Transient microbiota exposures activate dormant Escherichia coli infection in the bladder and drive severe outcomes of recurrent disease

The role of urine microbiota in culture-negative patients with pyuria

BACKGROUND

Pyuria is usually caused by bacteria and usually results in antibiotic prescriptions. However, traditional urine culture is time-consuming and has a high false negative possibility. Additionally, the role of urine viruses in pyuria is unclear. Metagenomics can enhance the precision and efficiency of diagnosis by directly sequencing the microbiota in urine. We aimed to determine the association of urine microbiota in patients with or without pyuria and culture negative.

METHODS

In this retrospective study, we screened urine samples from patients who received whole genome sequencing (WGS) and had a negative urine culture from October 2021 to May 2024. We compared differences in the top 10 detected genera of urine microbiota between the pyuria group and the non-pyuria group. Multivariable analysis was used for correlation analysis and performed to odds ratio (OR) and OR with 95% confidence interval (CI). The receiver operating characteristic (ROC) curve analyses tested the predictive ability of associated microbiota to pyuria.

RESULTS

We found 29 microbial genera including 2 viral genera. Escherichia [OR 11.688 (95%CI 2.190-62.362), p = 0.004], Gardnerella [OR 9.904 (95%CI 2.180-45.005), p = 0.003] or Polyomavirus [OR 5.205 (95%CI 1.295-20.919), p = 0.020] was associated with the independent risk factors of pyuria, while Lactobacillus was associated with a decreased risk of pyuria [OR 17.273 (95%CI 1.297-230.061), p = 0.031]. An integrated logistic regression model of Escherichia, Gardnerella, Polyomavirus, and Lactobacillus exhibited a predictive power for pyuria with the area under curve (AUC) of 0.8132 [95%CI (0.7098-0.9167), p < 0.001].

CONCLUSION

Urine microbiota is diverse. Escherichia, Gardnerella, or Polyomavirus are independently associated with pyuria, while Lactobacillus is a positive factor against pyuria.

Pneumocystis jirovecii is a potential pivotal ecological driver contributing to shifts in microbial equilibrium during the early-life lower airway microbiome assembly

Early life gut microbiota is being increasingly recognized as a major contributor to short and/or long-term human health and diseases. However, little is known about these early-life events in the human microbiome of the lower respiratory tract. This study aims to investigate fungal and bacterial colonization in the lower airways over the first year of life by analyzing lung tissue from autopsied infants. The fungal and bacterial communities of lung tissue samples from 53 autopsied infants were characterized by Next-Generation Sequencing (NGS), based on universal PCR amplification of the ITS region and the 16S rRNA gene, respectively. Our study highlights a high degree of inter-individual variability in both fungal and bacterial communities inhabiting the infant lung. The lower respiratory tract microbiota is mainly composed of transient microorganisms that likely travel from the upper respiratory tract and do not establish permanent residence. However, it could also contain some genera identified as long-term inhabitants of the lung, which could potentially play a role in lung physiology or disease. At 3-4 months of age, important dynamic changes to the microbial community were observed, which might correspond to a transitional time period in the maturation of the lung microbiome. This timeframe represents a susceptibility period for the colonization of pathogens such as Pneumocystis. The asymptomatic colonization of Pneumocystis was associated with changes in the fungal and bacterial communities. These findings suggest that the period of 2-4 months of age is a "critical window" early in life. Pneumocystis jirovecii could be a potential pivotal ecological driver contributing to shifts in microbial equilibrium during the early-life lower airway microbiome assembly, and to the future health of children.

Antibacterial compounds against non-growing and intracellular bacteria

Slow- and non-growing bacterial populations, along with intracellular pathogens, often evade standard antibacterial treatments and are linked to persistent and recurrent infections. This necessitates the development of therapies specifically targeting nonproliferating bacteria. To identify compounds active against non-growing uropathogenic Escherichia coli (UPEC) we performed a drug-repurposing screen of 6454 approved drugs and drug candidates. Using dilution-regrowth assays, we identified 39 compounds that either kill non-growing UPEC or delay its regrowth post-treatment. The hits include fluoroquinolones, macrolides, rifamycins, biguanide disinfectants, a pleuromutilin, and anti-cancer agents. Twenty-nine of the hits have not previously been recognized as active against non-growing bacteria. The hits were further tested against non-growing Pseudomonas aeruginosa and Staphylococcus aureus. Ten compounds - solithromycin, rifabutin, mitomycin C, and seven fluoroquinolones-have strong bactericidal activity against non-growing P. aeruginosa, killing >4 log10 of bacteria at 2.5 µM. Solithromycin, valnemulin, evofosfamide, and satraplatin are unique in their ability to selectively target non-growing bacteria, exhibiting poor efficacy against growing bacteria. Finally, 31 hit compounds inhibit the growth of intracellular Shigella flexneri in a human enterocyte infection model, indicating their ability to permeate the cytoplasm of host cells. The identified compounds hold potential for treating persistent infections, warranting further comparative studies with current standard-of-care antibiotics.

A bladder blueprint to build better models for understanding homeostasis and disease

The bladder is a complex organ that can be affected by various pathologies, such as cancer or infection. It has a specific tissue structure composed of many different cell types and layers, including urothelial and endothelial cells but also a muscle layer controlling stretch and contraction to void urine. The bladder has constitutive and induced immune responses to infection or damage and harbours a microbiome. Each of these features can be influenced by factors including age and biological sex, which makes modelling homeostasis and disease in the bladder complex and challenging. To model diseases that affect the bladder, mouse models are an invaluable tool to understand the bladder in situ. However, stark differences exist between mice and humans, and so mouse models of human disease have limitations. Thus, models that more closely approximate human physiology would be expected to contribute to improved understanding of bladder biology. As technology advances, improvements in model development and creation of 3D bladder structures are enabling scientists to recapitulate essential aspects of human bladder physiology to gain increased understanding of bladder homeostasis and diseases.

Interconnected microbiomes-insights and innovations in female urogenital health

The paradigm that the vaginal microbiota is a protective gateway for the urinary and reproductive systems has endured for more than a century and driven decades of probiotic research. Evidence robustly supports the notion that healthy urogenital microbiomes are predominantly colonized by lactobacilli, particularly Lactobacillus crispatus, which can acidify the local environment and protect against urogynecologic pathogen colonization. However, recent studies are beginning to delve deeper into the intricate mechanistic interactions connecting the microbiome, its diverse functional potential, host immunity, pathogens, and the development of urogenital diseases. Leveraging these emerging insights alongside past successes presents promising opportunities for future therapies aimed at enhancing the management of conditions such as bacterial vaginosis, urinary tract infections, bladder pain, urinary incontinence, and beyond.

Urinary tract infections: pathogenesis, host susceptibility and emerging therapeutics

Urinary tract infections (UTIs), which include any infection of the urethra, bladder or kidneys, account for an estimated 400 million infections and billions of dollars in health-care spending per year. The most common bacterium implicated in UTI is uropathogenic Escherichia coli, but diverse pathogens including Klebsiella, Enterococcus, Pseudomonas, Staphylococcus and even yeast such as Candida species can also cause UTIs. UTIs occur in both women and men and in both healthy and immunocompromised patients. However, certain patient factors predispose to disease: for example, female sex, history of prior UTI, or the presence of a urinary catheter or other urinary tract abnormality. The current clinical paradigm for the treatment of UTIs involves the use of antibiotics. Unfortunately, the efficacy of this approach is dwindling as the prevalence of antimicrobial resistance rises among UTI isolates, and the immense quantity of antibiotics prescribed annually for these infections contributes to the emergence of resistant pathogens. Therefore, there is an urgent need for new antibiotics and non-antibiotic treatment and prevention strategies. In this Review, we discuss how recent studies of bacterial pathogenesis, recurrence, persistence, host-pathogen interactions and host susceptibility factors have elucidated new and promising targets for the treatment and prevention of UTIs.

"Urinary tract infection: Conventional testing to developing Technologies"

Urinary tract infections (UTIs) present an escalating global health concern, precipitating increased hospitalizations and antibiotic utilization, thereby fostering the emergence of antimicrobial resistance. Current diagnostic modalities exhibit protracted timelines and substantial financial burdens, necessitating specialized infrastructures. Addressing these impediments mandates the development of a precise diagnostic paradigm to expedite identification and augment antibiotic stewardship. The application of biosensors, recognized for their transformative efficacy, emerges as a promising resolution. Recent strides in biosensor technologies have introduced pioneering methodologies, yielding pertinent biosensors and integrated systems with significant implications for point-of-care applications. This review delves into historical perspectives, furnishing a comprehensive delineation of advancements in UTI diagnostics, disease etiology, and biomarkers, underscoring the potential merits of these innovations for optimizing patient care.

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

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

Microbiota analysis of perimenopausal women experiencing recurrent vaginitis in conjunction with urinary tract infection

BACKGROUND

Recurrent vaginitis in conjunction with urinary tract infection (RV/UTI) in perimenopausal women is a common clinical condition that impacts both doctors and patients. Its pathogenesis is not completely known, but the urogenital microbiota is thought to be involved. We compared the urogenital and gut microbiotas of perimenopausal women experiencing RV/UTI with those of age-matched controls to provide a new microbiological perspective and scheme for solving clinical problems.

RESULTS

Fifty women of perimenopausal age who were diagnosed with RV/UTI and 50 age-matched healthy controls were enrolled. The urogenital and intestinal microbiota were analyzed via 16S ribosomal RNA gene sequencing by collecting samples from the mouth, anus, urine, cervix, and upper and lower vaginal ends. Among the microbiota of healthy perimenopausal women, the mouth had the highest richness, whereas the anus and mouth had the highest levels of diversity. Compared with those in healthy controls, in the microbiota of patients with RV/UTI, the evenness of the upper vaginal end, anus and cervix significantly increased, whereas the richness and diversity of the cervix significantly decreased. Lactobacillus accounted for 40.65% of the bacteria in the upper vaginal end and 39.85% of the bacteria in the lower vaginal end of healthy women of perimenopausal age, and there were no significant differences in Lactobacillus abundance among the patients with RV/UTI. The relative abundances of 54 genera and 97 species were significantly different between patients and healthy individuals, particularly in the cervix and urine. A total of 147 predicted pathways were significantly different between patients and healthy controls, with the microbiota of the anus exhibiting the greatest number of functional changes, followed by the urine microbiota. A random forest model composed of 16 genera in the lower vaginal end had the highest discriminatory power (AUC 81.48%) to predict RV/UTI.

CONCLUSIONS

Our study provides insight into the nature of the urogenital and intestinal microbiota in perimenopausal women, and reveals significant changes in the microbiota in patients with RV/UTI. This information will help characterize the relationship between the urogenital microbiota and RV/UTI, potentially aiding in the development of diagnostic and therapeutic strategies.

G. vaginalis increases HSV-2 infection by decreasing vaginal barrier integrity and increasing inflammation in vivo

Introduction

Clinically, a dysbiotic vaginal microbiota (VMB) colonized with anaerobic species such as Gardnerella vaginalis has been linked to increased susceptibility to viral sexually transmitted infections (STIs) such as Herpes Simplex Virus Type 2 (HSV-2). The mechanism is poorly understood due to the lack of small animal models.

Methods

Mice were inoculated with 107 CFU of the eubiotic bacteria Lactobacillus crispatus, the dysbiotic bacteria G. vaginalis, or PBS as a negative control every 48 h for ten days. On day ten, mice were inoculated with 105 PFU WT HSV-2 333 and survival, pathology, and viral titers were assessed. To elucidate changes in the vaginal microenvironment following bacterial inoculations, vaginal tissue and washes were collected following ten days of inoculations. To assess barrier integrity, tissue was fixed and stained for the barrier protein Desmoglein-1 (DSG-1). To evaluate the immune microenvironment, tissue was processed for flow cytometry to examine tissue-resident T cells and cytokine production by T cells. Vaginal washes were used for multiplex cytokine/chemokine analysis.

Results

G. vaginalis inoculated mice infected with HSV-2 had significantly decreased survival rates, increased pathology, and higher viral titers than PBS and L. crispatus inoculated mice. The vaginal epithelium of G. vaginalis inoculated mice showed decreased DSG-1 staining compared to other groups, indicating compromised barrier function. Decreased total numbers of CD4+ and CD8+ T cells expressing activated mucosal immune markers CD44, CD69, and CD103 were observed in the vaginal tract of G. vaginalis inoculated mice. They also showed increased proportions of T cells expressing inflammatory cytokines TNF-α and IFN-γ, while L. crispatus inoculated mice had increased proportions and absolute counts of T cells expressing the regulatory cytokine IL-10. In the multiplex assay, vaginal washes from G. vaginalis mice had increased inflammatory cytokines and chemokines compared to L. crispatus and PBS groups.

Discussion

These results suggest G. vaginalis inoculation may be increasing HSV-2 infection by disrupting the epithelial barrier, decreasing protective immune responses and increasing tissue inflammation in the vaginal tract.

Incidence and Recurrence of Urinary Tract Infections Caused by Uropathogenic Escherichia coli: A Retrospective Cohort Study

Purpose

Urinary tract infections (UTIs) are among the most common bacterial infections, with uropathogenic Escherichia coli (UPEC) as the main etiologic agent of uncomplicated UTIs (uUTIs). The prevalence of uUTis caused by organisms with antimicrobial resistance (AMR) is increasing worldwide, complexifying the disease management and increasing the risk of complications. In efforts to develop new strategies for uUTI prevention, it is imperative to understand factors associated with the occurrence of new episodes.

Patients and Methods

This retrospective cohort study aimed to assess the incidence of uUTIs caused by UPEC (UPEC-uUTIs) or unknown etiology (untested uUTIs) in adults aged ≥18 years receiving care in a San Francisco healthcare system.

Results

During 2014-2019, 1087 UPEC-uUTI and 4106 untested uUTI cases were documented, of which 324 (29.8%; 95% confidence interval: 27.1%-32.6%) and 1030 (25.1%; 95% confidence interval: 23.8%-26.4%) were followed by ≥1 new episode of uUTI within 12 months. In the UPEC-uUTI cohort, male gender, diagnosis of diabetes mellitus, and prior uUTI were risk factors for new episodes of uUTI. At the time of first UPEC-uUTI diagnosis, antimicrobial prescriptions were retrieved for 41.1% of cases. When tested, AMR was most frequently reported for trimethoprim/sulfamethoxazole or trimethoprim/sulfamethoxazole prescribed with other antimicrobials.

Conclusion

Our study provides important information on the incidence and risk of repeated episodes of uUTIs, as well as on AMR related to them.

Nur77 protects the bladder urothelium from intracellular bacterial infection

Intracellular infections by Gram-negative bacteria are a significant global health threat. The nuclear receptor Nur77 (also called TR3, NGFI-B, or NR4A1) was recently shown to sense cytosolic bacterial lipopolysaccharide (LPS). However, the potential role for Nur77 in controlling intracellular bacterial infection has not been examined. Here we show that Nur77 protects against intracellular infection in the bladder by uropathogenic Escherichia coli (UPEC), the leading cause of urinary tract infections (UTI). Nur77 deficiency in mice promotes the formation of UPEC intracellular bacterial communities (IBCs) in the cells lining the bladder lumen, leading to persistent infection in bladder tissue. Conversely, treatment with a small-molecule Nur77 agonist, cytosporone B, inhibits invasion and enhances the expulsion of UPEC from human urothelial cells in vitro, and significantly reduces UPEC IBC formation and bladder infection in mice. Our findings reveal a new role for Nur77 in control of bacterial infection and suggest that pharmacologic agonism of Nur77 function may represent a promising antibiotic-sparing therapeutic approach for UTI.

The Role of the Gut, Urine, and Vaginal Microbiomes in the Pathogenesis of Urinary Tract Infection in Women and Consideration of Microbiome Therapeutics

The gut, urine, and vaginal microbiomes play significant roles in the pathogenesis of recurrent urinary tract infections (rUTIs). Analysis of these microbiota has shown distinct associations with urinary tract infections. Encouraging data indicate that rUTIs may be responsive to microbiome treatments such as fecal microbiota transplantation, expanding potential treatments beyond antibiotics, hydration, and behavioral interventions. If successful, these nonantibiotic therapies have the potential to increase time between rUTI episodes and reduce the prevalence of multidrug-resistant organisms. In this review, we discuss the role of the 3 microbiomes in the pathogenesis of rUTI and utilization of live biotherapeutic products as therapy for rUTI.

Variability in cell division among anatomical sites shapes Escherichia coli antibiotic survival in a urinary tract infection mouse model

Urinary tract infection (UTI), mainly caused by Escherichia coli, are frequent and have a recurrent nature even after antibiotic treatment. Potential bacterial escape mechanisms include growth defects, but probing bacterial division in vivo and establishing its relation to the antibiotic response remain challenging. Using a synthetic reporter of cell division, we follow the temporal dynamics of cell division for different E. coli clinical strains in a UTI mouse model with and without antibiotics. We show that more bacteria are actively dividing in the kidneys and urine compared with the bladder. Bacteria that survive antibiotic treatment are consistently non-dividing in three sites of infection. Additionally, we demonstrate how both the strain in vitro persistence profile and the microenvironment impact infection and treatment dynamics. Understanding the relative contribution of the host environment, growth heterogeneity, non-dividing bacteria, and antibiotic persistence is crucial to improve therapies for recurrent infections.

Gentamicin loaded niosomes against intracellular uropathogenic Escherichia coli strains

Urinary tract infections (UTIs) are the most common bacterial infections and uropathogenic Escherichia coli (UPEC) is the main etiological agent of UTIs. UPEC can persist in bladder cells protected by immunological defenses and antibiotics and intracellular behavior leads to difficulty in eradicating the infection. The aim of this paper is to design, prepare and characterize surfactant-based nanocarriers (niosomes) able to entrap antimicrobial drug and potentially to delivery and release antibiotics into UPEC-infected cells. In order to validate the proposed drug delivery system, gentamicin, was chosen as "active model drug" due to its poor cellular penetration. The niosomes physical-chemical characterization was performed combining different techniques: Dynamic Light Scattering Fluorescence Spectroscopy, Transmission Electron Microscopy. Empty and loaded niosomes were characterized in terms of size, ζ-potential, bilayer features and stability. Moreover, Gentamicin entrapped amount was evaluated, and the release study was also carried out. In addition, the effect of empty and loaded niosomes was studied on the invasion ability of UPEC strains in T24 bladder cell monolayers by Gentamicin Protection Assay and Confocal Microscopy. The observed decrease in UPEC invasion rate leads us to hypothesize a release of antibiotic from niosomes inside the cells. The optimization of the proposed drug delivery system could represent a promising strategy to significatively enhance the internalization of antimicrobial drugs.

In vitro biofilm formation of Gardnerella vaginalis and Escherichia coli associated with bacterial vaginosis and aerobic vaginitis

Objective

To determine the optimum biofilm formation ratio of Gardnerella vaginalis (G. vaginalis) in a mixed culture with Escherichia coli (E. coli).

Methods

G. vaginalis ATCC14018, E. coli ATCC25922, as well as five strains of G. vaginalis were selected from the vaginal sources of patients whose biofilm forming capacity was determined by the Crystal Violet method. The biofilm forming capacity of E. coli in anaerobic and non-anaerobic environments were compared using the identical assay. The Crystal Violet method was also used to determine the biofilm forming capacity of a co-culture of G. vaginalis and E. coli in different ratios. After Live/Dead staining, biofilm thickness was measured using confocal laser scanning microscopy, and biofilm morphology was observed by scanning electron microscopy.

Results

The biofilm forming capacity of E. coli under anaerobic environment was similar to that in a 5% CO2 environment. The biofilm forming capacity of G. vaginalis and E. coli was stronger at 106:105 CFU/mL than at other ratios (P<0.05). Their thicknesses were greater at 106:105 CFU/mL than at the other ratios, with the exception of 106:102 CFU/mL (P<0.05), under laser scanning microscopy. Scanning electron microscopy revealed increased biofilm formation at 106:105 CFU/mL and 106:102 CFU/mL, but no discernible E. coli was observed at 106:102 CFU/mL.

Conclusion

G. vaginalis and E. coli showed the greatest biofilm forming capacity at a concentration of 106:105 CFU/mL at 48 hours and could be used to simulate a mixed infection of bacterial vaginosis and aerobic vaginitis in vitro.

The Role of Metabolomics and Microbiology in Urinary Tract Infection

One of the common illnesses that affect women's physical and mental health is urinary tract infection (UTI). The disappointing results of empirical anti-infective treatment and the lengthy time required for urine bacterial culture are two issues. Antibiotic misuse is common, especially in females who experience recurrent UTI (rUTI). This leads to a higher prevalence of antibiotic resistance in the microorganisms that cause the infection. Antibiotic therapy will face major challenges in the future, prompting clinicians to update their practices. New testing techniques are making the potential association between the urogenital microbiota and UTIs increasingly apparent. Monitoring changes in female urinary tract (UT) microbiota, as well as metabolites, may be useful in exploring newer preventive treatments for UTIs. This review focuses on advances in urogenital microbiology and organismal metabolites relevant to the identification and handling of UTIs in an attempt to provide novel methods for the identification and management of infections of the UT. Particular attention is paid to the microbiota and metabolites in the patient's urine in relation to their role in supporting host health.

Rapid-dissolving electrospun nanofibers for intra-vaginal antibiotic or probiotic delivery

The emergence of probiotics as an alternative and adjunct to antibiotic treatment for microbiological disturbances of the female genitourinary system requires innovative delivery platforms for vaginal applications. This study developed a new, rapid-dissolving form using electrospun polyethylene oxide (PEO) fibers for delivery of antibiotic metronidazole or probiotic Lactobacillus acidophilus, and performed evaluation in vitro and in vivo. Fibers did not generate overt pathophysiology or encourage Gardnerella growth in a mouse vaginal colonization model, inducing no alterations in vaginal mucosa at 24 hr post-administration. PEO-fibers incorporating metronidazole (100 µg MET/mg polymer) effectively prevented and treated Gardnerella infections (∼3- and 2.5-log reduction, respectively, 24 hr post treatment) when administered vaginally. Incorporation of live Lactobacillus acidophilus (107 CFU/mL) demonstrated viable probiotic delivery in vitro by PEO and polyvinyl alcohol (PVA) fibers to inhibit Gardnerella (108 CFU/mL) in bacterial co-cultures (9.9- and 7.0-log reduction, respectively, 24 hr post-inoculation), and in the presence of vaginal epithelial cells (6.9- and 8.0-log reduction, respectively, 16 hr post-inoculation). Administration of Lactobacillus acidophilus in PEO-fibers achieved vaginal colonization in mice similar to colonization observed with free Lactobacillus. acidophilus. These experiments provide proof-of-concept for rapid-dissolving electrospun fibers as a successful platform for intra-vaginal antibiotic or probiotic delivery.

RNA recording in single bacterial cells using reprogrammed tracrRNAs

Capturing an individual cell's transcriptional history is a challenge exacerbated by the functional heterogeneity of cellular communities. Here, we leverage reprogrammed tracrRNAs (Rptrs) to record selected cellular transcripts as stored DNA edits in single living bacterial cells. Rptrs are designed to base pair with sensed transcripts, converting them into guide RNAs. The guide RNAs then direct a Cas9 base editor to target an introduced DNA target. The extent of base editing can then be read in the future by sequencing. We use this approach, called TIGER (transcribed RNAs inferred by genetically encoded records), to record heterologous and endogenous transcripts in individual bacterial cells. TIGER can quantify relative expression, distinguish single-nucleotide differences, record multiple transcripts simultaneously and read out single-cell phenomena. We further apply TIGER to record metabolic bet hedging and antibiotic resistance mobilization in Escherichia coli as well as host cell invasion by Salmonella. Through RNA recording, TIGER connects current cellular states with past transcriptional states to decipher complex cellular responses in single cells.

RNA in situ hybridization of Escherichia coli in equine endometrial biopsies

Endometritis is one of the major causes of infertility in mares. Escherichia coli and β-haemolytic streptococci are among the bacterial species most frequently isolated from the equine uterus. Some bacteria such as β-hemolytic streptococci, can persist in dormant forms and cause prolonged, latent or recurrent infections. Dormant bacteria may be present despite negative bacterial cultures, and they are resistant to antimicrobial treatment due to their resting metabolic state. The purpose of this study was to study formalin-fixed paraffin-embedded equine endometrial biopsies for the presence and localization of E. coli-bacteria, with a chromogenic RNAscope^®-method for detection of E. coli-related 16S ribosomal RNA. Hematoxylin-eosin-stained endometrial biopsies were evaluated to determine the level of inflammation and degeneration. During estrus, samples were taken for endometrial culture and cytology with a double-guarded uterine swab. The samples included eight samples with moderate to severe endometrial inflammation detected in endometrial histopathology, and growth of E. coli in bacterial culture, six samples with moderate to severe endometrial inflammation but negative bacterial culture, and five samples with no endometrial pathology (grade I endometrial biopsy, negative endometrial culture and cytology) serving as controls. Positive and negative control probes were included in the RNA in situ hybridization, and results were confirmed with a fluorescence detection method (fluorescence in situ hybridization). Only unspecific signals of limited size and frequency of occurrence were detected in all samples, with random localization in the endometrium. No samples contained rod-shaped signals corresponding to bacterial findings. In conclusion, there was no evidence of bacterial invasion in the endometrium regardless of the inflammatory status of the biopsy or previous bacterial culture results. According to these findings on a small number of samples, invasion of E. coli is not a common finding in the lamina propria of mares, but these bacteria may also evade detection due to localized foci of infections, or supra-epithelial localization under the cover of biofilm. These bacteria and biofilm covering the epithelium may also be lost during formalin-fixation and processing.

Emerging Non-Antibiotic Options Targeting Uropathogenic Mechanisms for Recurrent Uncomplicated Urinary Tract Infection

Urinary tract infections (UTIs) are the most frequent bacterial infections in the clinical setting. Even without underlying anatomic or functional abnormalities, more than 40% of women experience at least one UTI in their lifetime, of which 30% develop recurrent UTIs (rUTIs) within 6 months. Conventional management with antibiotics for rUTIs may eventually lead to the development of multidrug-resistant uropathogens. Targeting of the pathogenicity of rUTIs, the evolution of uropathogenic Escherichia coli (UPEC), and inadequate host defenses by immune responses should be explored to provide non-antibiotic solutions for the management of rUTIs. The adaptive evolution of UPEC has been observed in several aspects, including colonization, attachment, invasion, and intracellular replication to invade the urothelium and survive intracellularly. Focusing on the antivirulence of UPEC and modulating the immunity of susceptible persons, researchers have provided potential alternative solutions in four categories: antiadhesive treatments (i.e., cranberries and D-mannose), immunomodulation therapies, vaccines, and prophylaxis with topical estrogen therapy and probiotics (e.g., Lactobacillus species). Combination therapies targeting multiple pathogenic mechanisms are expected to be a future trend in UTI management, although some of these treatment options have not been well established in terms of their long-term efficacy. Additional clinical trials are warranted to validate the therapeutic efficacy and durability of these techniques.

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.

Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies

The human microbiome is composed of a collection of dynamic microbial communities that inhabit various anatomical locations in the body. Accordingly, the coevolution of the microbiome with the host has resulted in these communities playing a profound role in promoting human health. Consequently, perturbations in the human microbiome can cause or exacerbate several diseases. In this Review, we present our current understanding of the relationship between human health and disease development, focusing on the microbiomes found across the digestive, respiratory, urinary, and reproductive systems as well as the skin. We further discuss various strategies by which the composition and function of the human microbiome can be modulated to exert a therapeutic effect on the host. Finally, we examine technologies such as multiomics approaches and cellular reprogramming of microbes that can enable significant advancements in microbiome research and engineering.

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.

Effects of aging on urinary tract epithelial homeostasis and immunity

A global increase in older individuals creates an increasing demand to understand numerous healthcare challenges related to aging. This population is subject to changes in tissue physiology and the immune response network. Older individuals are particularly susceptible to infectious diseases, with one of the most common being urinary tract infections (UTIs). Postmenopausal and older women have the highest risk of recurrent UTIs (rUTIs); however, why rUTIs become more frequent after menopause and during old age is incompletely understood. This increased susceptibility and severity among older individuals may involve functional changes to the immune system with age. Aging also has substantial effects on the epithelium and the immune system that led to impaired protection against pathogens, yet heightened and prolonged inflammation. How the immune system and its responses to infection changes within the bladder mucosa during aging has largely remained poorly understood. In this review, we highlight our understanding of bladder innate and adaptive immunity and the impact of aging and hormones and hormone therapy on bladder epithelial homeostasis and immunity. In particular, we elaborate on how the cellular and molecular immune landscape within the bladder can be altered during aging as aged mice develop bladder tertiary lymphoid tissues (bTLT), which are absent in young mice leading to profound age-associated change to the immune landscape in bladders that might drive the significant increase in UTI susceptibility. Knowledge of host factors that prevent or promote infection can lead to targeted treatment and prevention regimens. This review also identifies unique host factors to consider in the older, female host for improving rUTI treatment and prevention by dissecting the age-associated alteration of the bladder mucosal immune system.

Altering Microbiomes with Hydroxyapatite Nanoparticles: A Metagenomic Analysis

Hydroxyapatite (HAp), the most abundant biological material among mammals, has been recently demonstrated to possess moderate antibacterial properties. Metagenomics provides a series of tools for analyzing the simultaneous interaction of materials with larger communities of microbes, which may aid in optimizing the antibacterial activity of a material such as HAp. Here, a microbiome intrinsic to the sample of sandy soil collected from the base of an African Natal plum (Carissa macrocarpa) shrub surrounding the children's sandbox at the Arrowhead Park in Irvine, California was challenged with HAp nanoparticles and analyzed with next-generation sequencing for hypervariable 16S ribosomal DNA base pair homologies. HAp nanoparticles overwhelmingly reduced the presence of Gram-negative phyla, classes, orders, families, genera and species, and consequently elevated the relative presence of their Gram-positive counterparts. Thermodynamic, electrostatic and chemical bonding arguments were combined in a model proposed to explain this selective affinity. The ability of amphiphilic surface protrusions of lipoteichoic acid in Gram-positive bacteria and mycolic acid in mycobacteria to increase the dispersibility of the bacterial cells and assist in their resistance to capture by the solid phase is highlighted. Within the Gram-negative group, the variability of the distal, O-antigen portion of the membrane lipopolysaccharide was shown to be excessive and the variability of its proximal, lipid A portion insufficient to explain the selectivity based on chemical sequence arguments. Instead, flagella-driven motility proves to be a factor favoring the evasion of binding to HAp. HAp displayed a preference toward binding to less pathogenic bacteria than those causative of disease in humans, while taxa having a positive agricultural effect were largely captured by HAp, indicating an evolutionary advantage this may have given it as a biological material. The capacity to selectively sequester Gram-negative microorganisms and correspondingly alter the composition of the microbiome may open up a new avenue in environmental and biomedical applications of HAp.

Associations Between Bacterial Vaginosis And Urgency Urinary Incontinence In Women: An Analysis Of Nhanes 2001 To 2004

OBJECTIVE

To investigate the relationship between bacterial vaginosis (BV) and urinary incontinence (UI) in American women.

MATERIALS AND METHODS

Data from the National Health and Nutrition Examination Survey (NHANES) from 2001 to 2004 were merged. Self-collected vaginal swabs were used to assess BV. Urinary incontinence was determined by self-report. Multivariable logistic regression models were used to assess the association between BV and UI in American women, controlling for potential confounders.

RESULTS

Overall, 31.3% of female respondents tested positive for bacterial vaginosis. Women with bacterial vaginosis were more likely to report stress urinary incontinence (SUI) (22.78% vs 17.79%), urgency urinary incontinence (UUI) (12.86% vs 7.26%) and mixed urinary incontinence (MUI) (7.35% vs 4.42%) than women without bacterial vaginosis. In the adjusted analysis, women with bacterial vaginosis had 1.47 times greater odds of urgency urinary incontinence (OR 1.47, 95% CI 1.07 to 2.17, p=0.0160), and bacterial vaginosis did not increase the odds of stress urinary incontinence and mixed urinary incontinence in women.

CONCLUSION

After controlling for known risk factors, bacterial vaginosis seems to be significantly related to female urgency urinary incontinence. However, the cross-sectional nature of this study does not allow the conclusion of causality. Further basic and cohort studies are needed to examine the association of BV with UUI.

Hospital Urinary Tract Infections in Healthcare Units on the Example of Mazovian Specialist Hospital Ltd

Microbiological diagnostics is of great importance in limiting the spread of nosocomial infections. The information on etiological agents of infections and their susceptibility to antibiotics enables a quick response in the case of a suspected epidemic outbreak. The aim of this study is to analyze the incidence of nosocomial urinary tract infections among patients hospitalized in hospital wards over a period of 2 years and to determine the predominant etiological agent depending on the method of clinical specimen collection. Data from the Mazovian Specialist Hospital (MSH) in Radom constitute the material for the preparation of this study. Urine was collected using two methods. The first one was the method of collecting urine from the central stream, while the second method was urine collected from patients with a urinary catheter in place. The statistical calculations were conducted using the statistical software. Based on hospital data, it was shown that 5,870 urine tests were performed during the period under review, of which 2,070 were positive. The number of positive results in 2021 decreased by 2.84% compared to that in 2020. On the basis of the statistical analysis, differences in the occurrence of multiple strains were observed between catheter-based and midstream urine collection. Differences were observed especially for Acinetobacter baumannii, Candida albicans, Escherichia coli, and Pseudomonas aeruginosa. A. baumannii, C. albicans, and P. aeruginosa were significantly more frequently found in urine samples collected through the catheter than from the midstream. Furthermore, E. coli (51.56%) and Enterococcus species (25.46%) were more frequent when collected from the middle stream than when urine was collected through a catheter. However, for the strain K. pneumoniae, the results were comparable when urine was collected from catheterized patients (13.83%) and from midstream (13.35%). Urinary tract infection among hospitalized patients of the Mazovian Specialist Hospital in Radom was diagnosed quite frequently. In 2021, 32 more urine cultures were performed than in 2020. In the analyzed period, among all ordered urine cultures, 35.27% of samples were positive.

Gardnerella Exposures Alter Bladder Gene Expression and Augment Uropathogenic Escherichia coli Urinary Tract Infection in Mice

The anaerobic actinobacterium Gardnerella was first isolated from the bladder by suprapubic aspiration more than 50 years ago. Since then, Gardnerella has been increasingly recognized as a common and often abundant member of the female urinary microbiome (urobiome). Some studies even suggest that the presence of Gardnerella is associated with urological disorders in women. We recently reported that inoculation of Gardnerella into the bladders of mice results in urothelial exfoliation. Here, we performed whole bladder RNA-seq in our mouse model to identify additional host pathways involved in the response to Gardnerella bladder exposure. The transcriptional response to Gardnerella reflected the urothelial turnover that is a consequence of exfoliation while also illustrating the activation of pathways involved in inflammation and immunity. Additional timed exposure experiments in mice provided further evidence of a potentially clinically relevant consequence of bladder exposure to Gardnerella-increased susceptibility to subsequent UTI caused by uropathogenic Escherichia coli. Together, these data provide a broader picture of the bladder's response to Gardnerella and lay the groundwork for future studies examining the impact of Gardnerella on bladder health.

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.

Mixed Vaginitis in the Third Trimester of Pregnancy Is Associated With Adverse Pregnancy Outcomes: A Cross-Sectional Study

Mixed vaginitis is a complex vaginal dysbiosis that differs from single vaginitis. Vaginitis in the third trimester may lead to adverse maternal and neonatal outcomes. The clinical characteristics, microbiological characteristics, and adverse pregnancy outcomes of mixed vaginitis in late pregnancy are worth studying. Therefore, this study investigated the clinical and microbiological characteristics of vaginitis and adverse pregnancy outcomes of patients with mixed vaginitis. We studied 1,674 women in late pregnancy who attended the Tianjin Medical University General Hospital from November, 2019 to October, 2021. We administered standardized questionnaires, performed vaginal examination and sampling plus microscope examinations, and assessed follow-up pregnancy outcomes. We cultured the vaginal discharge of the patients with mixed vaginitis to isolate pathogens and performed antimicrobial susceptibility tests of the isolated pathogens. For the patients with peripartum infection, we collected a sample to isolate pathogens. Among the 1,674 women, 66 (3.9%) had mixed vaginitis. The independent risk factor for mixed vaginitis in late pregnancy was a history of vaginitis during early and middle pregnancy (OR = 5.637, 95% CI: 3.314-9.580). The signs of vaginal erythema (63.6% vs. 42.0%), yellow discharge (81.8% vs. 59.6%), and malodor (31.8% vs. 18.8%) (P <0.05) were significantly higher in patients with mixed vaginitis than in patients with single vaginitis. Bacterial isolates of the vaginal secretions of patients with mixed bacterial vaginitis were mainly the pathogens of aerobic vaginitis and bacterial vaginosis, such as Gardnerella vaginalis, Streptococcus anginosus, and Staphylococcus epidermidis. Pathogen isolation of the vaginal secretions of patients with mixed fungus and bacteria vaginitis mainly included Candida albicans, followed by S. anginosus, Enterococcus faecalis, Staphylococcus hemolyticus, Staphylococcus aureus, Streptococcus agalactiae and Staphylococcus simulans. Women with mixed vaginitis had an increased incidence and risk of peripartum infections (6.1% vs. 1.4%, P <0.05; OR = 3.985, 95% CI:1.214-13.079). Escherichia coli is the main pathogen that causes peripartum infection. Mixed vaginitis in late pregnancy is characterized by a severe and complex phenotype, complex vaginal dysbiosis, and a long course of vaginal dysbiosis. This can lead to an increased incidence and risk of peripartum infection. Therefore, more attention should be paid to patients with mixed vaginitis in the third trimester of pregnancy.

Urine and vaginal microbiota compositions of postmenopausal and premenopausal women differ regardless of recurrent urinary tract infection and renal transplant status

Postmenopausal women and renal transplant recipients are at increased risk of recurrent urinary tract infections (RUTI). Urine and vaginal microbiota of premenopausal controls (N = 18) and RUTI cases (18), and of postmenopausal controls (30) and RUTI cases (20) with and without a renal transplant, were characterized using 16S rRNA sequencing. Participants did not have UTI symptoms at the time of sampling. Gram-negative uropathobionts (predominantly Escherichia/Shigella, Pseudomonas, Klebsiella, and Acinetobacter) had a much higher mean relative abundance in urine than vaginal samples, especially in premenopausal women. No statistically significant differences in mean relative abundances of bacterial groups were found within the premenopausal group or within the postmenopausal group by RUTI or renal transplant status without chronic antibiotic use. Comparing postmenopausal to premenopausal women, mean relative abundances of lactobacilli (especially L. crispatus) in urine and vaginal samples and of Gram-negative uropathobionts in urine were lower, and of BV-anaerobes and Gram-positive uropathobionts in urine and vaginal samples were higher. While RUTI in premenopausal women is predominantly caused by Escherichia, the causative organisms in postmenopausal women are likely more diverse. The relative importance of individual organisms is currently unknown. We recommend that future studies, including intervention studies, include longitudinal microbiota assessments.

The impact of biological sex on diseases of the urinary tract

Biological sex, being female or male, broadly influences diverse immune phenotypes, including immune responses to diseases at mucosal surfaces. Sex hormones, sex chromosomes, sexual dimorphism, and gender differences all contribute to how an organism will respond to diseases of the urinary tract, such as bladder infection or cancer. Although the incidence of urinary tract infection is strongly sex biased, rates of infection change over a lifetime in women and men, suggesting that accompanying changes in the levels of sex hormones may play a role in the response to infection. Bladder cancer is also sex biased in that 75% of newly diagnosed patients are men. Bladder cancer development is shaped by contributions from both sex hormones and sex chromosomes, demonstrating that the influence of sex on disease can be complex. With a better understanding of how sex influences disease and immunity, we can envision sex-specific therapies to better treat diseases of the urinary tract and potentially diseases of other mucosal tissues.

Bladder Exposure to Gardnerella Activates Host Pathways Necessary for Escherichia coli Recurrent UTI

Recurrent urinary tract infections (rUTI) are a costly clinical problem affecting millions of women worldwide each year. The majority of rUTI cases are caused by uropathogenic Escherichia coli (UPEC). Data from humans and mouse models indicate that some instances of rUTI are caused by UPEC emerging from latent reservoirs in the bladder. Women with vaginal dysbiosis, typically characterized by high levels of Gardnerella and other anaerobes, are at increased risk of UTI. Multiple studies have detected Gardnerella in urine collected by transurethral catheterization (to limit vaginal contamination), suggesting that some women experience routine urinary tract exposures. We recently reported that inoculation of Gardnerella into the bladder triggers rUTI from UPEC bladder reservoirs in a mouse model. Here we performed whole bladder RNA-seq to identify host pathways involved in Gardnerella-induced rUTI. We identified a variety host pathways differentially expressed in whole bladders following Gardnerella exposure, such as pathways involved in inflammation/immunity and epithelial turnover. At the gene level, we identified upregulation of Immediate Early (IE) genes, which are induced in various cell types shortly following stimuli like infection and inflammation. One such upregulated IE gene was the orphan nuclear receptor Nur77 (aka Nr4a1). Pilot experiments in Nur77-/- mice suggest that Nur77 is necessary for Gardnerella exposure to trigger rUTI from UPEC reservoirs. These findings demonstrate that bladder gene expression can be impacted by short-lived exposures to urogenital bacteria and warrant future examination of responses in distinct cell types, such as with single cell transcriptomic technologies. The biological validation studies in Nur77-/- mice lay the groundwork for future studies investigating Nur77 and the Immediate Early response in rUTI.

Uropathogenic Escherichia coli Shows Antibiotic Tolerance and Growth Heterogeneity in an In Vitro Model of Intracellular Infection

Uropathogenic Escherichia coli (UPEC), the major causative agent of urinary tract infections, can invade different types of host cells. To compare the pharmacodynamic properties of antibiotics against intra- and extracellular UPEC, an in vitro model of intracellular infection was established in J774 mouse macrophages infected by the UPEC strain CFT073. We tested antibiotics commonly prescribed against urinary tract infections (gentamicin, ampicillin, nitrofurantoin, trimethoprim, sulfamethoxazole, and ciprofloxacin) and the investigational fluoroquinolone finafloxacin. The metabolic activity of individual bacteria was assessed by expressing the fluorescent reporter protein TIMERbac within CFT073. Concentration-response experiments revealed that all tested antibiotics were much less effective against intracellular bacteria than extracellular ones. Most antibiotics, except fluoroquinolones, were unable to reach a bactericidal effect intracellularly at clinically achievable concentrations. Ciprofloxacin and finafloxacin killed 99.9% of extracellular bacteria at concentrations around the MIC, while for intracellular bacteria, concentrations more than 100× over the MIC were required to achieve a bactericidal effect. Time-kill curves showed that finafloxacin was more rapidly bactericidal in acidic medium than at neutral pH, while the reverse observation was made for ciprofloxacin. Intracellularly, kill curves showed biphasic kinetics for both fluoroquinolones, suggesting the presence of drug-tolerant subpopulations. Flow cytometry analysis of TIMERbac fluorescence revealed a marked heterogeneity in intracellular growth of individual bacteria, suggesting that the presence of subpopulations reaching a state of metabolic dormancy was the main reason for increased antibiotic tolerance of intracellular UPEC.

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 mouse model displays host and bacterial strain differences in Aerococcus urinae urinary tract infection

In recent years, the clinical significance of Aerococcus urinae has been increasingly recognized. A. urinae has been implicated in cases of urinary tract infection (UTI; acute cystitis and pyelonephritis) in both male and female patients, ranging from children to older adults. Aerococcus urinae can also be invasive, causing urosepsis, endocarditis, and musculoskeletal infections. Mechanisms of pathogenesis in A. urinae infections are poorly understood, largely due to the lack of an animal model system. In response to this gap, we developed a model of A. urinae urinary tract infection in mice. We compared A. urinae UTI in female C3H/HeN and C57BL/6 mice and compared four clinical isolates of A. urinae isolated from patients with UTI, urgency urinary incontinence, and overactive bladder. Our data demonstrate that host genetic background modulates A. urinae UTI. Female C57BL/6 female mice rapidly cleared the infection. Female C3H/HeN mice, which have inherent vesicoureteral reflux that flushes urine from the bladder up into the kidneys, were susceptible to prolonged bacteriuria. This result is consistent with the fact that A. urinae infections most frequently occur in patients with underlying urinary tract abnormalities or disorders that make them susceptible to bacterial infection. Unlike uropathogens such as E. coli, which cause infection and inflammation both of the bladder and kidneys in C3H/HeN mice, A. urinae displayed tropism for the kidney, persisting in kidney tissue even after clearance of bacteria from the bladder. Aerococcus urinae strains from different genetic clades displayed varying propensities to cause persistent kidney infection. Aerococcus urinae infected kidneys displayed histological inflammation, neutrophil recruitment and increased pro-inflammatory cytokines. These results set the stage for future research that interrogates host-pathogen interactions between A. urinae and the urinary tract.

Summary:Aerococcus urinae clinical isolates are genetically diverse and display differential capacity to cause UTI in a mouse model. Infection was rapidly cleared from the bladder, but persisted and caused inflammation in the kidney.

Principles of seed banks and the emergence of complexity from dormancy

Across the tree of life, populations have evolved the capacity to contend with suboptimal conditions by engaging in dormancy, whereby individuals enter a reversible state of reduced metabolic activity. The resulting seed banks are complex, storing information and imparting memory that gives rise to multi-scale structures and networks spanning collections of cells to entire ecosystems. We outline the fundamental attributes and emergent phenomena associated with dormancy and seed banks, with the vision for a unifying and mathematically based framework that can address problems in the life sciences, ranging from global change to cancer biology.

Recurrent Urinary Tract Infections: Unraveling the Complicated Environment of Uncomplicated rUTIs

Urinary tract infections (UTIs) are frequent in humans, affecting the upper and lower urinary tract. Present diagnosis relies on the positive culture of uropathogenic bacteria from urine and clinical markers of inflammation of the urinary tract. The bladder is constantly challenged by adverse environmental stimuli which influence urinary tract physiology, contributing to a dysbiotic environment. Simultaneously, pathogens are primed by environmental stressors such as antibiotics, favoring recurrent UTIs (rUTIs), resulting in chronic illness. Due to different confounders for UTI onset, a greater understanding of the fundamental environmental mechanisms and microbial ecology of the human urinary tract is required. Such advancements could promote the tandem translation of bench and computational studies for precision treatments and clinical management of UTIs. Therefore, there is an urgent need to understand the ecological interactions of the human urogenital microbial communities which precede rUTIs. This review aims to outline the mechanistic aspects of rUTI ecology underlying dysbiosis between both the human microbiome and host physiology which predisposes humans to rUTIs. By assessing the applications of next generation and systems level methods, we also recommend novel approaches to elucidate the systemic consequences of rUTIs which requires an integrated approach for successful treatment. To this end, we will provide an outlook towards the so-called 'uncomplicated environment of UTIs', a holistic and systems view that applies ecological principles to define patient-specific UTIs. This perspective illustrates the need to withdraw from traditional reductionist perspectives in infection biology and instead, a move towards a systems-view revolving around patient-specific pathophysiology during UTIs.

The microbiome and host mucosal interactions in urinary tract diseases

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

Recurrent Urinary Tract Infection: A Mystery in Search of Better Model Systems

Urinary tract infections (UTIs) are among the most common infectious diseases worldwide but are significantly understudied. Uropathogenic E. coli (UPEC) accounts for a significant proportion of UTI, but a large number of other species can infect the urinary tract, each of which will have unique host-pathogen interactions with the bladder environment. Given the substantial economic burden of UTI and its increasing antibiotic resistance, there is an urgent need to better understand UTI pathophysiology - especially its tendency to relapse and recur. Most models developed to date use murine infection; few human-relevant models exist. Of these, the majority of in vitro UTI models have utilized cells in static culture, but UTI needs to be studied in the context of the unique aspects of the bladder's biophysical environment (e.g., tissue architecture, urine, fluid flow, and stretch). In this review, we summarize the complexities of recurrent UTI, critically assess current infection models and discuss potential improvements. More advanced human cell-based in vitro models have the potential to enable a better understanding of the etiology of UTI disease and to provide a complementary platform alongside animals for drug screening and the search for better treatments.

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.

What Is the Cause of Recurrent Urinary Tract Infection? Contemporary Microscopic Concepts of Pathophysiology

Urinary tract infections (UTIs) are the most common infectious disease and are mainly caused by Escherichia coli. In this review, we introduce the current concept of recurrent UTI (rUTI) based on recent research dealing with pathophysiology of the disease. Although urine is considered sterile, recent studies dealing with microbiome have proposed different ideas. UTIs have typically been considered as extracellular infections, but recently, uropathogenic Escherichia coli (UPEC) has been shown to bind and replicate in the urothelium to make intracellular bacterial communities. Binding UPECs might proceed in many ways including extracellular expulsion for clearance or survival and quiescent intracellular reservoirs that can cause rUTI. Moreover, it is also suggested that other important factors, such as lipopolysaccharide and multimicrobial infection, can be the cause of rUTI. This review article reveals a key mechanism of recurrence and discusses what makes a pathway of resolution or recurrence in a host after initial infection.

Gardnerella vaginalis promotes group B Streptococcus vaginal colonization, enabling ascending uteroplacental infection in pregnant mice

BACKGROUND

Group B Streptococcus is a common vaginal bacterium and the leading cause of invasive fetoplacental infections. Group B Streptococcus in the vagina can invade through the cervix to cause ascending uteroplacental infections or can be transmitted to the neonate during vaginal delivery. Some studies have found that women with a "dysbiotic" polymicrobial or Lactobacillus-depleted vaginal microbiota are more likely to harbor group B Streptococcus. Gardnerella vaginalis is often the most abundant bacteria in the vaginas of women with dysbiosis, while being detected at lower levels in most other women, and has been linked with several adverse pregnancy outcomes. Mouse models of group B Streptococcus and Gardnerella vaginalis colonization have been reported but, to the best of our knowledge, the two have not been studied together. The overarching idea driving this study is that certain members of the dysbiotic vaginal microbiota, such as Gardnerella vaginalis, may directly contribute to the increased rate of group B Streptococcus vaginal colonization observed in women with vaginal dysbiosis.

OBJECTIVE

We used a mouse model to test the hypothesis that vaginal exposure to Gardnerella vaginalis may facilitate colonization and/or invasive infection of the upper reproductive tract by group B Streptococcus during pregnancy.

STUDY DESIGN

Timed-pregnant mice were generated using an allogeneic mating strategy with BALB/c males and C57Bl/6 females. Dams were vaginally inoculated at gestational day 14 with group B Streptococcus alone (using a 10-fold lower dose than previously reported models) or coinoculated with group B Streptococcus and Gardnerella vaginalis. Bacterial titers were enumerated in vaginal, uterine horn, and placental tissues at gestational day 17. The presence (Fisher exact tests) and levels (Mann-Whitney U tests) of bacterial titers were compared between mono- and coinoculated dams in each compartment. Relative risks were calculated for outcomes that occurred in both groups. Tissue samples were also examined for evidence of pathophysiology.

RESULTS

Inoculation of pregnant mice with 10⁷ group B Streptococcus alone did not result in vaginal colonization or ascending infection. In contrast, coinoculation of group B Streptococcus with Gardnerella vaginalis in pregnant mice resulted in a 10-fold higher risk of group B Streptococcus vaginal colonization (relative risk, 10.31; 95% confidence interval, 2.710-59.04; P=.0006 [Fisher exact test]). Ascending group B Streptococcus infection of the uterus and placenta occurred in approximately 40% of coinoculated animals, whereas none of those receiving group B Streptococcus alone developed uterine or placental infections. Immunofluorescence microscopy revealed group B Streptococcus in both the maternal and fetal sides of the placenta. Histologic inflammation and increased proinflammatory cytokines were evident in the setting of group B Streptococcus placental infection. Interestingly, placentas from dams exposed to group B Streptococcus and Gardnerella vaginalis, but without recoverable vaginal or placental bacteria, displayed distinct histopathologic features and cytokine signatures.

CONCLUSION

These data suggest that Gardnerella vaginalis vaginal exposure can promote group B Streptococcus vaginal colonization, resulting in a greater likelihood of invasive perinatal group B Streptococcus infections. These findings suggest that future clinical studies should examine whether the presence of Gardnerella vaginalis is a risk factor for group B Streptococcus vaginal colonization in women. Because Gardnerella vaginalis can also be present in women without bacterial vaginosis, these findings may be relevant both inside and outside of the context of vaginal dysbiosis.