The urobiome, urinary tract infections, and the need for alternative therapeutics

Gut Microbiome Implication and Modulation in the Management of Recurrent Urinary Tract Infection

Urinary tract infections (UTIs) are one of the most common bacterial infections, affecting more than 150 million people each year in the world. UTIs have grown exponentially in the last few years. They represent a major load for both individuals and society. The highest incidence (about 55-60%) concerns women. Many pathogens are involved in UTIs, most of which are derived from the gut. Recent studies, together with recent diagnostic techniques (such as quantitative culture of urine or next-generation sequencing), have improved the knowledge of microbial communities in the urinary tract. It turned out that gut dysbiosis is strictly involved in the pathogenesis of UTIs. In particular, the human gut is the natural habitat for Escherichia coli (E. coli), the main bacterium responsible for UTIs. The overgrowth of E. coli pathogenic strains represents a risk factor for them. Furthermore, the human gut microbiota acts as a "global reservoir" for genes conferring resistance to clinically relevant antibiotics, thus influencing the treatment of UTIs. In addition, differently from the past, the idea of a sterile urinary environment has been replaced by the characterization of a urinary microbiome. The aim of our review is to explore recent studies on the association between gut microbiota and urinary microbiome and to summarize the current knowledge about the effects of interactions between gut and urinary microbial communities in the pathogenesis of UTIs, considering UTIs more as a "gut disease" and not only a urinary disease and providing new insight into the therapeutic options such as the use of probiotics.

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.

Genotypic and phenotypic characterisation of asymptomatic bacteriuria (ABU) isolates displaying bacterial interference against multi-drug resistant uropathogenic E. Coli

Escherichia coli can colonise the urogenital tract of individuals without causing symptoms of infection, in a condition referred to as asymptomatic bacteriuria (ABU). ABU isolates can protect the host against symptomatic urinary tract infections (UTIs) by bacterial interference against uropathogenic E. coli (UPEC). The aim of this study was to investigate the genotypic and phenotypic characteristics of five ABU isolates from midstream urine samples of adults. Comparative genomic and phenotypic analysis was conducted including an antibiotic resistance profile, pangenome analysis, and a putative virulence profile. Based on the genome analysis, the isolates consisted of one from phylogroup A, three from phylogroup B2, and one from phylogroup D. Two of the isolates, PUTS 58 and SK-106-1, were noted for their lack of antibiotic resistance and virulence genes compared to the prototypic ABU strain E. coli 83,972. This study provides insights into the genotypic and phenotypic profiles of uncharacterised ABU isolates, and how relevant fitness and virulence traits can impact their potential suitability for therapeutic bacterial interference.

Community context influences the conjugation efficiency of Escherichia coli

In urinary tract infections (UTIs), different bacteria can live in a polymicrobial community consisting of different species. It is unknown how community members affect the conjugation efficiency of uropathogenic Escherichia coli. We investigated the influence of individual species often coisolated from urinary infections (UTI) on the conjugation efficiency of E. coli isolates in artificial urine medium. Pairwise conjugation rate experiments were conducted between a donor E. coli strain containing the pOXA-48 plasmid and six uropathogenic E. coli isolates, in the presence and absence of five different species commonly coisolated in polymicrobial UTIs to elucidate their effect on the conjugation efficiency of E. coli. We found that the basal conjugation rates of pOXA-48, in the absence of other species, are dependent on the bacterial host genetic background. Additionally, we found that bacterial interactions have an overall positive effect on the conjugation rate of pOXA-48. Particularly, Gram-positive enterococcal species were found to enhance the conjugation rates towards uropathogenic E. coli isolates. We hypothesize that the nature of the coculture and physical interactions are important for these increased conjugation rates in an artificial urine medium environment.

The Study of Microbiome of the Female Genital Area in Relation to Pelvic Floor Dysfunction: A Systematic Review

INTRODUCTION AND HYPOTHESIS

The aim of this article is to present a systematic literature review focused on microbiome diversity in women experiencing pelvic floor dysfunction.

METHODS

Utilizing PubMed/MedLine and Scopus, 25 pertinent studies were meticulously selected for this review.

RESULTS

A key theme identified is the potential of microbiomes as diagnostic tools. The findings consistently highlight Lactobacillus as recurrent microbiota. Additionally, Gardnerella, Streptococcus, Prevotella, Aerococcus, Staphylococcus, Proteus, and Bifidobacterium species were frequently observed. This suggests the influential role of these microorganisms in shaping female urological and reproductive health. A deeper understanding of these predominant bacterial genera could offer invaluable insights into healthy physiological states and various disorders. The complex relationship between microbial compositions and diverse health conditions paves the way for novel diagnostic and therapeutic approaches. As we further explore the complexities of microbiomes, their role becomes increasingly crucial in transforming women's health care.

CONCLUSIONS

These findings emphasize the need for personalized care, integrating the microbiome into a comprehensive health assessment and treatment framework. This review lays the groundwork for future medical strategies where the microbiome is a pivotal element in both preventive and therapeutic care.

A critical assessment of microbial-based antimicrobial sanitizing of inanimate surfaces in healthcare settings

The global rise in antimicrobial resistance (AMR) poses a significant public health threat, especially in healthcare settings, where controlling the spread of antimicrobial genes is crucial. While person-to-person transmission remains the primary route for healthcare-associated infections (HAIs), hospital surfaces serve as key reservoirs for antimicrobial-resistant microorganisms. Regular cleaning and disinfection of these surfaces are essential. Microbial-based products for sanitizing hospital surfaces have emerged as promising tools to combat HAIs and AMR. However, a review of 32 publications found inconsistencies and potential risks. A total of 15 publications included hospital-based trials, while the rest were either in vitro or in situ assays, reviews, book chapters, or commentaries. In most of the hospital-based studies, specific strains of applied microorganisms were not identified, and the term "probiotic" was inaccurately used. These products mainly featured spores from Bacillus and Priestia genera, which was mainly hypothesized to work through competitive exclusion. Most hospital-based studies have shown that the application of microbial-based products resulted in a significant reduction in pathogens on surfaces, thereby contributing to a decrease in the incidence of healthcare-associated infections (HAIs). Further research is however needed to understand the effectiveness, mechanisms of action, and safety of microbial-based sanitizing agents. Strain-level identification is crucial for safety assessments, yet many reviewed products lacked this information. Consequently, there is a need for rigorous safety evaluations within existing regulatory frameworks to ensure the efficacy and safety of microbial-based cleaning products in healthcare settings.

An exploratory in silico analysis of bacteriocin gene clusters in the urobiome

Background: The role of the urobiome in health and disease remains an understudied area compared to the rest of the human microbiome. Enhanced culturing techniques and next-generation sequencing technologies have identified the urobiome as an untapped source of potentially novel antimicrobials. The aim of this study was to screen the urobiome for genes encoding bacteriocin production. Methods: The genomes of 181 bacterial urobiome isolates were screened in silico for the presence of bacteriocin gene clusters using the bacteriocin mining tool BAGEL4 and secondary metabolite screening tool antiSMASH7. Results: From these isolates, an initial 263 areas of interest were identified, manually annotated, and evaluated for potential bacteriocin gene clusters. This resulted in 32 isolates containing 80 potential bacteriocin gene clusters, of which 72% were identified as class II, 13.75% as class III, 8.75% as class I, and 5% as unclassified bacteriocins. Conclusion: Overall, 53 novel variants were discovered, including nisin, gassericin, ubericin, and colicins.

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.

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

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

Urinary Tract Infection and Microbiome

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

Vesicoureteral Reflux and Innate Immune System: Physiology, Physiopathology, and Clinical Aspects

Vesicoureteral reflux represents one of the most concerning topics in pediatric nephrology due to its frequency, clinical expression with the potential to evolve into chronic kidney disease, and last but not least, its socio-economic implications. The presence of vesicoureteral reflux, the occurrence of urinary tract infections, and the development of reflux nephropathy, hypertension, chronic kidney disease, and finally, end-stage renal disease represent a progressive spectrum of a single physiopathological condition. For the proper management of these patients with the best clinical outcomes, and in an attempt to prevent the spread of uropathogens' resistance to antibacterial therapy, we must better understand the physiopathology of urinary tract infections in patients with vesicoureteral reflux, and at the same time, we should acknowledge the implication and response of the innate immune system in this progressive pathological condition. The present paper focuses on theoretical aspects regarding the physiopathology of vesicoureteral reflux and the interconditionality between urinary tract infections and the innate immune system. In addition, we detailed aspects regarding cytokines, interleukins, antimicrobial peptides, and proteins involved in the innate immune response as well as their implications in the physiopathology of reflux nephropathy. New directions of study should focus on using these innate immune system effectors as diagnostic and therapeutic tools in renal pathology.

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.