Human urine is not sterile - shift of paradigm

Comparison of the urinary microbiome in men who have sex with men with and without Chlamydia trachomatis infection

PURPOSE

The urinary tract is colonized by microbial communities that impact urinary health. Previous studies have suggested that the bacterial composition of the male urinary microbiota is related to STIs. This study assessed the bacterial composition of the urinary microbiome in South African MSM with and without C. trachomatis.

METHODS

This study used urine samples from MSM attending care at the King Edward VIII hospital and the Aurum Institute in Durban, South Africa. A total of 200 samples were tested for C. trachomatis infection using the Applied Biosystems™ TaqMan® Assays. Urinary microbiomes of 23 samples were characterized using 16 S rRNA (V3 and V4) gene sequencing on the Illumina MiSeq platform.

RESULTS

Bacterial taxonomic analysis showed a high abundance of Streptococcus, Corynebacterium, and Staphylococcus in all the sequenced samples. Moreover, Prevotella and Lactobacillus were detected in urine samples of MSM. Alpha diversity metrics showed a slight increase in microbial diversity in C. trachomatis positive samples; however, this was not significant (ANOVA, P > 0.05). Principal coordinates analysis (PCoA) showed that the microbiome of C. trachomatis infected MSM was not clearly different from those uninfected. Distinct bacterial communities were not detected between positive and negative samples (PERMANOVA F1,22= 1.0284, R2 = 0.047%, P = 0.385).

CONCLUSION

Most microbiome studies on MSM to date have focused on the gut microenvironment. Few studies, however, have provided data regarding the normal composition of the male urethral microbiomes or if these microbiomes are associated with male STIs. This study adds to the growing body of knowledge highlighting the urinary microbiome in MSM.

Comprehensive insights into UTIs: from pathophysiology to precision diagnosis and management

Urinary tract infections (UTIs) are the second most common infectious disease, predominantly impacting women with 150 million individuals affected globally. It increases the socio-economic burden of society and is mainly caused by Escherichia coli, Proteus mirabilis, Klebsiella pneumoniae, Enterobacter spp., and Staphylococcus spp. The severity of the infection correlates with the host factors varying from acute to chronic infections. Even with a high incidence rate, the diagnosis is mainly based on the symptoms, dipstick analysis, and culture analysis, which are time-consuming, labour-intensive, and lacking sensitivity and specificity. During this period, medical professionals prescribe empirical antibiotics, which may increase the antimicrobial resistance rate. Timely and precise UTI diagnosis is essential for addressing antibiotic resistance and improving overall quality of life. In response to these challenges, new techniques are emerging. The review provides a comprehensive overview of the global burden of UTIs, associated risk factors, implicated organisms, traditional and innovative diagnostic methods, and approaches to UTI treatment and prevention.

The human microbiome and benign prostatic hyperplasia: Current understandings and clinical implications

The research of the human microbiome in the preceding decade has yielded novel perspectives on human health and diseases. Benign prostatic hyperplasia (BPH) is a common disease in middle-aged and elderly males, which negatively affects the life quality. Existing evidence has indicated that the human microbiome, including urinary, intra-prostate, gut, oral and blood microbiome may exert a significant impact on the natural progression of BPH. The dysbiosis of the microbiome may induce inflammation at either a local or systemic level, thereby affecting the BPH. Moreover, metabolic syndrome (MetS) caused by the microbiome can also be involved in the development of BPH. Additionally, alterations in the microbiome composition during the senility process may serve as another cause of the BPH. Here, we summarize the influence of human microbiome on BPH and explore how the microbiome is linked to BPH through inflammation, MetS, and senility. In addition, we propose promising areas of investigation and discuss the implications for advancing therapeutic approaches.

Preanalytical, Analytical and Postanalytical Analyses on Corynebacterium spp. and Actinomycetaceae in Urine Samples of Patients with Suspected Urinary Tract Infection-A Hypothesis-Forming Observational Study

A hypothesis-forming exploratory cross-sectional assessment was conducted to assess the occurrence and relevance of Gram-positive rod-shaped bacteria like Corynebacterium spp. and Actinomycetaceae in human urine samples. In total, 1170 urine samples from 1031 inpatients with suspected urinary tract infection were assessed for culture-based growth of Gram-positive rod-shaped bacteria applying API Coryne assays, matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF-MS), and in-house 16S rRNA gene sequencing. Overall, 502 different bacterial colonies from 346 urine samples taken from 324 inpatients were observed. The three quantitatively most abundant genera or genus clusters were Corynebacterium (254 isolates, 62%), Actinomyces/Winkia (79 isolates, 19%), and Actinotignum/Actinobaculum (29 isolates, 7%). Compared to sequencing, the diagnostic accuracy of all assessed competitor assays from the diagnostic routine was <80% for differentiation on the genus level and <30% for differentiation on the species level. Prolongated incubation for 4 days compared to 2 days resulted in additional detection of 15% of the totally recorded Gram-positive rod-shaped bacteria. An approximately 5-fold increased detection rate in mid-stream urine compared to urine acquired applying alternative sampling strategies was observed. In conclusion, in the rare event of the suspected clinical relevance of such findings, confirmatory testing with invasively sampled urine should be considered due to the high contamination rate observed in mid-stream urine. Confirmatory testing by DNA-sequencing methods should be considered if an exact identification of genus or species is regarded as relevant for the individual choice of the therapeutic strategy.

Stability of volatile organic compound metabolites in urine at various storage temperatures and freeze-thaw cycles for 8 months

The urinary concentrations of mercapturic acid metabolites of volatile organic compounds (VOCs) have been used as biomarkers of human exposure to this class of chemicals. However, long-term stability of these VOC metabolites (VOCMs) in urine at various storage conditions such as temperature, duration, and freeze-thaw cycles is not known. In this study, spot urine samples collected from three volunteers, stored at 22 °C (room temperature: RT), 4 °C (refrigerator) and -20 °C (freezer) for up to 240 days were analyzed at weekly to monthly interval for a total of 19 time points. Samples stored at 4 °C and -20 °C underwent 18 freeze-thaw cycles at RT for 30 min at each of the time points. Among 38 VOCMs analyzed, up to 18 metabolites were detected at concentrations above their respective detection limits on Day 0 (baseline concentration), and the concentrations of several VOCMs declined with the storage duration. Eight to ten VOCMs were lost completely within 240 days of storage at RT, compared to between two and five at 4 °C and between one and seven at -20 °C. The loss rate varied depending on the sample, storage temperature, VOCM, and number of freeze-thaw cycles. Storage of urine at RT led to a rapid loss of VOCMs in comparison to that stored at 4 °C or -20 °C. Among VOCMs measured, CEMA, SBMA, GAMA, DHBMA, AMCC, TCVMA, and HPMMA were lost more rapidly than the other metabolites. CMEMA, a major VOCM found in all three urines at baseline, exhibited a rapid loss in those of two volunteers but not of the other volunteer, suggesting sample to sample variation in lose rates. Freeze-thaw cycles considerably affected VOCM concentrations in urines stored at 4 °C or -20 °C. It is recommended that urine samples are analyzed for VOCMs within a couple of months of collection and stored at temperatures below -20 °C, with minimal or no freeze-thaw cycles. This study highlights the need for appropriate storage conditions to maintain the integrity of samples for biomonitoring studies.

The Urinary Microbiome in Health and Disease: Relevance for Bladder Cancer

Bladder cancer (BC) constitutes one of the most diagnosed types of cancer worldwide. Advancements in and new methodologies for DNA sequencing, leading to high-throughput microbiota testing, have pinpointed discrepancies in urinary microbial fingerprints between healthy individuals and patients with BC. Although several studies suggest an involvement of microbiota dysbiosis in the pathogenesis, progression, and therapeutic response to bladder cancer, an established direct causal relationship remains to be elucidated due to the lack of standardized methodologies associated with such studies. This review compiles an overview of the microbiota of the human urinary tract in healthy and diseased individuals and discusses the evidence to date on microbiome involvement and potential mechanisms by which the microbiota may contribute to the development of BC. We also explore the potential profiling of urinary microbiota as a biomarker for risk stratification, as well as the prediction of the response to intravesical therapies and immunotherapy in BC patients. Further investigation into the urinary microbiome of BC patients is imperative to unravel the complexities of the role played by host-microbe interactions in shaping wellness or disease and yield valuable insights into and strategies for the prevention and personalized treatment of BC.

Prophages: an integral but understudied component of the human microbiome

Phages integrated into a bacterial genome - called prophages - continuously monitor the vigour of the host bacteria to determine when to escape the genome and to protect their host from other phage infections, and they may provide genes that promote bacterial growth. Prophages are essential to almost all microbiomes, including the human microbiome. However, most human microbiome studies have focused on bacteria, ignoring free and integrated phages, so we know little about how these prophages affect the human microbiome. To address this gap in our knowledge, we compared the prophages identified in 14 987 bacterial genomes isolated from human body sites to characterize prophage DNA in the human microbiome. Here, we show that prophage DNA is ubiquitous, comprising on average 1-5 % of each bacterial genome. The prophage content per genome varies with the isolation site on the human body, the health of the human and whether the disease was symptomatic. The presence of prophages promotes bacterial growth and sculpts the microbiome. However, the disparities caused by prophages vary throughout the body.

Improving Patient Outcomes While Reducing Empirical Treatment with Multiplex-Polymerase-Chain-Reaction/Pooled-Antibiotic-Susceptibility-Testing Assay for Complicated and Recurrent Urinary Tract Infections

This study compared rates of empirical-therapy use and negative patient outcomes between complicated and recurrent urinary tract infection (r/cUTI) cases diagnosed with a multiplex polymerase chain reaction or pooled antibiotic susceptibility testing (M-PCR/P-AST) vs. standard urine culture (SUC). Subjects were 577 symptomatic adults (n = 207 males and n = 370 females) presenting to urology/urogynecology clinics between 03/30/2022 and 05/24/2023. Treatment and outcomes were recorded by the clinician and patient surveys. The M-PCR/P-AST (n = 252) and SUC (n = 146) arms were compared after patient matching for confounding factors. The chi-square and Fisher's exact tests were used to analyze demographics and clinical outcomes between study arms. Reduced empirical-treatment use (28.7% vs. 66.7%), lower composite negative events (34.5% vs. 46.6%, p = 0.018), and fewer individual negative outcomes of UTI-related medical provider visits and UTI-related visits for hospitalization/an urgent care center/an emergency room (p < 0.05) were observed in the M-PCR/P-AST arm compared with the SUC arm. A reduction in UTI symptom recurrence in patients ≥ 60 years old was observed in the M-PCR/P-AST arm (p < 0.05). Study results indicate that use of the M-PCR/P-AST test reduces empirical antibiotic treatment and negative patient outcomes in r/cUTI cases.

A bacterial signature-based method for the identification of seven forensically relevant human body fluids

Detection and identification of body fluids plays a crucial role in criminal investigation, as it provides information on the source of the DNA as well as corroborative evidence regarding the crime committed, scene, and/or association with persons of interest. Historically, forensic serological methods have been chemical, immunological, catalytic, spectroscopic, and/or microscopic in nature. However, most of these methods are presumptive, with few robust confirmatory exceptions. In recent years several new molecular methods (mRNA, miRNA, DNA methylation, etc.) have been proposed; although promising, these methods require high quality human DNA or RNA. Additional steps are required in RNA based methods. Additionally, RNA based methods cannot be used for old cases where only DNA extracts remain to sample from. In this study, a novel non-human DNA (microbiome) based method was developed for the identification of the majority of forensically relevant human biological samples. Eight hundred and twelve (n = 812) biological samples (semen, vaginal fluid, menstrual blood, saliva, feces, urine, and blood) were collected and preserved using methods commonly used in forensic laboratories for evidence collection. Variable region four (V4) of 16 S ribosomal DNA (16 S rDNA) was amplified using a dual-indexing strategy and then sequenced on the MiSeq FGx sequencing platform using the MiSeq Reagent Kit v2 (500 cycles) and following the manufacturer's protocol. Machine learning prediction models were used to assess the classification accuracy of the newly developed method. As there was no significant difference in bacterial communities between vaginal fluid, menstrual blood, and female urine, these were combined as female intimate samples. Except in urine, the bacterial structures associated with male and female body fluid samples were not significantly different from one another. The newly developed method accurately identified human body fluid samples with an overall accuracy of more than 88%. This newly developed bacterial signature-based method is fast (no additional steps are needed as the same DNA can be used for both body fluid identification and STR typing), efficient (consume less sample as a single test can identify all major body fluids), sensitive (needs only 5 pg of bacterial DNA), accurate, and can be easily added into a forensic high throughput sequencing (HTS) panel.

Prophage rates in the human microbiome vary by body site and host health

Phages integrated into a bacterial genome-called prophages-continuously monitor the health of the host bacteria to determine when to escape the genome, protect their host from other phage infections, and may provide genes that promote bacterial growth. Prophages are essential to almost all microbiomes, including the human microbiome. However, most human microbiome studies focus on bacteria, ignoring free and integrated phages, so we know little about how these prophages affect the human microbiome. We compared the prophages identified in 11,513 bacterial genomes isolated from human body sites to characterise prophage DNA in the human microbiome. Here, we show that prophage DNA comprised an average of 1-5% of each bacterial genome. The prophage content per genome varies with the isolation site on the human body, the health of the human, and whether the disease was symptomatic. The presence of prophages promotes bacterial growth and sculpts the microbiome. However, the disparities caused by prophages vary throughout the body.

The Innovative Approach in Functional Bladder Disorders: The Communication Between Bladder and Brain-Gut Axis

Functional bladder disorders including overactive bladder and interstitial cystitis may induce problems in many other parts of our body such as brain and gut. In fact, diagnosis is often less accurate owing to their complex symptoms. To have correct diagnosis of these diseases, we need to understand the pathophysiology behind overlapped clinical presentation. First, we focused on reviewing literatures that have reported the link between bladder and brain, as the patients with bladder disorders frequently accompanied mood disorders such as depression and anxiety. Second, we reviewed literatures that have described the relationship between bladder and gut. There exist many evidences of patients who suffered from both bladder and intestinal diseases, such as irritable bowel syndrome and inflammatory bowel disease, at the same time. Furthermore, the interaction between brain and gut, well-known as brain-gut axis, might be a key factor that could change the activity of bladder and vice versa. For example, the affective disorders could alter the activity of efferent nerves or autonomic nervous system that modulate the gut itself and its microbiota, which might cause the destruction of homeostasis in bladder eventually. In this way, the communication between bladder and brain-gut axis might affect permeability, inflammation, as well as infectious etiology and dysbiosis in bladder diseases. In this review, we aimed to find an innovative insight of the pathophysiology in the functional bladder disorders, and we could provide a new understanding of the overlapped clinical presentation by elucidating the pathophysiology of functional bladder disorders.

Ejaculatory Abstinence Affects the Sperm Quality in Normozoospermic Men-How Does the Seminal Bacteriome Respond?

This study was designed to describe bacterial profiles of ejaculates collected following a long and short ejaculatory abstinence set in the context of changes in the conventional, oxidative, and immunological characteristics of semen. Two specimens were collected in succession from normozoospermic men (n = 51) following 2 days and 2 h, respectively. Semen samples were processed and analyzed according to the World Health Organization (WHO) 2021 guidelines. Afterwards, sperm DNA fragmentation, mitochondrial function, levels of reactive oxygen species (ROS), total antioxidant capacity, and oxidative damage to sperm lipids and proteins were evaluated in each specimen. Selected cytokine levels were quantified using the ELISA method. Bacterial identification by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry revealed that samples collected following two days of abstinence presented with a higher bacterial load and diversity, and a greater prevalence of potentially uropathogenic bacteria including Escherichia coli, Staphylococcus aureus and Enterococcus faecalis. Only staphylococci and Escherichia coli remained present in specimens obtained after 2 h of abstinence. Whilst all samples accomplished the criteria set by WHO, a significantly higher motility (p < 0.05), membrane integrity (p < 0.05), mitochondrial membrane potential (p < 0.05), and DNA integrity (p < 0.0001) were detected following 2 h of ejaculatory abstinence. On the other hand, significantly higher ROS levels (p < 0.001), protein oxidation (p < 0.001), and lipid peroxidation (p < 0.01) accompanied by significantly higher concentrations of tumor necrosis factor alpha (p < 0.05), interleukin-6 (p < 0.01), and interferon gamma (p < 0.05) were observed in specimens collected after two days of abstinence. It may be summarized that shorter ejaculatory abstinence does not compromise sperm quality in normozoospermic men, while it contributes to a decreased occurrence of bacteria in semen which is accompanied by a lower probability of damage to spermatozoa by ROS or pro-inflammatory cytokines.

Uromycobiome in infants and toddlers with and without urinary tract infections

BACKGROUND

The bacterial components of the urobiome have been described in children, both with and without urinary tract infections (UTI). However, less is known about the pediatric uromycobiome: the community of fungi in the urine. The objectives of this study were to describe the uromycobiome in children and determine whether the uromycobiome differs between children with and without UTI.

METHODS

This was a cross-sectional study of febrile children less than 3 years of age who presented to the Emergency Department and had a catheterized urine sample sent as part of clinical care. We obtained residual urine for use in this study and identified components of the uromyobiome through amplification and sequencing of the fungal ITS2 region. We then compared the uromycobiome between those with and without UTI.

RESULTS

We included 374 children in this study (UTI = 50, no UTI = 324). Fungi were isolated from urine samples of 310 (83%) children. Fungi were identified in a higher proportion of children with UTI, compared to those without UTI (96% vs. 81%, p = 0.01). Shannon diversity index was higher in children with UTI, compared to those without (p = 0.04). Although there were differences in the most abundant taxa between children with and without UTI, there was no significant difference in beta diversity between groups.

CONCLUSIONS

Fungi were detected in the majority of catheterized urine samples from children. While a higher proportion of children with UTI had fungi in their urine, compared to children without UTI, there was no difference in the composition of these groups. A higher resolution version of the Graphical abstract is available as Supplementary information.

The Potential Role of Urinary Microbiome in Benign Prostate Hyperplasia/Lower Urinary Tract Symptoms

Historically, urine in the urinary tract was considered “sterile” based primarily on culture-dependent methods of bacterial detection. Rapidly developing sequencing methods and analytical techniques have detected bacterial deoxyribonucleic acid and live bacteria in urine, improving our ability to understand the urinary tract microbiome. Recently, many studies have revealed evidence of a microbial presence in human urine in the absence of clinical infections. In women, fascinating evidence associates urinary tract microbiota with lower urinary tract symptoms (LUTS). However, the association between urinary tract microbiota and men with LUTS, particularly those with benign prostate hyperplasia (BPH), has not been established. In addition, the identification of the proinflammatory cytokines and pathogens responsible for the clinical progression of BPH is still underway. This review article aimed to address microbiome-related evidence for BPH. Further studies are required for a comprehensive understanding of the relationship between the urogenital microbiome and BPH pathogenesis to facilitate the development of preventive and therapeutic approaches for male LUTS.

The Urobiome and Its Role in Overactive Bladder

Urine is no longer considered to be sterile. After the existence of the microbiome was revealed through metagenomic analysis using next-generation sequencing, the relationship between characteristics of the microbiome and diseases have been studied and published in various journals. A microbiome exists in the urinary tract and is associated with urinary tract infection, malignancy of the genitourinary tract, and lower urinary tract symptoms. Based on the urine sampling method, sampling site, culture method, and sex, the characteristics of the microbiome vary. Most of the Lactobacillus species are identified mainly in women, and various other species are identified in men. These microorganisms can cause or prevent various diseases. Variations in the microbiome are seen in those with and without disease, and an asymptomatic status does not indicate the absence of microbes. This microbiome has been implicated in a variety of lower urinary tract symptoms and diseases, in particular, overactive bladder. The microbiome differs between patients with urgency and urge urinary incontinence and healthy individuals. There are many aspects of the microbiome yet to be studied in relation to other lower urinary tract symptoms.

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.

β-Defensin 2, an Antimicrobial Peptide, as a Novel Biomarker for Ulcerative Interstitial Cystitis; Can β-Defensin 2 Suspect the Dysbiosis of Urine Microbiota?

As urine is not sterile, inflammatory reactions caused by dysbiosis of the urinary microbiota may induce interstitial cystitis. A study was conducted to determine whether β-defensin 2 (BD-2), a specific antimicrobial peptide in the bladder, could be used as a novel diagnostic marker for ulcerative interstitial cystitis (IC). Urine samples from three female groups were examined: healthy controls (n = 34, Control group), non-Hunner type IC (n = 40, NHIC group), and Hunner type IC (n = 68, HIC group). Urine samples were collected via a transurethral catheter and assayed for BD-2 levels using enzyme linked immunosorbent assay. Under general or regional anesthesia, cystoscopy with diagnostic and therapeutic hydrodistension was performed in NHIC and HIC groups patients. These patients underwent a biopsy of the bladders. Based on the urinary specimens from 142 patients, BD-2 expression was found to be 18-fold higher in patients with Hunner type IC than in patients with non-Hunner type IC. The enhanced secretion of BD-2 exhibited a strong correlation with increased mast cell counts associated with bladder IC pathology. Enhanced urinary secretion of the antimicrobial peptide BD-2 from Hunner type IC patients associated with clinical phenotypes and demonstrated relatively robust levels to be used as a potential biomarker. Moreover, the increased urinary level of BD-2 may suggest a new possibility of biomarkers caused by dysbiosis of the urinary microbiota in ulcerative IC.

Acute Cystitis Symptom Score questionnaire for measuring patient-reported outcomes in women with acute uncomplicated cystitis: Clinical validation as part of a phase III trial comparing antibiotic and nonantibiotic therapy

PURPOSE

The Acute Cystitis Symptom Score (ACSS) used in a clinical trial comparing the phytodrug Canephron®N (BNO 1045) with an antibacterial agent (fosfomycin trometamol [FT]) in the treatment of acute uncomplicated cystitis (AC) in women was evaluated as a patient-reported outcome measure in a post hoc analysis.

MATERIALS AND METHODS

This double-blind, randomized, multicenter, phase III noninferiority trial was performed in 51 centers in Europe. The ACSS questionnaire was used to assess severity and course of symptoms.

RESULTS

The post hoc analysis included 325 patients treated with BNO 1045 and 332 patients treated with FT (total of 657 patients). The mean sum-scores of the ACSS-typical domain were comparable between groups on day 1 (BNO 1045: 10.2; FT: 10.1), and then decreased on day 4 (BNO 1045: 5.1; FT: 4.5), at end of treatment on day 8 (BNO 1045: 2.1; FT: 2.1), and at late follow-up on day 38 (BNO 1045: 0.8; FT: 0.9). Predefined thresholds using the scoring system of the ACSS could be established and validated to define "clinical cure."

CONCLUSIONS

Evaluating not only antibacterial but also nonantibacterial agents indicated for the treatment of AC in women, clinical criteria for diagnostics, and measures of patient-reported outcomes are more important as main objectives than microbiological criteria. In this post hoc evaluation, we showed that the ACSS questionnaire, validated in several languages, has the potential to be used as a suitable instrument for diagnostics and patient-reported outcomes in well-designed, international, clinical studies investigating different treatment modalities of uncomplicated urinary tract infections.

Urinary Microbiome: Yin and Yang of the Urinary Tract

The application of next generation sequencing techniques has allowed the characterization of the urinary tract microbiome and has led to the rejection of the pre-established concept of sterility in the urinary bladder. Not only have microbial communities in the urinary tract been implicated in the maintenance of health but alterations in their composition have also been associated with different urinary pathologies, such as urinary tract infections (UTI). Therefore, the study of the urinary microbiome in healthy individuals, as well as its involvement in disease through the proliferation of opportunistic pathogens, could open a potential field of study, leading to new insights into prevention, diagnosis and treatment strategies for urinary pathologies. In this review we present an overview of the current state of knowledge about the urinary microbiome in health and disease, as well as its involvement in the development of new therapeutic strategies.

Assessment of bacterial and fungal populations in urine from clinically healthy dogs using next-generation sequencing

BACKGROUND

Urine from clinically healthy dogs is not sterile. Characterizing microbial diversity and abundance within this population of dogs is important to define normal reference ranges for healthy urine.

OBJECTIVES

To establish composition and relative representation of bacterial and fungal microbiomes in urine of clinically healthy dogs.

ANIMALS

Fifty clinically healthy dogs.

METHODS

Analytic study. Urine sampling via cystocentesis. Comprehensive evaluation of urine including standard urinalysis, culture and sensitivity, next-generation sequencing (NGS), and bioinformatics to define bacterial and fungal microbiome.

RESULTS

Culture did not yield positive results in any samples. Next-generation sequencing of urine established low presence of bacteria, fungi, or both in all samples. Diversity and abundance of bacterial and fungal communities varied between urine samples from different dogs. Struvite crystals were associated with bacterial community structure (P = .07) and there was a positive correlation between struvite crystals and pH.

CONCLUSIONS AND CLINICAL IMPORTANCE

The microbiome in urine of clinically healthy dogs has diverse bacterial and fungal species These findings highlight limitations of conventional culture testing and the need for culture-independent molecular diagnostics to detect microorganisms in urine.

Alterations in Urobiome in Patients With Bladder Cancer and Implications for Clinical Outcome: A Single-Institution Study

Numerous studies indicate that resident microbiome exists in urine of healthy individuals and dysbiosis of the urobiome (urinary microbiome) may be associated with pathological conditions. This study was performed to characterize the alterations in urobiome and explore its implications of clinical outcome in male patients with bladder cancer. 62 male patients with bladder cancer and 19 non-neoplastic controls were recruited. The follow-up study cohort included 40 patients who were diagnosed with non-muscle invasive bladder cancer (NMIBC) and underwent transurethral resection of bladder tumor (TURBT). Mid-stream urine samples were collected from all the participants the day before cystoscopy. DNA was extracted from urine pellet samples and processed for high throughput 16S rRNA amplicon sequencing of the V4 region using Illumina MiSeq. Sequencing reads were filtered using QIIME and clustered using UPARSE. We found bacterial richness indices (Observed Species index, Chao1 index, Ace index; all P < 0.01) increased in cancer group when compared with non-neoplastic group, while there were no differences in Shannon and Simpson index between two groups. During a median follow-up time of 12 (5.25–25) months, 5/40 (12.5%)of the patients developed recurrence and no patient suffered from progression to muscle-invasive disease. Species diversity of the microbiome was significantly higher in the recurrence group compared with non-recurrence group in patients with NMIBC after TURBT. The LEfSe analysis demonstrated that 9 genera were increased (e.g., Micrococcus and Brachybacterium) in recurrence group. To our knowledge we report the relative comprehensive study to date of the male bladder cancer urinary microbiome and its relationship to pathogenesis and clinical outcomes. Given our preliminary data, additional studies evaluating the urine microbiome in relation to clinical outcomes are warranted to improve our understanding of tumor recurrence after TURBT.

Pre-analytical and analytical variables that influence urinary volatile organic compound measurements

There has been rapidly accelerating interest in the utilization of volatile organic compounds (VOCs) as non-invasive methods for rapid point-of-care medical diagnostics. There is widespread variation in analytical methods and protocols, with little understanding of the effects of sample storage on VOC profiles. This study aimed to determine the effects on VOC profiles of different storage times, at room temperature, prior to freezing, of sealed urine samples from healthy individuals. Analysis using Field Asymmetric Ion Motility Spectrometry (FAIMS) determined the alterations in VOC and total ion count profiles as a result of increasing room temperature storage times. Results indicated that increasing exposure time to room temperature prior to freezing had a threefold effect. Firstly, increased urinary VOC profile variability, with a plateau phase between 12 and 48 hours, before further degradation. Secondly, an increase in total ion count with time exposed to room temperature. Finally, a deterioration in VOCs with each sample run during the analysis process. This provides new insight into the effect of storage of urine samples for VOC analysis using FAIMS technology. Results of this study provide a recommendation for a 12-hour maximum duration at room temperature prior to storage.

UTI − quo vadis? New alternatives to treat uncomplicated urinary tract infections

Urinary tract infections (UTI) are one of the most common problems in urology clinics. The European Association of Urology (EAU) has been pioneering in its efforts to disseminate the latest clinical findings through the organization of the annual EAU congresses. At this year’s congress (EAU Barcelona 2019), various satellite symposia were organized, focusing on specific issues in the field of urology. "UTI − quo vadis? New alternatives to treat uncomplicated urinary tract infections" was one of the industry-sponsored symposia, organized with the aim of evaluating the current scenario and also throwing light on the paradigm shift in the treatment of acute, uncomplicated lower urinary tract infections (uUTI). Several interlinking topics were presented during this symposium. The topics covered antibiotic resistance, involving a presentation of the current data from the Global Prevalence Study on Infections in Urology (GPIU-study). This discussion was followed by case reports on the impact of antibiotic resistance on the management of patients with UTI/uUTI and treatment options for UTI/uUTI according to current guidelines. The highlight of the symposium was the presentation of very recent data from a gold standard phase III clinical trial (double-blind, double-dummy randomized study), demonstrating the non-inferiority of a herbal medicine (BNO 1045) versus antibiotic therapy (fosfomycin trometamol (FT), as a single dose = 3 g) for the treatment of acute, uncomplicated cystitis.

Recentrifuge: Robust comparative analysis and contamination removal for metagenomics

Metagenomic sequencing is becoming widespread in biomedical and environmental research, and the pace is increasing even more thanks to nanopore sequencing. With a rising number of samples and data per sample, the challenge of efficiently comparing results within a specimen and between specimens arises. Reagents, laboratory, and host related contaminants complicate such analysis. Contamination is particularly critical in low microbial biomass body sites and environments, where it can comprise most of a sample if not all. Recentrifuge implements a robust method for the removal of negative-control and crossover taxa from the rest of samples. With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications. In addition to contamination-subtracted samples, Recentrifuge provides shared and exclusive taxa per sample, thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics. Regarding the first area, Recentrifuge's novel approach has already demonstrated its benefits showing that microbiomes of Arctic and Antarctic solar panels display similar taxonomic profiles. In the clinical field, to confirm Recentrifuge's ability to analyze complex metagenomes, we challenged it with data coming from a metagenomic investigation of RNA in plasma that suffered from critical contamination to the point of preventing any positive conclusion. Recentrifuge provided results that yielded new biological insight into the problem, supporting the growing evidence of a blood microbiota even in healthy individuals, mostly translocated from the gut, the oral cavity, and the genitourinary tract. We also developed a synthetic dataset carefully designed to rate the robust contamination removal algorithm, which demonstrated a significant improvement in specificity while retaining a high sensitivity even in the presence of cross-contaminants. Recentrifuge's official website is www.recentrifuge.org. The data and source code are anonymously and freely available on GitHub and PyPI. The computing code is licensed under the AGPLv3. The Recentrifuge Wiki is the most extensive and continually-updated source of documentation for Recentrifuge, covering installation, use cases, testing, and other useful topics.

The local microbiome after pediatric bladder augmentation: intestinal segments and the native urinary bladder host similar mucosal microbiota

INTRODUCTION

Next-generation sequencing (NGS) techniques have provided novel insights into the microbiome of the urinary bladder (UB). In children after bladder augmentation using either ileum (ileocystoplasty, ICP) or colon (colocystoplasty, CCP), the fate of the mucosal microbiome introduced into the urinary tract remains unknown.

OBJECTIVE

The aim was to compare the mucosal microbiome of the native UB vs the augmented intestinal segment (IS) using NGS.

STUDY DESIGN

Twelve children after bladder augmentation (ICP n = 6, CCP n = 6) were included. Biopsies were taken during routine postoperative cystoscopy from the native UB and the IS. Specimens underwent whole-genome DNA extraction, 16S rRNA gene amplification, NGS, and Quantitative Insights Into Microbial Ecology (QIIME) data analysis. Downstream statistical data analyses were performed in Calypso.

RESULTS

Patients' median age at the time of surgery was 11 years (6-17 years), and the median interval between augmentation and sampling was 7 years (4-13 years). α-Diversity (Shannon diversity index) was not significantly different between IS vs UB, ICP vs CCP, and male vs female. No general differences in the overall bacterial pattern (β-diversity) were found between IS, UB, ICP, and CCP groups. The groups overlapped in principal coordinate analysis (PCoA) and non-metric multidimensional scaling (NMDS) analysis (Figure). Age at sampling had a statistically significant influence on β-diversity at the genus level. Corynebacterium, Pseudoxanthomonas, Lactobacillus, Flavobacterium, and Micrococcus were the most dominating taxa detected over all samples. There was an obvious dominance of the genus Corynebacterium in the samples taken from the UB and IS in both ICP and CCP patients. Limitations of this study include the relatively small number of patients.

CONCLUSION

After bladder augmentation, the native UB and augmented ISs (ICP and CCP) host similar microbiota despite their distinct differences of originating mucosal anatomy.

Presence of anaerobic bacteria in the urinary tract of catheterized ICU patients

The purpose of our study was to examine the extent of anaerobic bacteriuria in catheterized patients in the intensive care unit (ICU) and to search for risk factors for anaerobic bacteriuria. A urine culture was collected from each patient every 2 days during their ICU stay and incubated under aerobic and anaerobic conditions. Aerobic and anaerobic blood cultures were collected as well. Demographic, clinical, and laboratory data were collected from patient files. Ninety patients were included in this study, 32 women (35.6%) and 58 men (64.4%). A total of 663 cultures were obtained. Twenty-three patients (25.6%) had growth of anaerobic bacteria in a urinary culture at some point during ICU stay, with Bifidobacterium being the most common pathogen. Aerobic urinary cultures were positive in 38 patients (42.2%). A significant statistical correlation was found between the presence of aerobic and anaerobic bacteria in urine culture (p = 0.0004). Treatment with glycopeptides was found to be inversely associated with anaerobic bacteriuria (p = 0.0292), and treatment with imidazoles was associated with an increased risk of anaerobic bacteriuria (p = 0.0186). None of the patients developed bacteremia with the same anaerobic pathogen that was isolated from their urine. Anaerobic bacteriuria is a common phenomenon in catheterized patients in the ICU. Further studies are needed in order to define the clinical significance of these findings in such patients and in other patient groups as well as in healthy people.

Harnessing fertilizer potential of human urine in a mesocosm system: a novel test case for linking the loop between sanitation and aquaculture

Human urine (HU) is a biogenic fertilizer which has raised immense interest owing to its capacity of combining sanitation and nutrient recovery. In search of an alternative organic fertilizer for fish culture, the nutrient potential of HU was evaluated. Fries of Indian carps and larvae of freshwater prawn were reared for 120 days under six conditions: (a) aerated and (b) non-aerated fresh HU (0.01%), (c) cattle manure (CM; 1.8 kg tank^-1), mixed treatment with CM and HU under (d) iso-phosphorus and (e) iso-nitrogenous condition and (f) control. Monitoring of water quality and biological parameters revealed that total fish yield was the highest in CM (621.5 g tank^-1) followed by mixed treatments under iso-nitrogenous (428 g tank^-1) and iso-phosphorus (333 g tank^-1) conditions, aerated HU (321 g tank^-1) and HU (319 g tank^-1). The gross primary productivity (GPP) in HU was satisfactory (601.8 mg C m^-2 h^-1) and superior to all but CM treatment. The abundance of heterotrophic bacteria (HB) was highest in CM and lowest in HU. Both GPP and HB population were correlated positively with fish yield per tank. Although pH in all treatments remained high (pH 8.4-8.9), no ammonia toxicity was observed. No E. coli infestation in any fish muscle was encountered. The concentrations of cadmium and lead in fish muscle were within respective safe level. The study established that high fertilizer potential of HU could be exploited as an alternative organic fertilizer or as a candidate to be blended with cattle manure.

Gender differences in the bacteriology of rhinosinusitis

Evaluating gender differences in pathogens involving sinonasal tract disease in patients undergoing nasal surgery for chronic and recurrent rhinosinusitis (C/R RS). Retrospective analysis of 164 positive sinonasal swab cultures taken during endoscopic sinonasal surgery between the years 2006 and 2013. Study population included 79 (48.8%) female patients and 84 (51/2%) males with a mean age of 47.3 (13-88) years. Positive Staphylococcal growth was found in 38 (23.2%) patients, positive anaerobic growth in 25 (15.2%) patients and 67 (40.9%) patients had polymicrobial growth. Staphylococcal growth in the male population was significantly higher compared to the female population (p = 0.04). Odds ratio for a polymicrobial infection in males over 60 years old compared to females was 2.17 (CI 0.63-8.08, 95%). Anaerobes were found to be more frequent in males (17.9%) than in females (12.5%). Species of Streptococci showed no difference between gender and age groups. The results obtained suggest a difference between the causing pathogens in C/R RS between females and males. In the male population, staphylococcal species were found to be significantly more common with a greater tendency to polymicrobial pathogens and higher rates of anaerobes. These results might suggest different management protocols perioperatively in males and females.

Diversity of Bacterial Urine and Prostate Gland Tissue Cultures in Patients Undergoing Transurethral Prostate Gland Resection

INTRODUCTION

The objective of this study was to identify the types of bacterial colonization of the prostate gland tissue and urine pre- and postoperatively in patients undergoing a transurethral resection (TUR) of the prostate gland. In addition, clinical symptoms and histopathological findings were included.

MATERIAL AND METHODS

Forty three patients were investigated. Urine test strips and urine cultures were taken pre- and postoperatively and intraoperatively prostate resection chips were taken for culture.

RESULTS

A positive bacterial culture was found in 20 of 43 (46.5%) patients. Preoperatively, a positive bacterial culture was found in 12 patients and postoperatively in 7 patients. Thirteen patients showed a positive culture of the prostate gland tissue. No patient showed the same bacterial isolates in all 3 samples. Postinterventionally, 6 patients of the group with positive bacterial cultures developed complications. From the group of patients without bacterial growth, only one patient developed a postoperative complication.

CONCLUSION

The bacterial colonization in the 3 different cultures showed an inhomogeneous spectrum of bacteria without a reproducible pattern. Nevertheless, it clearly demonstrates that the group with a positive culture is at great risk to develop postoperative complications.

Letter to the Editor: Diagnostic Criteria in Urological Diseases do not Always Match with Findings by Extended Culture Techniques and Metagenomic Sequencing of 16S rDNA

Some diseases of the urinary tract are defined by the presence of microorganisms while others are defined by their absence. The underlying idea has always been that urine from healthy subjects is sterile and a negative urine culture has usually been taken as discriminative for an infection to be absent. Several disorders with symptoms that resemble infections are regarded as separate entities based on the exclusion of bacterial growth such as overactive neurogenic bladder and pelvic pain syndromes. During the recent years two paradigmata related to the role of bacteria in urological disease classification have changed completely. Firstly, bacteriuria does not necessarily mean an infection, and secondly, if extended sets of culture media for identification of fastidious and anaerobic bacteria or culture-independent metagenomic sequencing (MGS) is applied, a broad range of even non-culturable bacteria has been detected in the ”sterile” bladder urine in healthy individuals. The aim of this editorial is to initiate a discussion to redefine the criteria for urinary tract infections and non-infectious urological disorders with similar symptoms. Clinical studies, in which extended sets of culture media and MGS are integrated, are needed to clarify the pathogenesis of urological disorders where bacteria may play a role. The pure detection of bacteria in the urine does not by itself prove an infectious etiology of a specific disorder. It is important to avoid that results of new technologies lead to unnecessary antibiotic consumption with unwanted collateral damage and adverse events.

Complications after prostate biopsies in men on active surveillance and its effects on receiving further biopsies in the Prostate cancer Research International: Active Surveillance (PRIAS) study

OBJECTIVE

To study the risk of serial prostate biopsies on complications in men on active surveillance (AS) and determine the effect of complications on receiving further biopsies.

PATIENTS AND METHODS

In the global Prostate cancer Research International: Active Surveillance (PRIAS) study, men are prospectively followed on AS and repeat prostate biopsies are scheduled at 1, 4, and 7 years after the diagnostic biopsy, or once yearly if prostate-specific antigen-doubling time is <10 years. Data on complications after biopsy, including infection, haematuria, haematospermia, and pain, were retrospectively collected for all biopsies taken during follow-up in men from several large participating centres. Generalised estimating equations were used to test predictors of infection after biopsy. Competing risk analysis was used to compare the rates of men receiving further biopsies between men with and without previous complications.

RESULTS

In all, 2 184 biopsies were taken in 1 164 men. Infection was reported after 55 biopsies (2.5%), and one in five men reported any form of complication. At multivariable analysis, the number of previous biopsies was not a significant predictor of infection (odds ratio 1.04, 95% confidence interval 0.76-1.43). The only significant predictor for infection was the type of prophylaxis used. Of all men with a complication at the diagnostic or first repeat biopsy, 21% did not have a repeat biopsy at the time a repeat biopsy was scheduled according to protocol, vs 12% for men without a previous biopsy complication.

CONCLUSION

In our present cohort of men on AS, we found no evidence that repeat prostate biopsy in itself posed a risk of infection. However, complications after biopsy were not uncommon and after a complication men were less likely to have further biopsies. We should aim to safely reduce the amount of repeat biopsies in men on AS.