis. The study found that PCR has a 99% sensitivity and a 94% specificity for diagnosing UTIs. Furthermore, NGS was shown to have a sensitivity of 90% for identifying UTIs and a specificity of 86%. The odds ratio (OR) for PCR to detect Gram-positive bacteria is 0.50 (95% confidence interval [CI] 0.41-0.61), while the OR for NGS to detect Gram-negative bacteria is 0.23 [95% CI 0.09-0.59]. UTIs are typically caused by Gram-negative bacteria like Escherichia coli and Gram-positive bacteria like Staphylococci and Streptococci. PCR and NGS are reliable, culture-free molecular diagnostic methods that, despite being expensive, are essential for UTI diagnosis and prevention due to their high sensitivity and specificity.

A Bird's-Eye View of the Pathophysiologic Role of the Human Urobiota in Health and Disease: Can We Modulate It?

For a long time, urine has been considered sterile in physiological conditions, thanks to the particular structure of the urinary tract and the production of uromodulin or Tamm-Horsfall protein (THP) by it. More recently, thanks to the development and use of new technologies, i.e., next-generation sequencing and expanded urine culture, the identification of a microbial community in the urine, the so-called urobiota, became possible. Major phyla detected in the urine are represented by Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Particularly, the female urobiota is largely represented by Lactobacillus spp., which are very active against urinary pathogenic Escherichia (E.) coli (UPEC) strains via the generation of lactic acid and hydrogen peroxide. Gut dysbiosis accounts for recurrent urinary tract infections (UTIs), so-called gut-bladder axis syndrome with the formation of intracellular bacterial communities in the course of acute cystitis. However, other chronic urinary tract infections are caused by bacterial strains of intestinal derivation. Monomicrobial and polymicrobial infections account for the outcome of acute and chronic UTIs, even including prostatitis and chronic pelvic pain. E. coli isolates have been shown to be more invasive and resistant to antibiotics. Probiotics, fecal microbial transplantation, phage therapy, antimicrobial peptides, and immune-mediated therapies, even including vaccines for the treatment of UTIs, will be described.

Urogenital urobiome of healthy children does not differ from that of children with bladder and bowel dysfunction

INTRODUCTION

The pediatric urinary microbiome (urobiome) has been studied in the context of healthy children and children with genitourinary pathologies including neuropathic bladder, urinary tract infection (UTI) and nephrolithiasis. Little is known about the urobiome of children with bladder and bowel dysfunction (BBD), a condition that is an established risk factor of UTI. We hypothesized that the symptoms of a child with BBD may be related to urobiome composition.

OBJECTIVE

To evaluate the urogenital urobiome's role in BBD, we compared the urogenital urobiomes of children with and without BBD.

STUDY DESIGN

We performed a prospective case-control pilot study at a single large, academic children's hospital. Cases included toilet trained prepubertal females over 2 years of age with BBD established through a validated scoring system and controls included asymptomatic, presumably healthy, children. Children were excluded if they had symptoms or lab work consistent with a concurrent UTI or antibiotic course for any reason within the prior 14 days. We performed 16 S ribosomal RNA gene sequencing and expanded quantitative urine culture on clean catch urine samples. To compare within sample (alpha) diversity, we used the Kruskal-Wallis test. To compare between sample (beta) diversity, we calculated the Bray-Curtis distance and performed the PERMANOVA test.

RESULTS

Data from 25 children with BBD and 8 asymptomatic controls were analyzed. The demographic and clinical characteristics of the two comparison groups were similar, though a higher proportion of Black children were included in the asymptomatic control group. Neither alpha diversity nor beta diversity was significantly different between the two groups. The core microbiome of the BBD group included all the genera in the core urogenital urobiome of the controls, plus additional genera associated with opportunistic infection and/or UTI, including Escherichia, Campylobacter and Streptococcus.

DISCUSSION

The results of both the 16 S sequencing and expanded quantitative urine culture in this small study suggest that the urogenital urobiomes of children with BBD do not differ significantly from those of asymptomatic children. However, the core urogenital urobiome of children with BBD included genera associated with opportunistic infection and/or UTI. This study was limited by the sample collection method ("clean catch" midstream voided urine samples, which introduce the possibility of vulvovaginal contamination), small sample size, and unequal balance of patient characteristics between the two study groups.

CONCLUSION

The urogenital urobiomes of children with and without BBD do not appear to significantly differ. Larger studies are needed to confirm these findings.

Urinary Tract Infection and Microbiome

Urinary tract infection is one of the most common bacterial infections and can cause major burdens, not only to individuals but also to an entire society. Current knowledge of the microbial communities in the urinary tract has increased exponentially due to next-generation sequencing and expanded quantitative urine culture. We now acknowledge a dynamic urinary tract microbiome that we once thought was sterile. Taxonomic studies have identified the normal core microbiota of the urinary tract, and studies on the changes in microbiome due to sexuality and age have set the foundation for microbiome studies in pathologic states. Urinary tract infection is not only caused by invading uropathogenic bacteria but also by changes to the uromicrobiome milieu, and interactions with other microbial communities can also contribute. Recent studies have provided insights into the pathogenesis of recurrent urinary tract infections and antimicrobial resistance. New therapeutic options for urinary tract infections also show promise; however, further research is needed to fully understand the implications of the urinary microbiome in urinary tract infections.

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.

Menopausal Changes in the Microbiome-A Review Focused on the Genitourinary Microbiome

A balanced interaction between the host and its microbiome is crucial to health. Research regarding the significance of the gut and vaginal microbiomes in female health is substantial. However, less data regarding the urinary microbiome are available. Interactions between the gut, vaginal, and urinary microbiomes are also currently being researched. Hormone-induced dysbiosis after menopause is believed to have effects on physical changes and health consequences. Postmenopausal changes in the gut microbiome are associated with increased short-chain fatty acids and hydrogen sulfide levels. Increased vaginal pH caused by reduced estrogen alters the vaginal microbiome, resulting in reduced levels of Lactobacillus. Such changes influence the vaginal structure and functions, contributing to the onset of genitourinary syndrome of menopause. A dysbiosis of the urinary microbiome is associated with urgency and urinary incontinence and also related to interstitial cystitis/bladder pain syndrome and neuropathic bladder. As these diseases commonly affect postmenopausal women, hormone-induced changes in the microbiome may play a role. Menopause increases the alpha diversity of the urinary microbiome and lowers the percentage of Lactobacillus in urine, and such changes precede recurrent cystitis. More research regarding the effects of changes in the urinary microbiome due to menopause on urinary tract diseases is needed.

Microbiome in urological diseases: Axis crosstalk and bladder disorders

Since the identification of the human urinary microbiome, numerous studies have characterized this microbial community and improved our knowledge of its association with urinary diseases. This association between urinary diseases and microbiota is not confined to the urinary microbiota; it is interconnected with the microbiota of other organs. The gastrointestinal, vaginal, kidney, and bladder microbiota all affect urinary diseases because they work with their respective organs to control the growth and operation of the immune, metabolic, and nervous systems through dynamic bidirectional communication along the bladder-centered axis. Therefore, disturbances in the microbial communities may result in the emergence of urinary diseases. In this review, we describe the increasing and intriguing evidence of complicated and critical relationships that may contribute to the development and progression of urinary diseases through disruption of the microbiota in various organs.

Microbiota Ecosystem in Recurrent Cystitis and the Immunological Microenvironment of Urothelium

Urinary tract infections (UTIs) represent one of the most frequent low genital tract diseases in the female population. When UTIs occur with a frequency of at least three times per year or two times in the last six month, we speak of recurrent UTI (rUTI) and up to 70% of women will have rUTI within 1 year. It was previously thought that antibiotic resistance was principally responsible for the recurrence of UTIs, but nowadays new diagnostic technologies have shown the role of microbiota in the pathophysiology of these diseases. Much research has been conducted on the role of gut microbiome in the development of rUTI, while little is known yet about vaginal and urinary microbiome and the possible immunological and microscopical mechanisms through which they trigger symptoms. New discoveries and clinical perspectives are arising, and they all agree that a personalized, multi-modal approach, treating vaginal and urinary dysbiosis, may reduce rUTIs more successfully.

The Recurrent Urinary Tract Infection Symptom Scale: Development and validation of a patient‐reported outcome measure

Objectives

This study aimed to develop and validate a tailored patient-reported outcome measure (PROM) evaluating the patient experience of recurrent urinary tract infection (rUTI) symptom severity. This measure was designed to supplement clinical testing methods, allowing full assessment of the patient experience of rUTI symptom burden, while enhancing patient-centred UTI management and monitoring.

Subjects and Methods

The Recurrent Urinary Tract Infection Symptom Scale (RUTISS) was developed and validated using a three-stage methodology, in accordance with gold-standard recommendations. Firstly, a two-round Delphi study was conducted to gain insights from 15 international expert clinicians working in rUTI, developing an initial pool of novel questionnaire items, assessing content validity and making item refinements. Next, two phases of one-to-one semi-structured cognitive interviews were conducted with a diverse sample of 28 people experiencing rUTI to assess questionnaire comprehensiveness and comprehensibility, making refinements after each phase. Finally, a comprehensive pilot of the RUTISS was conducted with 240 people experiencing rUTI across 24 countries, providing data for psychometric testing and item reduction.

Results

Exploratory factor analysis indicated a four-factor structure comprising: 'urinary pain and discomfort', 'urinary urgency', 'bodily sensations' and 'urinary presentation', together accounting for 75.4% of the total variance in data. Qualitative feedback from expert clinicians and patients indicated strong content validity for items, which was supported by high content validity indices in the Delphi study (I-CVI > 0.75). Internal consistency and test-retest reliability of the RUTISS subscales were excellent (Cronbach's α = 0.87-0.94 and ICC = 0.73-0.82, respectively), and construct validity was strong (Spearman's ρ = 0.60-0.82).

Conclusion

The RUTISS is a 28-item questionnaire with excellent reliability and validity, which dynamically assesses patient-reported rUTI symptoms and pain. This new PROM offers a unique opportunity to critically inform and strategically enhance the quality of rUTI management, patient-clinician interactions, and shared-decision making by monitoring key patient-reported outcomes.

Application of Various Techniques to Gain Insights Into the Complex Urinary Tract Microbial Communities of Renal Transplant Recipients

Urinary tract infections (UTIs) are prevalent in renal transplant (RT_X) recipients and associated with worse outcomes. Early detection by sensitive diagnostic tests and appropriate treatment strategies in this cohort is therefore crucial, but evidence has shown that current methods may miss genuine infections. Research has shed light on the urinary tract microbial ecology of healthy individuals and nontransplant patients with UTI, but information on the RTx cohort is scant. We conducted a cross-sectional study to (i) compare the gold standard diagnostic culture with alternative techniques and (ii) characterize RTx patient urinary microbial communities.

Methods

Midstream urine specimens were collected from 51 RTx patients attending a renal transplant clinic and 27 asymptomatic controls. Urinary microscopy, dipstick, and routine culture were performed. To improve sensitivity of microbial detection, we cultured the urinary cell sediment and performed 16S rRNA gene sequencing on urine. Uroplakin-positive urothelial cells shed in urine were analyzed by immunofluorescence staining for any bacterial association.

Results

Sediment culture and 16S rRNA sequencing confirmed detection deficiencies of diagnostic culture and revealed differences in the urobiomes of RTx patients and controls. Specifically, Gardnerella, Escherichia, and Lactobacillus were most abundant in patients, whereas Lactobacillus, Streptococcus, and Gardnerella were most abundant in controls. The application of both culture and sequencing provided a more nuanced view of the urinary microbial communities.

Conclusions

This study provides insight into the potential problems of diagnostic culture within RTx patients and sheds light on their urinary microbial inhabitants. Further work may identify key microbial signatures and facilitate the development of better tools for UTI detection within this cohort, which could allow targeted intervention before an infection leads to serious consequences. http://links.lww.com/TXD/A479.

Possibilities and limitations of using low biomass samples for urologic disease and microbiome research

With the dogma of sterile urine no longer held as truth, numerous studies have implicated distinct changes in microbial diversity and composition to diseased subgroups in both benign and malignant urological diseases, ranging from overactive bladder to bladder and prostate cancer. Further facilitated by novel and effective techniques of urine culture and sequencing, analysis of the genitourinary microbiome holds high potential to identify biomarkers for disease and prognosis. However, the low biomass of samples included in microbiome studies of the urinary tract challenge researchers to draw definitive conclusions, confounded by technical and procedural considerations that must be addressed. Lack of samples and adequate true negative controls can lead to overestimation of microbial influence with clinical relevance. As such, results from currently available studies and assessment of their limitations required a thorough understanding. The purpose of this narrative review was to summarize notable microbiome studies in the field of urology with a focus on significant findings and limitations of study design. Methodological considerations in future research are also discussed.

Molecular Diagnostic Methods Versus Conventional Urine Culture for Diagnosis and Treatment of Urinary Tract Infection: A Systematic Review and Meta-analysis

Context

Objective

Evidence acquisition

Evidence synthesis

Conclusions

Patient summary

The detection of urinary viruses is associated with aggravated symptoms and altered bacteriome in female with overactive bladder

Although it is known that changes in bacterial components of the urinary microbiome are associated with overactive bladder (OAB), the specific role of viruses is still insufficiently investigated. The aim of the present study is to evaluate the role of urinary viruses in woman with OAB, and analyze the potential relationship between viruses, bacteria and disease. Catheterized urine samples were collected from 55 women with OAB and 18 control individuals. OAB patients fulfilling the following criteria were considered eligible for this study: female, 18 years of age or older; presented with classic OAB symptoms defined by the International Continence Society; and OAB Symptom Score (OABSS) total score ≥ 3 points and question 3 (urgency) score ≥ 2 points. Based on results of metagenomic next-generation sequencing (mNGS), all participants were divided into virus-infected and virus-uninfected groups for analysis. The results of mNGS showed that the diversity of the OAB group was lower than that of the control group when focused on bacterial sequences, which was consistent with our previous study. According to the questionnaire filled out by the patients, OABSS and 8-item OAB questionnaire, female OAB patients who had viruses detected in their urine had more severe symptoms. In parallel, John Cunningham virus (mainly subtype 7 and subtype 2) was the most frequently detected virus in urine. Correlation analysis indicated that risk factors for virus infection in OAB patients include age, habit of holding urine and pelvic surgery history. Given our preliminary data, viral infection can aggravate OAB severity and affect the composition of bacterial. Further research is required to explain how viral infections can aggravate OAB patient symptoms and cause bacterial changes.

Lactobacillus crispatus Limits Bladder Uropathogenic E. coli Infection by Triggering a Host Type I Interferon Response

Many urinary tract infections (UTIs) are recurrent because uropathogens persist within the bladder epithelial cells (BECs) for extended periods between bouts of infection. Because persistent uropathogens are intracellular, they are often refractive to antibiotic treatment. The recent discovery of endogenous Lactobacillus spp. in the bladders of healthy humans raised the question of whether these endogenous bacteria directly or indirectly impact intracellular bacterial burden in the bladder. Here, we report that in contrast to healthy women, female patients experiencing recurrent UTIs have a bladder population of Lactobacilli that is markedly reduced. Exposing infected human BECs to L. crispatus in vitro markedly reduced the intracellular uropathogenic Escherichia coli (UPEC) load. The adherence of Lactobacilli to BECs was found to result in increased type I interferon (IFN) production, which in turn enhanced the expression of cathepsin D within lysosomes harboring UPECs. This lysosomal cathepsin D-mediated UPEC killing was diminished in germ-free mice and type I IFN receptor-deficient mice. Secreted metabolites of L. crispatus seemed to be responsible for the increased expression of type I IFN in human BECs. Intravesicular administration of Lactobacilli into UPEC-infected murine bladders markedly reduced their intracellular bacterial load suggesting that components of the endogenous microflora can have therapeutic effects against UTIs.

Application of Next-Generation Sequencing in Infections After Allogeneic Haematopoietic Stem Cell Transplantation: A Retrospective Study

This retrospective study aimed to determine the characteristics of infection and diagnostic efficacy of next-generation sequencing (NGS) in patients with fever after allogeneic hematopoietic stem cell transplantation (allo-HSCT). A total of 71 patients with fever after HSCT were enrolled in this study. Compared with conventional microbiological test (CMT), we found that the sensitivity of NGS versus CMT in peripheral blood samples was 91.2% vs. 41.2%, and that NGS required significantly less time to identify the pathogens in both monomicrobial infections (P=0.0185) and polymicrobial infections (P= 0.0027). The diagnostic performance of NGS was not affected by immunosuppressant use. Viruses are the most common pathogens associated with infections. These results indicated that the sensitivity, timeliness, and clinical significance of NGS are superior for the detection of infections. Although NGS has the advantage of identifying a wide range of potential pathogens, the positive rate is related closely to the sample type. Therefore, we recommend that, in the clinical application of NGS to detect pathogens in patients after allo-HSCT, an appropriate sample type and time should be selected and submitted to improve the positive rate and accuracy of NGS. NGS holds promise as a powerful technology for the diagnosis of fever after HSCT.

Differential Urinary Microbiota Composition Between Women With and Without Recurrent Urinary Tract Infection

Background

Recurrent urinary tract infection (RUTI) is common and burdensome in women. Due to the low concentration or slow-growing of uropathogens in RUTI, standard urine cultures (SUCs) are often negative. Next-generation sequencing (NGS) of bacterial 16S rRNA gene is more sensitive and could be used to reveal the differential microbiota between patients with RUTI and asymptomatic controls.

Methods

Women (aged ≥ 18 years) with clinically diagnosed RUTI with negative SUC and age-matched women asymptomatic controls with normal urinalysis were enrolled. Their midstream voided urine specimens were collected and processed for NGS (Illumina MiSeq) targeting the bacterial 16S rRNA gene V3-V4 region. The dataset was clustered into operational taxonomic units (OTUs) using QIIME. Taxonomic analysis, alpha diversity, beta diversity, multivariate statistical analysis, and linear discriminant analysis effect size (LEfSe) for differential analysis were performed and compared between patients with RUTI and asymptomatic controls.

Results

A total of 90 patients with RUTI and 62 asymptomatic controls were enrolled in this study. Among them, 74.4% (67/90) and 71.0% (44/62) were successfully amplified and sequenced their bacterial 16S rRNA gene. In the alpha diversity analysis, the chao1 index and observed species index were significantly lower in the RUTI group than in the control group (P = 0.015 and 0.028, respectively). In the beta diversity analysis, there was a significant difference between the 2 groups [Analysis of similarities (ANOSIM), R = 0.209, P = 0.001]. The relative abundance of 36 bacterial taxa was significantly higher, and another 24 kinds of bacteria were significantly lower in the RUTI group compared with the control group [LEfSe analysis, P < 0.05, linear discriminative analysis (LDA) score > 3], suggesting that Ralstonia, Prevotella, Dialister, and Corynebacterium may play an important role in RUTI.

Conclusion

The urinary microbiota of women with clinically diagnosed RUTI were significantly different from age-matched asymptomatic controls.

Gardnerella vaginalis in Recurrent Urinary Tract Infection Is Associated with Dysbiosis of the Bladder Microbiome

Recent studies on the urine microbiome have highlighted the importance of the gut–vagina–bladder axis in recurrent urinary tract infection (rUTI). In particular, the role of Gardnerella as a covert pathogen that activates E. coli in animal experiments has been reported. Herein, we conducted a human bladder microbiome study to investigate the effect of Gardnerella on rUTI. Urine 16S ribosomal RNA gene sequencing via transurethral catheterization was conducted in the normal control group (NC) (n = 18) and rUTI group (n = 78). The positive detection rate of Gardnerella species did not differ between the NC and rUTI groups (22.2% vs. 18.0%, p = 0.677). In addition, the Gardnerella-positive NC and Gardnerella-positive rUTI groups showed similar levels of microbiome diversity. The Gardnerella-positive group was categorized into three subgroups: the Escherichia-dominant group, Gardnerella-dominant group, and Lactobacillus-dominant group. All of the Escherichia-dominant groups were associated with rUTI. The Gardnerella-dominant or Lactobacillus-dominant groups expressed rUTI with symptoms when risk factors such as the degree of Gardnerella proliferation or causative agents of bacterial vaginosis were present. The presence of Gardnerella in the urine is considered to be related to rUTI depending on other risk factors. New guideline recommendations regarding antibiotic selection based on a novel method to detect the cause of rUTI may be required to reduce antibiotic resistance.

Bladder Microbiome in the Context of Urological Disorders—Is There a Biomarker Potential for Interstitial Cystitis?

Since the development of modern cultivation and sequencing techniques, the human microbiome has increasingly become the focus of scientific attention. Even in the bladder, long considered to be a sterile niche, a highly variable and complex microbial colonization has now been demonstrated. Especially in the context of diseases such as interstitial cystitis, whose etiopathogenesis is largely unknown, and whose diagnosis is based on a process of exclusion of confusable diseases, science hopes to gain far-reaching insights for etiology and diagnosis, including the identification of potential biomarkers. While for functional disorders such as urge urinary incontinence and overactive bladder syndrome, initial associations have been demonstrated between reduced microbial diversity and increased symptomatology, as well as shifts in the abundance of specific microorganisms such as Lactobacillus or Proteus, studies in interstitial cystitis show conflicting results and have failed to identify a putative organism or urotype that clearly distinguishes the urinary microbiome of patients with IC/BPS from that of healthy controls. At the present time, therefore, the new insights into the bladder microbiome and its potential influence on urologic disease cannot yet be used in the context of elucidating possible etiopathogenetic causes, as well as in the use of a biomarker for diagnostic or prognostic purposes. Further studies should focus primarily on uniform procedures and detection methods to achieve better comparability of results and increase the likelihood of detecting hidden patterns.

Urobiome: An outlook on the metagenome of urological diseases

The urinary tract likely plays a role in the development of various urinary diseases due to the recently recognized notion that urine is not sterile. In this mini review, we summarize the current literature regarding the urinary microbiome and mycobiome and its relationship to various urinary diseases. It has been recently discovered that the healthy urinary tract contains a host of microorganisms, creating a urinary microbiome. The relative abundance and type of bacteria varies, but generally, deviations in the standard microbiome are observed in individuals with urologic diseases, such as bladder cancer, benign prostatic hyperplasia, urgency urinary incontinence, overactive bladder syndrome, interstitial cystitis, bladder pain syndrome, and urinary tract infections. However, whether this change is causative, or correlative has yet to be determined. In summary, the urinary tract hosts a complex microbiome. Changes in this microbiome may be indicative of urologic diseases and can be tracked to predict, prevent, and treat them in individuals. However, current analytical and sampling collection methods may present limitations to the development in the understanding of the urinary microbiome and its relationship with various urinary diseases. Further research on the differences between healthy and diseased microbiomes, the long-term effects of antibiotic treatments on the urobiome, and the effect of the urinary mycobiome on general health will be important in developing a comprehensive understanding of the urinary microbiome and its relationship to the human body.

The Microbiome’s Function in Disorders of the Urinary Bladder

The introduction of next generation sequencing techniques has enabled the characterization of the urinary tract microbiome, which resulted in the rejection of the long-held notion of urinary bladder sterility. Since the discovery and confirmation of the human bladder microbiome, an increasing number of studies have defined this microbial community and understand better its relationship to urinary pathologies. The composition of microbial communities in the urinary tract is linked to a variety of urinary diseases. The purpose of this review is to provide an overview of current information about the urinary microbiome and diseases as well as the development of novel treatment methods.

A New Gold Rush: A Review of Current and Developing Diagnostic Tools for Urinary Tract Infections

Urinary tract infections (UTIs) are one of the most common infections in the United States and consequently are responsible for significant healthcare expenditure. The standard urine culture is the current gold standard for diagnosing urinary tract infections, however there are limitations of the test that directly contribute to increased healthcare costs. As a result, new and innovative techniques have been developed to address the inefficiencies of the current standard-it remains to be seen whether these tests should be performed adjunctly to, or perhaps even replace the urine culture. This review aims to analyze the advantages and disadvantages of the newer and emerging diagnostic techniques such as PCR, expanded quantitative urine culture (EQUC), and next generation sequencing (NGS).

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.

Polymicrobial interactions in the urinary tract: is the enemy of my enemy my friend?

The vast majority of research pertaining to urinary tract infection has focused on a single pathogen in isolation, and predominantly Escherichia coli. However, polymicrobial urine colonization and infection are prevalent in several patient populations, including individuals with urinary catheters. The progression from asymptomatic colonization to symptomatic infection and severe disease is likely shaped by interactions between traditional pathogens as well as constituents of the normal urinary microbiota. Recent studies have begun to experimentally dissect the contribution of polymicrobial interactions to disease outcomes in the urinary tract, including their role in development of antimicrobial-resistant biofilm communities, modulating the innate immune response, tissue damage, and sepsis. This review aims to summarize the epidemiology of polymicrobial urine colonization, provide an overview of common urinary tract pathogens, and present key microbe-microbe and host-microbe interactions that influence infection progression, persistence, and severity.

Microbiological profile of urinary tract infections in a tertiary medical facility in Western Mexico: An update

Urinary tract infections (UTIs) are one of the most important issues in modern medicine. In developing countries, the use of antibiotics is a common practice, and due to this, antibiotic resistance has increased. The objective of this research was to update and report on the microbiological profile of urinary tract infections based on the number of positive urine cultures (UCs), resistance, sensitivity, and the prevalence of bacterial strains. The results were obtained from the database of a tertiary medical facility in Western Mexico. The number of positive UCs was 1769 from inpatients and outpatients who were users of medical services in the hospital from January to December of 2017. The most commonly isolated microorganism was E. coli, with 1225 cases, of which 603 (49.2%) were ESBL (Extended-Spectrum Beta-Lactamase-producing bacteria) strains. The resistance rate of nitrofurantoin was 36.6%, and meropenem showed the most promising results with a resistance rate of only 7.1%. Resistances to quinolones and cephalosporins among the isolates investigated were 51%-67%. Based on our results, it is necessary to increase controls and to improve management protocols in order to achieve better medical practices by reducing antibiotic resistance.

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.