Detection of eubacteria in interstitial cystitis by 16S rDNA amplification

Urinary Microbiome in Bladder Diseases-Review

The microbiome is the totality of microorganisms found in a specific biological niche. It has been proven that in the human body, the microbiome is responsible for its proper functioning. Dysbiosis, i.e., a disturbance in the composition of the microbiome, may be associated with the pathogenesis of many human diseases. Until recently, studies did not focus on the microbiome of the urinary tract, because, since the 19th century, there had been a dogma that urine in healthy people is sterile. Yet, advances in molecular biology techniques have allowed this dogma to be overthrown. The use of DNA sequencing has shown that the urinary tract has its own endogenous microbiome. This discovery enabled further research on the characteristics of the urine microbiomes of healthy people, as well as on the role of the urine microbiome in the pathogenesis of many urological diseases, including bladder diseases. The aim of this review is to summarize the current knowledge on the urinary microbiome in bladder diseases and to identify potential directions for further research.

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.

Sex Differences in Bladder Cancer Immunobiology and Outcomes: A Collaborative Review with Implications for Treatment

CONTEXT

Urothelial carcinoma of the bladder (UCB) exhibits significant sexual dimorphism in the incidence, etiology, and response to intravesical immunotherapy. Environmental factors such as tobacco use and clinical management issues such as delayed presentation have widely been associated with sex differences in UCB outcomes. Emerging findings from immune checkpoint blockade trials are suggestive of differential outcomes in females compared with males. Sex-specific differences in the way immune system functions and responds to pathogenic insults are well established. As such, an in-depth understanding of the genetic and epigenetic factors contributing to sex-associated differences in response to immunomodulatory therapies is needed urgently for improved management of UCB.

OBJECTIVE

To review the associations between patient sex and clinical outcomes, with a focus on the incidence, host intrinsic features, and response to therapies in UCB.

EVIDENCE ACQUISITION

Using the PubMed database, this narrative review evaluates published findings from mouse model-based and clinical cohort studies to identify factors associated with sex and clinical outcomes in bladder cancer. A scoping review of the key findings on epidemiology, genetic, hormonal, immune physiology, and clinical outcomes was performed to explore potential factors that could have implications in immunomodulatory therapy design.

EVIDENCE SYNTHESIS

Sex-associated differences in UCB incidence and clinical outcomes are influenced by sex hormones, local bladder resident immune populations, tumor genetics, and bladder microbiome. In the context of therapeutic outcomes, sex differences are prominent in response to bacillus Calmette-Guérin immunotherapy used in the treatment of non-muscle-invasive bladder cancer. Similarly, with respect to tumor molecular profiles in muscle-invasive bladder cancer, tumors from females show enrichment of the basal subtype.

CONCLUSIONS

Among proposed tumor/host intrinsic factors that may influence response to immune-based therapies, patient sex remains a challenging consideration that deserves further attention. Evidence to date supports a multifactorial origin of sexual dimorphism in the incidence and outcomes of UCB.

PATIENT SUMMARY

In this review, we highlight the sex-associated host and tumor intrinsic features that may potentially drive differential disease progression and therapeutic response in urothelial carcinoma of the bladder.

Urinary microbiome in uncomplicated and interstitial cystitis: is there any similarity?

PURPOSE

Acute/uncomplicated cystitis is the most common bacterial infection causing inflammation in the bladder tissues and predominantly diagnosed in women. Interstitial cystitis may too, cause inflammation in the bladder but its etiology has been elusive. Even though the site and symptoms of both diseases are largely shared, state of the urinary microbiome in these disorders have not been comparatively evaluated before. The purpose of this review is to assess and qualitatively compare structure and composition of the urinary microbiome in acute/uncomplicated cystitis and interstitial cystitis.

METHODS AND RESULTS

The available literature in MEDLINE are extensively searched using keywords and screened. Pertinent evidence is carefully assessed and synthesized. We included the original studies with a cohort of medically stable, non-pregnant women with otherwise functionally normal urinary tract and excluded the original articles if the infection in a patient's cohort is accompanied by urinary syndromes such as incontinence and overactive bladder syndrome. A total of six original papers reporting on the urinary microbiome in acute cystitis and nine papers on the interstitial cystitis met the selection criteria.

CONCLUSION

The evidence we have gleaned from the literature on the urinary microbiome associated with the acute and interstitial cystitis does not point to convergence of microbiome similarities between the two diseases. More studies with direct sampling of the bladder tissues besides sampling bladder surfaces are warranted for accurate comparison of microbiome similarity between the two conditions. The future research on interstitial cystitis microbiome should include stratified cohorts with prospective design.

A Culture-Independent Analysis of the Microbiota of Female Interstitial Cystitis/Bladder Pain Syndrome Participants in the MAPP Research Network

We surveyed urine microbiota of females diagnosed with interstitial cystitis/bladder pain syndrome (IC/BPS) and matched control participants enrolled in the National Institutes of Health (NIH) Multidisciplinary Approach to the Study of Chronic Pelvic Pain (MAPP) Research Network using the culture-independent methodology. Midstream urine specimens were analyzed with the Plex-ID molecular diagnostic platform that utilizes polymerase chain reaction⁻electrospray ionization⁻time-of-flight⁻mass spectrometry (PCR-ESI-TOF MS) to provide a comprehensive identification of bacterial and select fungal species. IC/BPS and control participants were evaluated for differences (presence, diversity, and abundance) in species and genus. Urine specimens obtained from 181 female IC/BPS and 182 female control participants detected a total of 92 species (41 genera). Mean (SD) species count was 2.49 (1.48) and 2.30 (1.28) among IC/BPS and control participants, respectively. Overall species composition did not significantly differ between IC/BPS and control participants at any level (p = 0.726 species level, p = 0.222 genus level). IC/BPS participants urine trended to an overabundance of Lactobacillus gasseri (p = 0.09) detected but had a lower prevalence of Corynebacterium compared with control participants (p = 0.002). The relative abundance data analysis mirrored the prevalence data differences with no significant differences in most species or genus abundance other than Lactobacillus gasseri and Corynebacterium (p = 0.08 and p = 0.001, respectively). No cause and/or effect conclusion can be drawn from this observation, but it suggests that a more comprehensive evaluation (vaginal, bowel, catheterized bladder and/or tissue-based specimens) of the lower urinary tract microbiota in IC/BPS patients is warranted.

Mycobacterium Fortuitum Bloodstream Infection in a Very Low Birth Weight Preterm Neonate

Mycobacterium fortuitum is a rapidly growing Mycobacterium species that is a rare cause of disease, primarily in immunocompromised patients. We present a very low birth weight preterm neonate who developed M. fortuitum bloodstream infection, where 16S rDNA sequencing allowed accurate identification. Cure was achieved by line removal and adjuvant combination treatment with amikacin, ciprofloxacin and clarithromycin.

Alterations of microbiota in urine from women with interstitial cystitis

Background

Interstitial Cystitis (IC) is a chronic inflammatory condition of the bladder with unknown etiology. The aim of this study was to characterize the microbial community present in the urine from IC female patients by 454 high throughput sequencing of the 16S variable regions V1V2 and V6. The taxonomical composition, richness and diversity of the IC microbiota were determined and compared to the microbial profile of asymptomatic healthy female (HF) urine.

Results

The composition and distribution of bacterial sequences differed between the urine microbiota of IC patients and HFs. Reduced sequence richness and diversity were found in IC patient urine, and a significant difference in the community structure of IC urine in relation to HF urine was observed. More than 90% of the IC sequence reads were identified as belonging to the bacterial genus Lactobacillus, a marked increase compared to 60% in HF urine.

Conclusion

The 16S rDNA sequence data demonstrates a shift in the composition of the bacterial community in IC urine. The reduced microbial diversity and richness is accompanied by a higher abundance of the bacterial genus Lactobacillus, compared to HF urine. This study demonstrates that high throughput sequencing analysis of urine microbiota in IC patients is a powerful tool towards a better understanding of this enigmatic disease.

Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons

Background

Urine within the urinary tract is commonly regarded as "sterile" in cultivation terms. Here, we present a comprehensive in-depth study of bacterial 16S rDNA sequences associated with urine from healthy females by means of culture-independent high-throughput sequencing techniques.

Results

Sequencing of the V1V2 and V6 regions of the 16S ribosomal RNA gene using the 454 GS FLX system was performed to characterize the possible bacterial composition in 8 culture-negative (<100,000 CFU/ml) healthy female urine specimens. Sequences were compared to 16S rRNA databases and showed significant diversity, with the predominant genera detected being Lactobacillus, Prevotella and Gardnerella. The bacterial profiles in the female urine samples studied were complex; considerable variation between individuals was observed and a common microbial signature was not evident. Notably, a significant amount of sequences belonging to bacteria with a known pathogenic potential was observed. The number of operational taxonomic units (OTUs) for individual samples varied substantially and was in the range of 20 - 500.

Conclusions

Normal female urine displays a noticeable and variable bacterial 16S rDNA sequence richness, which includes fastidious and anaerobic bacteria previously shown to be associated with female urogenital pathology.

Urinary tract infection and inflammation at onset of interstitial cystitis/painful bladder syndrome

OBJECTIVES

Interstitial cystitis/painful bladder syndrome (IC/PBS) is a chronic disease primarily in women that is of low incidence and unknown etiology and manifests as bladder pain and urinary symptoms. Acute urinary tract infection (UTI) is of high incidence in women, presents as dysuria and urinary symptoms, and is caused by uropathogenic bacteria. We hypothesized that UTI is present at the onset of IC/PBS in some women.

METHODS

For a case-control study seeking risk factors for IC/PBS, women with IC/PBS symptoms of 12 months or less were recruited and evaluated by interview and medical record review. The date of symptom onset was identified by a six-step process. Three evidence-based methods using culture, urinalysis, and symptoms were used separately and in combination to diagnose UTI at IC/PBS onset.

RESULTS

Of 1177 screened women, 314 with recent-onset IC/PBS, including numerous confirming characteristics, were enrolled in the study; 98% of the requested medical records were obtained and reviewed. Evidence of a UTI at the onset of IC/PBS was found in 18% to 36% of women. Common UTI features not used in its diagnosis (short interval to medical care, hematuria, antibiotic treatment, and improvement after antibiotics) were significantly more common in those with onset UTI than in those without.

CONCLUSIONS

These retrospective data suggest that a proportion, probably a minority, of women at IC/PBS onset had evidence of UTI or inflammation. Our results indicate that UTI is present at the onset of IC/PBS in some women and might reveal clues to IC/PBS pathogenesis.

Absence of bacterial and viral DNA in bladder biopsies from patients with interstitial cystitis/chronic pelvic pain syndrome

PURPOSE

We examined bladder biopsies from women with interstitial cystitis/chronic pelvic pain syndrome (IC/CPPS) for the presence of bacterial and viral DNA sequences using polymerase chain reaction.

MATERIALS AND METHODS

Bladder biopsies were taken during cystoscopy from patients under investigation for IC/CPPS, or controls undergoing colposuspension for stress incontinence. Biopsies were snap frozen to -70C. After DNA extraction, polymerase chain reaction (PCR) using specific primers for the hypoxanthine-guanine phosphoribosyl transferase gene confirmed the presence of human DNA. PCR for bacterial and viral gene sequences was performed using specific primers. Positive reactions were repeated to confirm the signal.

RESULTS

A total of 92 patients with IC/CPPS (12 who met the National Institute of Diabetes and Digestive and Kidney Diseases criteria and 80 who did not) and 91 controls were recruited. PCR for hypoxanthine-guanine phosphoribosyl transferase gene was positive in all samples. PCR for the 16S ribosomal RNA gene, as well as for adenovirus, cytomegalovirus, herpes simplex virus types I and II, human papillomavirus (all subtypes) and Chlamydia trachomatis were negative in all samples.

CONCLUSIONS

IC/CPPS is not associated with persistence of viral and bacterial DNA in the bladder. A chronic infective etiology for the condition is excluded by these findings.

Rapidly progressive dementia due to Mycobacterium neoaurum meningoencephalitis

Dementia developed in a patient with widespread neurologic manifestations; she died within 5 months. Pathologic findings showed granulomatous inflammation with caseation necrosis, foreign body–type giant cells, and proliferative endarteritis with vascular occlusions. Broad-range polymerase chain reaction identified Mycobacterium neoaurum as the possible pathogen. Central nervous system infection by M. neoaurum may result in rapidly progressive dementia.

Detection of Helicobacter pylori in bladder biopsy specimens of patients with interstitial cystitis by polymerase chain reaction

The cause of interstitial cystitis (IC) is still unknown. Several features suggest that it may be an infectious disease and it has compelling similarities to chronic gastritis. The identification of Helicobacter pylori as the cause of chronic gastritis focused attention on this organism. Many studies have been done investigating the role of H. pylori in the etiology of IC. Previous studies mostly determined the presence of H.pylori with antibodies in the serum samples of IC patients, but these methods may lead to false positive or negative results. We therefore investigated the presence of H.pylori in bladder biopsy specimens by using polymerase chain reaction (PCR), which is accepted as the most sensitive and specific test for detecting this organism. A total of 32 patients with IC were enrolled into the study. The PCR assay was performed on cold cup bladder biopsies of IC patients. Both positive and negative controls were included in each set of PCR reactions. Gastric biopsy specimens of peptic ulcer patients with proven H. pylori infection were used as positive controls. Bladder biopsies of all IC patients were negative for H. pylori DNA. PCR showed the presence of H. pylori in the positive controls in each cycle demonstrating that the PCR assay was working properly. Thus, there is no evidence that IC is the result of H. pylori infection. This study does not negate the possibility that other infectious agents may play a role in the etiology of IC.

Interstitial cystitis: a chronic pelvic pain syndrome

Interstitial cystitis, an enigmatic chronic pelvic pain syndrome that occurs primarily in women, is much more common than originally believed. Its etiology is unknown, its evaluation and diagnosis remain controversial, and its treatment is largely empiric. Recent basic and clinical research is unlocking some of the mystery surrounding this clinical syndrome. Diagnostic awareness, willingness to consider recently studied therapies, and reasonable therapeutic expectations on the part of both the physician and the patient seem to be the key to successful management of this condition.

Detection and identification of Bartonella species pathogenic for humans by PCR amplification targeting the riboflavin synthase gene (ribC)

Several Bartonella species have now been implicated as human pathogens. The recovery of these fastidious organisms in the clinical microbiology laboratory remains difficult, and current methods are still relatively insensitive. Thus, the bartonellae are good candidates for detection by PCR. We have developed a PCR assay which uses a single primer pair targeting the riboflavin synthase gene (ribC) and detected six Bartonella species that have been implicated in human disease, B. henselae, B. quintana, B. bacilliformis, B. clarridgeiae, B. elizabethae, and B. vinsonii subsp. berkhoffii. Species identification is achieved simply by restriction enzyme digestion of the amplicon. This PCR assay appears to be specific for the Bartonella genus because it failed to amplify DNA from several other bacterial species.

Molecular methods for diagnosis of infective endocarditis

The culture of viable microorganisms from the blood or from cardiac tissue is currently the most important test for diagnosis of IE. This is followed by phenotypic identification methods used for taxonomic positioning of isolates. However, in those cases where the invading microorganism is difficult or impossible to culture (including instances of prior antimicrobial treatment), molecular methods provide the best means for detection. Molecular identification methods, either nucleic acid target or signal amplification alone or in combination with sequence analysis can offer a more specific and in some cases a more rapid alternative to the phenotypic methods. We propose revised Duke criteria of IE, including positive identification of an organism by molecular biology methods.

Is interstitial cystitis an infectious disease?

Interstitial cystitis (IC) is a chronic bladder disorder of unknown aaetiology. Although several investigators have attempted to identify an infectious cause for IC, none has yet been found. Our own studies to search for an infectious cause discovered instead, a toxic factor in the urine of approximately 95% of IC patients that is made by and inhibits, the normal proliferation of bladder epithelial cells. Additional research is necessary to determine whether this factor is encoded by the eucaryotic cells themselves or an unidentified intracellular microorganism.