Quantitative Urine Culture Research Articles

Alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method

Considerable variation exists in the methodology of urinary microbiota studies published so far including the cornerstone of any biomedical analysis: sample collection. The aim of this study was to compare the urinary microbiota of first-catch voided urine (FCU), mid-stream voided urine (MSU) and aseptically catheterised urine in men and define the most suitable urine sampling method. Forty-nine men (mean age 71.3 years) undergoing endoscopic urological procedures were enrolled in the study. Each of them contributed three samples: first-catch urine (FCU), mid-stream urine (MSU) and a catheterised urine sample. The samples were subjected to next-generation sequencing (NGS, n = 35) and expanded quantitative urine culture (EQUC, n = 31). Using NGS, Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant phyla in our population. The most abundant genera (in order of relative abundance) included: Prevotella, Veillonella, Streptococcus, Porphyromonas, Campylobacter, Pseudomonas, Staphylococcus, Ezakiella, Escherichia and Dialister. Eighty-two of 105 samples were dominated by a single genus. FCU, MSU and catheterised urine samples differed significantly in three of five alpha-diversity measures (ANOVA, p < 0.05): estimated number of operational taxonomic units, Chao1 and abundance-based coverage estimators. Beta-diversity comparisons using the PIME method (Prevalence Interval for Microbiome Evaluation) resulted in clustering of urine samples according to the mode of sampling. EQUC detected cultivable bacteria in 30/31 (97%) FCU and 27/31 (87%) MSU samples. Only 4/31 (13%) of catheterised urine samples showed bacterial growth. Urine samples obtained by transurethral catheterisation under aseptic conditions seem to differ from spontaneously voided urine samples. Whether the added value of a more exact reflection of the bladder microbiota free from urethral contamination outweighs the invasiveness of urethral catheterisation remains to be determined.

Dysbiosis of the Human Urinary Microbiome and its Association to Diseases Affecting the Urinary System.

The human urinary microbiome, also termed urobiome, has been overlooked due to the clinical dogma of sterile urine, as reported by routine culture. However, evolving sensitive tools such as expanded quantitative urine culture, 16S ribosomal RNA gene sequencing, and next-generation sequencing have discovered a vast number of microorganisms present in urine, even in healthy individuals. Microbiome dysbiosis and its links to disease is a heavily explored area in several microbial niches. Presently, urobiome dysbiosis and its correlation to urinary system-related diseases is at its infancy but rapidly emerging, as it provides potential therapeutic insights. This review outlines the changes in the human urinary microbiome concerning globally prevalent diseases affecting kidney function, such as chronic kidney disease (CKD), diabetes mellitus (DM), hypertension (HT), and urinary tract infection (UTI). Alterations to urine microbial diversity, including differences in the abundance and species richness of particular microbial genera, notably Lactobacillus, Prevotella, Streptococcus, Staphylococcus, Klebsiella, Enterococcus, between diseased and healthy samples are discussed utilising studies to date. Subsequent research needs to move beyond correlation to understand the roles of the urinary microbiota in diseases, thereby clarifying whether urinary dysbiosis has causal contributions that may provide important insight for diagnostics, pathophysiology, and therapy in renal pathologies.

Microbiome of Genitourinary Tumors: Especially in Prostate Cancer and Kidney Cancer

Human body contains diverse microbes. Different microbes are identified at different organs. Urine was thought as sterile, but according to progression in important technologies like 16S rRNA gene sequencing and expanded quantitative urine culture, it is known that diverse microbes exist in genitourinary tract. Microbiome contains the microbes and surrounding microenvironments. In addition to urologic difficulties like interstitial cystitis or chronic prostatitis, malignancies are thought to be related to microbiomes. In this review, we summarized several studies in urologic malignancies, especially prostate cancer and kidney cancer.

This Month in Adult Urology

This Month in Adult Urology

The Urinary Microbiome in Postmenopausal Women with Recurrent Urinary Tract Infections.

The etiology of postmenopausal recurrent urinary tract infection (UTI) is not completely known, but the urinary microbiome is thought to be implicated. We compared the urinary microbiome in menopausal women with recurrent UTIs to age-matched controls, both in the absence of acute infection. This is a cross-sectional analysis of baseline data from 64 women enrolled in a longitudinal cohort study. All women were using topically applied vaginal estrogen. Women >55 years of age from the following groups were enrolled: 1) recurrent UTIs on daily antibiotic prophylaxis, 2) recurrent UTIs not on antibiotic prophylaxis and 3) age-matched controls without recurrent UTIs. Catheterized urine samples were collected at least 4 weeks after last treatment for UTI and at least 6 weeks after initiation of vaginal estrogen. Samples were evaluated using expanded quantitative urine culture (EQUC) and 16S rRNA gene sequencing. With EQUC, there were no significant differences in median numbers of microbial species isolated among groups (p=0.96), even when considering Lactobacilli (p=0.72). However, there were trends toward different Lactobacillus species between groups. With 16S rRNA sequencing, the majority of urine samples contained Lactobacillaceae, with nonsignificant trends in relative abundance among groups. Using a Bayesian analysis, we identified significant differences in anaerobic taxa associated with phenotypic groups. Most of these differences centered on Bacteroidales and the family Prevotellaceae, although differences were also noted in Actinobacteria and certain genera of Clostridiales. Associations between anaerobes within the urinary microbiome and postmenopausal recurrent UTI warrants further investigation.

Recurrent urinary tract infection: Association of clinical profiles with urobiome composition in women.

Clinical profiles of women with recurrent urinary tract infection (RUTI) are correlated with their urinary microbes. This IRB-approved, cross-sectional study enrolled adult women with RUTI. Urine samples (catheterized and voided) underwent culture by expanded quantitative urine culture (EQUC) and standard urine culture (SUC) methods. A validated symptom questionnaire, relevant clinical variables, and EQUC were used to identify symptom clusters and detect associations with specific urinary microbes. Most (36/43) participants were postmenopausal; the average age was 67 years. 51% reported vaginal estrogen use; 51% reported sexual activity. Although single symptoms were not associated with specific urinary microbes, EQUC results were correlated with five distinct clinical profile clusters: Group A: odor, cloudiness, and current vaginal estrogen use (no culture result association). Group B: frequency, low back pain, incomplete emptying, and vaginal estrogen (significantly increased proportion of Lactobacillus-positive cultures). Group C: pain/burning, odor, cloudiness, and urgency (high proportions of UTI-associated microbe-positive cultures). Group D: frequency, urgency, pain/burning, and current vaginal estrogen use (increased number of no growth cultures). Group E: frequency, urgency, pain/burning, odor, overactive bladder, and sexually active (significantly increased proportion of Klebsiella-positive cultures). Distinct clinical profiles are associated with specific urinary microbes in women with RUTI. Refined assessments of clinical profiles may provide useful insights that could inform diagnostic and therapeutic considerations.

Urinary microbiota of women with recurrent urinary tract infection: collection and culture methods.

Many clinicians utilize standard culture of voided urine to guide treatment for women with recurrent urinary tract infections (RUTI). However, despite antibiotic treatment, symptoms may persist and events frequently recur. The cyclic nature and ineffective treatment of RUTI suggest that underlying uropathogens pass undetected because of the preferential growth of Escherichia coli. Expanded quantitative urine culture (EQUC) detects more clinically relevant microbes. The objective of this study was to assess how urine collection and culture methods influence microbial detection in RUTI patients. This cross-sectional study enrolled symptomatic adult women with an established RUTI diagnosis. Participants contributed both midstream voided and catheterized urine specimens for culture via both standard urine culture (SUC) and EQUC. Presence and abundance of microbiota were compared between culture and collection methods. Forty-three symptomatic women participants (mean age 67years) contributed specimens. Compared to SUC, EQUC detected more unique bacterial species and consistently detected more uropathogens from catheterized and voided urine specimens. For both collection methods, the most commonly detected uropathogens by EQUC were E. coli (catheterized: n = 8, voided: n = 12) and E. faecalis (catheterized: n = 7, voided: n = 17). Compared to catheterized urine samples assessed by EQUC, SUC often missed uropathogens, and culture of voided urines by either method yielded high false-positive rates. In women with symptomatic RUTI, SUC and assessment of voided urines have clinically relevant limitations in uropathogen detection. These results suggest that, in this population, catheterized specimens analyzed via EQUC provide clinically relevant information for appropriate diagnosis.

A prospective study on the pathogenesis of catheter-associated bacteriuria in critically ill patients

BackgroundUpdating the pathogenesis of catheter-associated bacteriuria (CA-bacteriuria) in the intensive care unit (ICU) is needed to adapt prevention strategies. Our aim was to determine whether the main pathway of CA-bacteriuria in ICU patients was endoluminal or exoluminal.In a prospective study, quantitative urine cultures were sampled from catheter sampling sites, collector bags and the catheter outer surface near the meatus from days 1 to 15 after catheterization. The endoluminal pathway was CA-bacteriuria (defined as 102 CFU/mL) first in collector bags and then in catheters. The exoluminal pathway was CA-bacteriuria first in catheters, on day 1 in early cases and after day 1 in late cases.ResultsOf 64 included patients, 20 had CA-bacteriuria. Means of catheterization days and incidence density were 6.81 days and 55.2/1000 catheter-days. Of 26 microorganisms identified, 12 (46.2%) were Gram positive cocci, 8 (30.8%) Gram negative bacilli and 6 yeasts. Three (11.5%) CA-bacteriuria were endoluminal and 23 (88.5%) exoluminal, of which 10 (38.5%) were early and 13 (50%) late. Molecular comparison confirmed culture findings. A quality audit showed good compliance with guidelines.ConclusionThe exoluminal pathway of CA-bacteriuria in ICU patients predominated and surprisingly occurred early despite good implementation of guidelines. This finding should be considered in guidelines for prevention of CA-bacteriuria.

English

BACKGROUND Urinary tract Infection (UTI) are the most common clinical conditions in general practice and gynaecological department. Men and women of all age groups are affected by UTI, but its overall prevalence is higher in women. The major causative agents are Escherichia coli and other Enterobacteriaceae. In majority of the cases, empirically treatment is started with antimicrobials before the urine culture and sensitivity reports become available. This has led to an increase in antibiotic resistance in urinary pathogens. Hence, the present study was undertaken to determine the antimicrobial susceptibility pattern of uropathogens to commonly used antimicrobials in treating UTIs. METHODS A total of 200 urine samples were obtained from patients with signs and symptoms suggestive of UTIs attending Bapuji and Chigateri General Hospital which are attached to Jagadguru Jayadeva Murugarajendra Medical College (JJMMC), Davangere for a period of 3 months that is from May 2016 to July 2016. Urine samples were processed within 2 hours of reaching the laboratory. Semi quantitative urine culture was done. Isolation and identification were done by performing standard biochemical tests and the antimicrobial susceptibility testing was done using the standard disc diffusion method by Kirby-Bauer technique. RESULTS There were 170 urinary isolates from 200 samples. Children less than 10 years were more affected 54 (27 %). Female patients were more, 119 (59.5 %) compared to males 81 (40.5 %). Escherichia coli was the most predominant isolate, 71 (41.8 %) followed by Enterococcus species 22 (1.9 %). Organisms were resistant to commonly used antibiotics i.e., cotrimoxazole, ciprofloxacin, norfloxacin and amoxicillin. Both gram negative and gram-positive isolates were sensitive to amikacin and nitrofurantoin. CONCLUSIONS In present study Escherichia coli is the predominant pathogen. Uncomplicated UTIs can be empirically treated by nitrofurantoin. Occurrence of treatment failure with commonly used antimicrobials is more often in Indian setting. Hence, antimicrobial susceptibility testing must be employed routinely. KEY WORDS UTIs, Uropathogens, E. coli, Antimicrobial Susceptibility Pattern

A New Gold Rush: A Review of Current and Developing Diagnostic Tools for Urinary Tract Infections.

Urinary tract infections (UTIs) are one of the most common infections in the United States and consequently are responsible for significant healthcare expenditure. The standard urine culture is the current gold standard for diagnosing urinary tract infections, however there are limitations of the test that directly contribute to increased healthcare costs. As a result, new and innovative techniques have been developed to address the inefficiencies of the current standard—it remains to be seen whether these tests should be performed adjunctly to, or perhaps even replace the urine culture. This review aims to analyze the advantages and disadvantages of the newer and emerging diagnostic techniques such as PCR, expanded quantitative urine culture (EQUC), and next generation sequencing (NGS).

Risk factors for urinary bacterial growth in dogs with congenital portosystemic shunts: 66 cases (1997-2019).

To identify risk factors for urinary bacterial growth in dogs with confirmed congenital portosystemic shunts on which a quantitative urine culture was performed. Sixty-six dogs were included in this retrospective cross-sectional study. Medical records were reviewed from 1997 through 2019. Variables of interest included age, sex and sexual status, clinical signs for a urinary tract infection, blood urea concentration, urinalysis abnormalities, ultrasound abnormalities of the urinary tract, and previous treatment. Univariable and multivariable analyses were performed. The median age of the dogs was one year (range: 0.2-11.0 years). Urinary tract ultrasound abnormalities (cystic calculi and cystic debris) were reported in 50 dogs (75.7%). Abnormalities on urinalysis included pyuria in nine dogs (13.6%), bacteriuria in 13 dogs (19.7%), and haematuria in 26 dogs (39.4%). The median urine specific gravity was 1.021 (range: 1.004-1.052). Sixteen dogs (24.2%) had a positive quantitative urine culture. Based on multivariable analysis, bacteriuria (Odds ratio, 116; 95% CI, 9.6-1393; P=< 0.001) was the only variable significantly associated with a significantly increased odds for a positive quantitative urine culture. Clinical and subclinical bacteriuria can occur in dogs with congenital portosystemic shunts. In this group of dogs, bacteriuria was a risk factor for urinary bacterial growth.

Culture-Dependent and Sequencing Methods Revealed the Absence of a Bacterial Community Residing in the Urine of Healthy Cats.

A growing number of studies suggest that the lower urinary tract of humans and dogs can harbor a urinary microbiota. Nevertheless, a certain concern has developed that the microbiota reported could be due to unaccounted contamination, especially in low-biomass samples. The aim of this study was to investigate the bacterial community which populates the urine of healthy cats using two approaches: a culture-dependent approach which consisted of the expanded quantitative urine culture (EQUC) techniques capable of identifying live bacteria not growing in standard urine cultures, and a culture-independent approach which consisted of 16S ribosomal RNA next generation sequencing (16S rRNA NGS) capable of identifying bacterial DNA and exploring microbial diversity with high resolution. To avoid confounding factors of possible bacterial contamination, the urine was sampled using ultrasound-guided cystocentesis, and several sample controls and negative controls were analyzed. The urine sampled from the 10 cats included in the study showed no bacterial growth in the EQUC procedure. Although several reads were successfully originated using 16S rRNA NGS, a comparable pattern was observed between urine samples and the negative control, and no taxa were statistically accepted as non-contaminant. Taken together, the results obtained allowed stating that no viable bacteria were present in the urine of healthy cats without lower urinary tract disease and urinary tract infections, and that the bacterial DNA detected was of contaminant origin.

Let’s Explore: Predictive Ability of Urinalysis for Diagnosis of Urinary Tract Infection in CKD Patients

Background: Immuno-compromised Chronic Kidney Disease (CKD) patients are more vulnerable to infection. Among all infections, Urinary Tract Infection (UTI) is the main culprit of increased morbidity and mortality. So to combat this and to retard disease progression, control of UTI is a prime concern for this group of patients. Quantitative urine culture is the 'gold standard' method for definitive diagnosis of urinary-tract infections, but it is intensively time and labor consuming. For initiating early empirical treatment even in absence of localizing symptoms, the same day result is very helpful. Culture may lead to delaying of diagnosis. The microscopy of urine thus may be an essential tool for the diagnosis of patients with urinary tract infections. The aim of this study was to evaluate the diagnostic performance of the common urinalysis parameters in comparison to urine culture as the reference method.&#x0D; Materials and methods: We evaluated 1000 urine samples, submitted for urine analysis and culture admitted in Nephrology ward, Chattogram Medical College Hospital, a large tertiary care hospital for one year from 1st January 2017 to 31st December 2017. A cross-sectional study was done. Different Cut-off values were determined from different studies obtained by comparing the results with urine cultures. The test characteristics by the sensitivity, specificity, PPV and NPV were calculated for bacteria and White Blood Cells (WBCs) Red Blood Cells (RBC) glucose in urine and albuminuria. A practical diagnostic threshold of bacteriuria was determined. The diagnostic performance of culture was compared with different parameters of urinalysis.&#x0D; Results: Among the 1000 urine specimens submitted for culture, 618 cultures (61.8%) were positive, and 382 were (38.2%) negative. The cut-off value for pyuria was determined ³10 pus cell/HPF and compared for bacteriuria (Sensitivity: 69%, specificity: 36%, PPV: 64%, NPV: 42%) and presence of sugar and albumin in urine were found associated significantly with culture positivity at 95% CI (Sensitivity: 15%, specificity: 90%, PPV: 70%, NPP: 39% and sensitivity: 97%, specificity: 6%, PPV: 62%, NPP: 59%) respectively. And association between RBC and pus cell in urine microscopy was significant.&#x0D; Conclusions: UTI is a common infection in CKD patients with high incidence. Though culture is the gold standard, but urinalysis by cell count for pyuria, dipsticks for the presence of sugar or albumin may be helpful to diagnose UTI. The association of these all characteristics with growth in culture was statistically significant.&#x0D; JCMCTA 2020 ; 31 (1) : 26-30

Bladder bacterial diversity differs in continent and incontinent women: a cross-sectional study

Since the discovery of the bladder microbiome (urobiome), interest has grown in learning whether urobiome characteristics have a role in clinical phenotyping and provide opportunities for novel therapeutic approaches for women with common forms of urinary incontinence. This study aimed to test the hypothesis that the bladder urobiome differs among women in the control cohort and women affected by urinary incontinence by assessing associations between urinary incontinence status and the cultured urobiome. With institutional review board oversight, urine specimens from 309 adult women were collected through transurethral catheterization. These women were categorized into 3 cohorts (continent control, stress urinary incontinence [SUI], and urgency urinary incontinence [UUI]) based on their responses to the validated Pelvic Floor Distress Inventory (PFDI) questionnaire. Among 309 women, 150 were in the continent control cohort, 50 were in the SUI cohort, and 109 were in the UUI cohort. Symptom severity was assessed by subscale scoring with the Urinary Distress Inventory (UDI), subscale of the Pelvic Floor Distress Inventory. Microbes were assessed by expanded quantitative urine culture protocol, which detects the most common bladder microbes (bacteria and yeast). Microbes were identified to the species level by matrix-assisted laser desorption and ionization time-of-flight mass spectrometry. Alpha diversity indices were calculated for culture-positive samples and compared across the 3 cohorts. The correlations of UDI scores, alpha diversity indices, and species abundance were estimated. Participants had a mean age of 53 years (range 22-90); most were whites (65%). Women with urinary incontinence were slightly older (control, 47; SUI, 54; UUI, 61). By design, UDI symptom scores differed (control, 8.43 [10.1]; SUI, 97.95 [55.36]; UUI, 93.71 [49.12]; P<.001). Among 309 participants, 216 (70%) had expanded quantitative urine culture-detected bacteria; furthermore, the urinary incontinence cohorts had a higher detection frequency than the control cohort (control, 57%; SUI, 86%; UUI, 81%; P<.001). In addition, the most frequently detected species among the cohorts were as follows: continent control, Lactobacillus iners (12.7%), Streptococcus anginosus (12.7%), L crispatus (10.7%), and L gasseri (10%); SUI, S anginosus (26%), L iners (18%), Staphylococcus epidermidis (18%), and L jensenii (16%); and UUI, S anginosus (30.3%), L gasseri (22%), Aerococcus urinae (18.3%), and Gardnerella vaginalis (17.4%). However, only Actinotignum schaalii (formerly Actinobaculum schaalii), A urinae, A sanguinicola, and Corynebacterium lipophile group were found at significantly higher mean abundances in 1 of the urinary incontinence cohorts when compared with the control cohort (Wilcoxon rank sum test; P<.02), and no individual genus differed significantly between the 2 urinary incontinence cohorts. Both urinary incontinence cohorts had increased alpha diversity similar to continent control cohort with indices of species richness, but not evenness, strongly associated with urinary incontinence. In adult women, the composition of the culturable bladder urobiome is associated with urinary incontinence, regardless of common incontinence subtype. Detection of more unique living microbes was associated with worsening incontinence symptom severity. Culturable species richness was significantly greater in the urinary incontinence cohorts than in the continent control cohort.

Assessment of asymptomatic bacteriuria and sterile pyuria among antenatal attendants in hospitals in northern Ghana

BackgroundAsymptomatic bacteriuria (ASB) and sterile pyuria (SP) are complexities of UTI whose prevalence are not known in the northern sector of Ghana. Our aim was to determine the occurrence of sterile pyuria and asymptomatic bacteriuria among pregnant women accessing antenatal care at a secondary and tertiary care hospitals in Tamale, northern Ghana.MethodsA cross sectional study was conducted by screening 530 pregnant women with no signs of acute urinary tract infection attending antenatal clinic for a period of 6 months. Midstream urine was collected for microscopy, quantitative urine culture and antibiotic susceptibility testing. Data analysis was carried out using the Statistical Package for Social Sciences version 20.ResultsAsymptomatic bacteriuria was respectively 20 and 35.5% at Tamale Central and Tamale Teaching Hospital out of the 390 and 90 women screened. Sterile pyuria was found among 66% of the 50 women presenting at Tamale Central Hospital. More than 64% of isolates recovered from ASB patients were S. aureus and coagulase negative Staph. (CoNS). Escherichia coli was the dominant species among members of the enterobacteriaceae isolated. Highest susceptibility was recorded against gentamicin and amikacin while most resistance was to Ampicillin, cotrimoxazole, chloramphenicol and nitrofurantoin. Resistance to imipenem and vancomycin were 28.8 and 52%, with strains showing multiple drug resistance of between 81 and 92%.ConclusionThe prevalence of asymptomatic bacteriuria is appreciably higher (20–35.5%) than documented rates in the southern sector of the country. The presence of sterile pyuria which may be an indication of asymptomatic renal impairment and most often overlooked in antenatal management is 66%. Empirical treatment of UTIs at the Tamale Central and Teaching Hospital without confirmation of susceptibility may result in treatment failure. It is necessary to screen and treat pregnant women for ASB and SP due to the complications associated with these conditions.

Cultivable Bacteria in Urine of Women With Interstitial Cystitis: (Not) What We Expected.

Multiple studies show cultivatable bacteria in urine of most women. The existence of these bacteria challenges interstitial cystitis (IC)/painful bladder syndrome (PBS) diagnosis, which presumes a sterile bladder. The aims of this study were (1) to compare the female bladder microbiomes in women with IC/PBS and unaffected controls and (2) to correlate baseline bladder microbiome composition with symptoms. This cross-sectional study enrolled 49 IC/PBS and 40 controls. All provided catheterized urine samples and completed validated questionnaires. A subset of the IC/PBS cohort provided voided and catheterized urine samples. All samples from both cohorts were assessed by the expanded quantitative urine culture (EQUC) protocol; a subset was assessed by 16S rRNA gene sequencing. Of the IC/PBS cohort, 49.0% (24/49) were EQUC positive; in these EQUC-positive samples, the most common urotypes were Lactobacillus (45.8%) and Streptococcus (33.3%). Of the controls, 40.0% were EQUC positive; of these EQUC-positive samples, the most common urotype was Lactobacillus (50.0%). The urotype distribution was significantly different (P < 0.05), as 16% of the IC/PBS cohort, but 0% of controls, were Streptococcus urotype (P < 0.01). Symptom-free IC/PBS participants were less likely to be EQUC positive (12.5%) than IC/PBS participants with moderate or severe symptoms (68.8% and 46.2%) and the control cohort (60%; P < 0.05). Lactobacillus was the most common urotype. However, the presence of Lactobacillus did not differ between cohorts, and it did not impact IC/PBS symptom severity. Bacteria were not isolated from most participants with active IC/PBS symptoms. These findings suggest that bacteria may not be an etiology for IC/PBS.

The Urethral Microbiota: A Missing Link in the Female Urinary Microbiota.

We examined the urethral microbiota, determined if it differs from the bladder urinary microbiota, and assessed if its composition differs based on patient demographic factors and presence of lower urinary tract symptoms. Patients presenting to our urogynecology clinic were enrolled in the study. Demographic information and responses to the Pelvic Floor Distress Inventory questionnaire were collected. All participants provided midstream voided urine, periurethral swab, transurethral swab and catheterized urine samples, which were analyzed by Expanded Quantitative Urine Culture and MALDI-TOF mass spectrometry. Bray-Curtis dissimilarity analysis assessed diversity between sample types for each participant. Kruskal-Wallis, chi-square, McNemar, Wilcoxon signed rank and Fisher's exact tests tested for significance. A total of 49 patients participated in the study. Bladder microbiota were dissimilar to urethral, periurethral and voided urine microbiota (p <0.0001). Urethral and periurethral microbiota were similar (p >0.05), but the urethral microbiota were dissimilar to voided urine microbiota (p=0.001) while the periurethral microbiota were not (p >0.05). Women less than 55 years old were more likely to be sexually active, premenopausal and Hispanic compared to women 55 years old or older. Women in the younger cohort had Lactobacillus and Gardnerella cultured from urethral samples more frequently and more abundantly than women in the older cohort. There was no significant association between lower urinary tract symptoms and the frequency or abundance of urethral bacteria species. Niches of microbiota along the female lower urinary tract may be influenced by age, menopausal status and sexual activity. More research is needed to determine the function and clinical significance of the urethral microbiome.

Characteristics associated with bacterial growth in urine in 451 proteinuric dogs (2008-2018).

BackgroundUrine cultures are frequently recommended to rule out infection as a postrenal cause of proteinuria.ObjectiveIdentify characteristics associated with bacterial growth in urine in proteinuric dogs.AnimalsFour hundred and fifty‐one dogs admitted to a teaching hospital between January 2008 and January 2018 with urine protein‐to‐creatinine ratios (UPCs) >0.5.MethodsRetrospective study included dogs with a UPC, urinalysis, and quantitative urine culture (QUC) performed within a 72‐hour period by searching electronic records. Dogs with recent antimicrobial therapy, urine collected by methods other than cystocentesis, or UPC ≤0.5 were excluded. Signalment, comorbidities, serum BUN and creatinine concentrations, urinalysis findings, and QUC results were recorded. The association between these characteristics and presence of bacterial growth in urine was assessed by univariable and multivariable analysis.ResultsThirty of four hundred fifty‐one dogs (6.7%) had bacterial growth in urine. Of these, 18 (60.0%) had active urine sediment. Bacterial growth in urine was associated with pyuria (odd ratio [OR] 25.1, 95% confidence interval [CI] 7.9‐79.6, P < .001), bacteriuria (OR 11.1, 95% CI 3.2‐39.1, P < .001), and lower urinary tract disease (OR 6.7, 95% CI 1.9‐23.0; P = .0028). If QUC was prompted based on these criteria, 8/451 (1.8%) of proteinuric dogs would have had undetected bacterial growth.Conclusions and Clinical ImportanceThe proportion of proteinuric dogs with both inactive urine sediment and bacterial growth in urine was low, suggesting that QUC might not be necessary in the evaluation of all proteinuric dogs. An active urine sediment or lower urinary tract disease should prompt QUC for proteinuric dogs.

Utility of DNA Next-Generation Sequencing and Expanded Quantitative Urine Culture in Diagnosis and Management of Chronic or Persistent Lower Urinary Tract Symptoms.

Many patients suffer from chronic, irritative lower urinary tract symptoms (LUTS). The evaluation and management of these patients have proven difficult with the use of standard diagnostic tools, including urinalysis and urine culture. The growing body of literature on the urinary microbiome has looked at the possible implications of the bladder microbiome and dysbiosis, or perturbations in the microbiome, in conditions associated with chronic LUTS. Disorders such as recurrent urinary tract infections (UTIs) and interstitial cystitis have been studied utilizing 16S rRNA rapid next-generation gene sequencing (NGS) and expanded quantitative urine culture (EQUC). In this article, we first present a brief review of the literature describing the current understanding of the urinary microbiome and the features and applications of NGS and EQUC. Next, we discuss the conditions most commonly associated with chronic, persistent LUTS and present the limitations of current diagnostic practices utilized in this patient population. We then review the limited data available surrounding treatment efficacy and clinical outcomes in patients who have been managed based on results provided by these two recently established diagnostic tools (DNA NGS and/or EQUC). Finally, we propose a variety of clinical scenarios in which the use of these two techniques may affect patients' clinical outcomes.

The prevalence of positive urine cultures in 100 dogs with an inactive urine sediment

Objective: The purpose of this study was to determine the prevalence of positive quantitative urine cultures in dogs with an inactive urine sediment.&#x0D; Background: A urinalysis is a useful screening tool for the evaluation of evidence of bacterial cystitis and a quantitative urine culture is used for definitive diagnosis.&#x0D; Evidentiary value: A retrospective chart review from June 2012 to December 2017 at three private practice emergency and specialty referral hospitals examined urine samples obtained from 100 client-owned dogs.&#x0D; Methods: The signalment and clinicopathologic data was recorded for all canine patients that had urine samples obtained by cystocentesis that had an inactive sediment exam on urinalysis and subsequent quantitative urine cultures were performed.&#x0D; Results: The prevalence of positive quantitative urine cultures in all dogs with an inactive urine sediment at the aforementioned institutions was 6% (6/100). Escherichia coli was the most commonly isolated bacteria.&#x0D; Conclusion: Given the low prevalence of positive quantitative urine cultures in dogs with an inactive urine sediment and current guideline recommendations for management of subclinical bacteriuria, we do not recommend urine cultures for dogs without lower urinary tract signs. Further prospective study of patient subgroups, as well as controlled studies evaluating urine sample handling techniques using methods available to private practice practitioners are sorely needed.&#x0D; Application: Emergency and general practicing veterinarians should consider a quantitative urine culture for dogs with lower urinary tract signs, even with an inactive sediment examination, and on a case-by-case basis for dogs with pertinent systemic diseases or known risk factors for bacterial cystitis.&#x0D; &#x0D;