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Kim, D.S.; Lee, J.W. Urinary Tract Infection and Microbiome. Encyclopedia. Available online: (accessed on 01 December 2023).
Kim DS, Lee JW. Urinary Tract Infection and Microbiome. Encyclopedia. Available at: Accessed December 01, 2023.
Kim, Dong Soo, Jeong Woo Lee. "Urinary Tract Infection and Microbiome" Encyclopedia, (accessed December 01, 2023).
Kim, D.S., & Lee, J.W.(2023, June 06). Urinary Tract Infection and Microbiome. In Encyclopedia.
Kim, Dong Soo and Jeong Woo Lee. "Urinary Tract Infection and Microbiome." Encyclopedia. Web. 06 June, 2023.
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. 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. 

microbiome urinary tract infection cystitis urobiome

1. Introduction

Urinary tract infections (UTIs) are among the most common bacterial infections worldwide and encompass a broad spectrum of diseases, ranging from uncomplicated cystitis to life-threatening urosepsis [1]. Studies using data from the Global Burden of Disease (GBD) show that in 2019 the absolute number of UTI cases had increased by 60.50% since 1990, to a total of 404.61 million patients. The age-standardized incidence of UTIs was 3.6 times higher for females, and UTI incidences increased with age in teenagers, peaking around 35 years. Mortality and disability-adjusted life years (DALYs) were significantly higher in patients aged 65–75 years in both sexes [2]. Due to their high frequency and severity in complex cases, UTIs pose a significant burden for healthcare systems [1][3]. Repetitive use of antibiotics can lead to multidrug-resistant strains, and the cost of treatment can escalate steeply, especially in patients with comorbidities, catheter-associated infections, and septic shock [4].
In-depth evaluation into the micro-organisms involved in UTI has opened doors to a whole new perception of the human urinary tract. Using novel 16S rRNA rapid next-generation gene sequencing (NGS) and expanded quantitative urine culture (EQUC) we now know that the urine is not sterile [5][6]. Over 100 species from more than 50 genera have been identified [7]. The urinary tract is home to a rich and complex microbial community and changes in its composition are thought to be implicated in diverse urinary tract symptoms and diseases [8][9].
Research on the human microbiome and its influence on individual physiology and pathology has increased in recent years [8][10][11][12][13][14]. The implications of microbiome ecology in healthy and diseased patients are yet to be fully understood but future research promises new diagnostic and therapeutic options that include efforts to preserve and restore the integrity of the urinary microbiome [12][13][15][16][17].

2. Urinary Tract Infection and Microbiome

2.1. Urinary Microbiome

2.1.1. EQUC and NGS Technology

NGS refers to diverse new methods of rapid and cost-effective sequencing of DNA and RNA. NGS methods were used to identify bacteria without cultures. Through polymerase chain reaction (PCR) amplification and sequencing, the hypervariable regions of the 16s rRNA gene is analyzed to distinguish between different bacterial species [18]. Using NGS methods, the bladder was proven to be a non-sterile medium [6].
After discovering the presence of urinary tract microbiomes, EQUC was developed as way to detect microbiomes that were not found with standard urine culture methods. Standard urine cultures used to detect uropathogens in patients with UTI are usually performed using 1 μL of urine in blood agar plates (BAP) and MacConkey agar plates under aerobic conditions at 35 °C. EQUC uses up to 100 μL of urine in BAP, MacConkey, chocolate, colistin–nalidixic acid (NAC) agars, and also CDC anaerobe BAP agars under anaerobic conditions and different gas mixtures at 35 °C. While standard urine culture detects organism growth higher that 1000 CFU/mL, EQUC can detect growth as low as 10 CFU/mL [18]. This enhanced protocol allows detection of up to 92% of bacteria not seen in standard tests [6]. Different protocols using diverse combinations of medium and cultivating environment (extended spectrum) or a concise combination (streamlined) have been reported showing detections rates much higher than standard methods [19].

2.1.2. Uncovering the Urinary Tract Microbiome

Many studies have put their efforts in primarily taxonomically profiling urinary tract microbiomes. For healthy humans, research has mainly been focused on female participants [6][20][21][22][23]. An early study by Siddiqui et al. in 2011 analyzed midstream urine from eight healthy adult female volunteers with confirmed negative cultures. In their study, 16s rRNA sequencing revealed 45 different genera with over 80% assigned to Lactobacillus, Prevotella, and Gardnerella. Variations between individuals were considerable and no common microbial signature was noticeable [21]. Wolfe et al. also analyzed the urine of adult women with no UTIs. The control group consisted of patients with benign gynecologic conditions reporting no urinary symptoms and the comparison group included patient with pelvic floor dysfunction, such as pelvic organ prolapse or urinary incontinence. Urine samples were collected via clean-catch midstream voiding, transurethral catheterization, and suprapubic aspiration and analyzed using bacterial culture, light microscopy, and polymerase chain reaction (PCR) amplification. The presence of bacteria (both Gram negative and positive) was confirmed even in culture-negative transurethral catharized samples. Taxonomical analysis showed Lactobacillus was most frequently detected, with additional findings of Gardnerella, Prevotella, Actinobaculum, Aerococcus, and Streptococcus [20].
Sex is a major factor that can contribute to differences in baseline individual microbiomes. Compared to women, only a number studies have evaluated male urinary tract microbiomes and most were conducted in the clinical setting of sexually transmitted infections (STIs) [24][25][26][27]. Nelson et al. used 16s rRNA sequencing on first-catch urine in males visiting an STI clinic without symptoms of urethritis. Lactobacillus, Corynebacteria, and Streptococcus were among the most frequently detected genera. Clustering analysis showed that STI were associated with organisms not usually related to the male urinary tract such as Sneathia, Gemella, and Prevotella [24]. They also compared microbiomes in urine and urethral samples from 32 men. They were found to be nearly identical regardless of inflammation or infection. For non-STI patients Lactobacillus, Sneathia, and Veillonella were most abundant, while for STI patients Neisseria, Streptococcus, and Corynebacterium were most common [25]
As for differences due to age, Price et al. showed that Gardnerella was found more often in younger women (mean age 36 ± 13, p < 0.001) and those with fewer median vaginal parities, while women with Escherichia were older (mean age 60 ± 13, p = 0.005) and more likely to be postmenopausal [23]. Lewis et al. studied microbiota from healthy individuals using 16s rRNA sequencing. Although there were only 6 males included in the study, the numbers of genera were analyzed against age. The number of genera in microbiota increased while the average total number of bacteria decreased [28].

2.2. Implications of Urinary Tract Microbiome in UTIs

2.2.1. Urinary Microbiome and UTIs

UTIs can occur when the equilibrium between the host and urinary tract microbiome is disrupted [29][30]. Wilner et al. profiled microbial communities in 50 patients with acute uncomplicated UTIs using 16s rRNA sequencing and fimH amplicon pyrosequencing from midstream urine samples. UTI microbial communities showed differences according to age with younger individuals dominated with Escherichia coli (E. coli) and older patients with high abundances of Pseudomonas. In females with UTIs, a relatively higher proportion of Enterobacteriaceae was observed while in male UTI patients Streptococcus, Lactobacillus, and Staphylococcus were not detected [31]. Garretto et al. used EQUC and 16s rRNA to analyze the genomes of E. coli strains from catheterized urine collected from women with lower urinary tract symptoms, including symptomatic UTIs. The presence of E. coli and genomic variations in E. coli could not predict UTI symptoms. Urobiome analysis showed E. coli was a weak predictor of UTI [32].
Few studies have investigated how the urinary microbiome changes during urinary tract infection. Hasman et al. used whole-genome sequencing (WGS) to evaluate bacteria cultivated from random urine samples of patients with suspected urinary tract infection. WGS aided in identifying cultivated bacteria, especially in polymicrobial samples, and predicted antimicrobial susceptibility. In addition, some putative pathogenic strains were observed in culture-negative samples [33]
These studies show that multiple factors are involved in UTIs. The urobiome composition appears to play a greater role in urinary tract defense, and its disequilibrium may contribute to infection as much as the invading uropathogen itself. In addition, the virome [34] and mycobiome [35] can also affect the microbiome and should be explored for their role in calibrating the urinary tract milieu. Interactions between different microbial communities, such as the gut and vagina, are also major contributors to tract infection [36]. Metagenomic sequencing of the female urinary tract and vagina showed similar microbiota, suggesting crosstalk between these communities [37].

2.2.2. Recurrent Urinary Tract Infections and the Effects of Antibiotics on the Microbiome

Recurrent UTIs pose a significant burden on both personal and social aspects, from decreasing the quality of life (QOL) to socio-economic issues [1]. The pathogenesis of recurrent UTIs is yet to be defined; however, two major theories and supporting studies have been proposed for both [38]. First, repeated infections via an ascending fecal–perineal–urethral route are supported by studies that show similarities between urine and gut microbiomes and evidence of an intestinal reservoir for recurrence [39][40]. Magruder et al. used 16s rRNA sequencing and metagenomics on fecal and urine specimens of kidney transplant recipients and found that the gut abundance of Escherichia and Enterococcus were independent risk factors for bacteriuria. Strain analysis also showed a close strain-level alignment in the gut/urine specimens [39].
Along with recurrent UTI, the emergence of multidrug resistance (MDR) is a global problem. Diagnostic and antimicrobial stewardship are crucial to avoid unnecessary diagnostic testing and to prevent antibiotic misuse [41][42]. Microbiota are thought to gain MDR by acquiring genotypes through horizontal gene transfer or mutations to resist treatment [36][43]. Antibiotic treatment is still the mainstay for urinary tract infections, and these regimens can cause long-term changes in the microbiome. Gottschick et al. compared the urinary microbiota of healthy participants with those of patients with bacterial vaginosis during infection and after antibiotic treatment [44]. Antibiotic treatment reduced Gardnerella vaginalis, Atopobium vaginae, and Sneathia amnii abundance, while Lactobacillus iners, which has a controversial role in bacterial vaginosis, was seen to increase to numbers two times higher than those in healthy women. Antibiotic treatment was unable to restore the infected urinary tract microbiome to its pre-infection status. Mulder et al. used 16s rRNA sequencing in elderly participants and analyzed the results against antimicrobial drug use [45]

2.3. Microbiome and Emerging Treatments for Recurrent UTIs

Research on recurrent UTIs and antimicrobial resistance using cutting-edge technology has provided new insights and an understanding of how microbial communities interact and change pathological states. This knowledge can translate to the development of urinary tract microbiome modulation as a possible method for UTI treatment.
The effectiveness of protective bacteria, such as Lactobacilli, on enhancing the defensive mechanisms of the urinary tract have been widely evaluated [12]. These probiotics, when delivered in sufficient amounts, are thought to benefit the host through antimicrobial components such as bacteriocins, biosurfactants, and lactic acids [10]. L. crispatus is one of the well-known strains in maintaining a healthy microbiome. Stapleton et al. performed a randomized double-blind placebo-controlled phase 2 trial for an L. crispatus intravaginal suppository probiotic (Lactin-V). A total of 100 premenopausal women with a history of recurrent UTIs, were treated for acute infection and randomized for Lactin-V or a placebo. After 10 weeks, UTI recurrence was seen in 15% of the women receiving Lactin-V against 27% of the placebo group (relative risk 0.5, 95% confidence interval, 0.2–1.2). Higher amounts of vaginal colonization by L. crispatus were associated with significant reduction in UTI for the Lactin-V group [46].
There have also been studies on using different strains of E. coli for bacterial interference [47][48]. E. coli 83972, first isolated from a young girl with asymptomatic bacteriuria [49], has mutations which decrease its virulence compared to other E. coli strains that can cause symptomatic infection [50]. Bacterial interference is thought to occur from competition for nutrients, bacteriocin production, competition for attachment sites, and prevention of biofilm formation [51]
Fecal microbiota transplantation (FMT) transfers microbiota from a healthy donor to the patient’s intestine, restoring a healthy microbiome constitution [52]. A few studies have shown that FMT has a role in reducing recurrent UTIs [53][54][55]. Tariq et al. identified patients with more than three UTIs in the year preceding FMT for three or more episodes of PCR-positive C. difficile infection (CDI). They were compared against a control group with three or more UTI episodes in the year prior to their third CDI. FMT was associated with a significant decrease in UTI frequency, and all patients had complete resolution of CID with no recurrence within a 1-year follow up. Additionally, post-FMT antibiotic-susceptibility profiling of urine cultures showed susceptibility to ciprofloxacin and trimethoprim-sulfamethoxazole which were observed to be resistant in earlier cultures [53].
Antimicrobial peptides such as human cathelicidins, defensins, and bacteriocins are secreted from the urothelium and exert direct antibiotic activity as well as immunomodulatory effects. Especially bacteriocins, which are peptides produced by bacteria to eradicate competing organisms, have gained renewed interest as a new target for treatment in this era of growing multidrug resistance [10]. E. coli produces two types of bacteriocins; high-molecular-weight colicins and small microcins. Colicins damage target cells by membrane permeabilization through voltage-dependent channels, cellular nuclease degradation, and inhibition of peptidoglycan synthesis [56]. They have been reported as a way to inhibit and reduce biofilm formation on urinary catheters [57][58]
Other interesting candidates for treatment are the urinary virome and phages [59]. Studies on the virome community are even scarcer than on microbiomes and current analyses are centered on eukaryotic viruses, namely the human papilloma virus (HPV) [34][60]. However, viruses within the human microbiota far outnumber bacterial cells, with the most abundant viruses being those that infect bacteria (bacteriophages) [61], implicating the existence of a large undiscovered viral community. Natural or genetically engineered phages and their lytic enzymes could be considered alternatives to antibiotic treatment or synergistic additives to conventional treatment. However, due to their high specificity, there is an increased risk of bacteria evolving into phage-resistant strains, and most phage therapies are developed in combination with other antimicrobial agents or as phage cocktails [59]

3. Conclusions

NGS technology, EQUC, and large metagenomic projects have helped us detect and identify the microbiome community of the urinary tract. These discoveries will hopefully give mankind new insights on managing recurrent UTIs and a desperately needed boost in catching up on multidrug resistance in uropathogenic bacteria. New treatment modalities that use microbiomes as probiotics or competitive substitutes may help prevent recurrent UTIs. In addition to antimicrobial proteins, bacteriophages show promising results as an adjunctive treatment modality to combat antibiotic resistance.


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