Multiplex PCR Based Urinary Tract Infection (UTI) Analysis Compared to Traditional Urine Culture in Identifying Significant Pathogens in Symptomatic Patients

Concanavalin A-assisted multiplex digital PCR assay for rapid capture and accurate quantification detection of foodborne pathogens

Multiplex, sensitive, and rapid detection of pathogens is crucial for ensuring food safety and safeguarding human health, however, it remains a significant challenge. This study proposes a concanavalin A-assisted multiplex digital amplification (CAMDA) assay for simultaneous quantitative detection of multiple foodborne bacteria. The CAMDA assay enables the simultaneous detection of six foodborne pathogens within 1.1 h and the limit of detection is 101 CFU/mL. Furthermore, the CAMDA assay exhibits high specificity, with a rate of 97 % for Bacillus cereus and 100 % for other pathogens tested in this study. Moreover, practical application validation using eight milk powder samples demonstrates that the accuracy of the CAMDA assay reaches 100 % when compared to qPCR results. Therefore, our developed CAMDA assay holds great potential for accurate and rapid detection of multiple pathogens in complex food matrices while also promoting the utilization of microfluidic chips in food investigation.

The Application of Next-Generation Sequencing in Preoperative Evaluation for Urologic Stone Surgery

Introduction: Next-generation sequencing (NGS) is a new molecular technique for identifying microorganisms. Treating bacteriuria in patients undergoing stone removal procedures is important for preventing postoperative urinary tract infection (UTI). The objective of this study is to assess the usefulness of preoperative urine NGS testing by comparing NGS with standard urine culture in predicting postoperative UTI after ureteroscopic lithotripsy (URSL) and percutaneous nephrolithotomy (PCNL). Materials and Methods: This prospective study was conducted from February 16, 2022, to January 11, 2024. Sixty subjects who underwent URSL or PCNL were included. Preoperative voided urine samples were collected for urine culture and tested by MicroGenDX for urine polymerase chain reaction (PCR) and urine NGS. Stone specimens obtained intraoperatively were also sent for stone culture and MicrogenDx. Patients were monitored for 4 weeks post-operation for recording clinical outcomes related to infections and complications. Results: Twenty-six (43.3%) male and 34 (56.7%) female participants were included. Twenty-six (43.3%) patients underwent PCNL (15 standard PCNL and 11 mini PCNL), and 34 (56.7%) underwent URSL. Standard urine culture identified positive results in 26 cases (43.3%), PCR for 17 cases (28.3%), and NGS for 31 cases (51.7%). The overall postoperative UTI rate was 6 (10%). Standard urine culture demonstrated a sensitivity of 50%, specificity of 57.4%, and accuracy of 56.7%. Positive predictive value (PPV) was notably poor at 11.5%. Urine NGS showed a higher sensitivity of 83.3%, specificity of 53.7%, accuracy of 55%, and PPV of 16.7%. Conclusion: Urine NGS significantly improves the sensitivity of detecting microorganisms in preoperative urine compared with standard urine culture. Despite its high sensitivity and capability to identify nonculturable bacteria, using NGS alongside standard urine culture is recommended. This parallel approach harnesses the strengths of both methods. Integrating NGS into standard practice could elevate the quality of care, especially for patients at high risk of UTIs, such as those undergoing invasive stone removal procedures.

The Urinary Microbiome: Improving Diagnostics and Management of Urinary Tract Infections in Adult Females

This article discusses the urinary microbiome in relation to urinary tract infection (UTI) in women. It makes biologic sense that the microbiota of different niches (bladder, vagina, and gut) interact with each other in health, as well as during a UTI event; however, these relationships remain poorly understood. Future research should close knowledge gaps regarding the interactions between the urinary microbiota and the host, amongst the microbiota of adjacent niches, and between the microbes within the same microbiota. The new knowledge should result in improved UTI treatment in the age of antibiotic stewardship.

Rapid Molecular Testing for UTIs: A Diagnostic Stewardship Perspective

With increased focus on antimicrobial stewardship in post-acute, long-term care (PALTC) settings, optimization of diagnostic testing is essential. Molecular diagnostics are currently being offered and used for the diagnosis of urinary tract infections (UTIs) in community and PALTC settings. Yet, no studies to date explore the role of rapid diagnostics such as polymerase chain reaction and other molecular methods in the stewardship efforts of PALTC settings, specifically compared with standard testing with urinalysis and culture with antimicrobial susceptibility testing. This article outlines a framework of diagnostic stewardship to critically evaluate the use of molecular diagnostics for the diagnosis of UTIs in PALTC and the impact on patient outcomes and antimicrobial stewardship. The authors suggest a 5-step process for evaluating the role of novel diagnostics in the PALTC setting. Understanding the shortcomings of newer diagnostic tests may identify needs for further investigation before their widespread use.

Comparison of polymerase chain reaction and next-generation sequencing with conventional urine culture for the diagnosis of urinary tract infections: A meta-analysis

The limitations of conventional urine culture methods can be avoided by using culture-independent approaches like polymerase chain reaction (PCR) and next-generation sequencing (NGS). However, the efficacy of these approaches in this setting is still subject to contention. PRISMA-compliant searches were performed on MEDLINE/PubMed, EMBASE, Web of Sciences, and the Cochrane Database until March 2023. The included articles compared PCR or NGS to conventional urine culture for the detection of urinary tract infections (UTIs). RevMan performed meta-analysis, and the Cochrane Risk of Bias Assessment Tool assessed study quality. A total of 10 selected studies that involved 1,291 individuals were included in this meta-analysis. The study found that PCR has a 99% sensitivity and a 94% specificity for diagnosing UTIs. Furthermore, NGS was shown to have a sensitivity of 90% for identifying UTIs and a specificity of 86%. The odds ratio (OR) for PCR to detect Gram-positive bacteria is 0.50 (95% confidence interval [CI] 0.41-0.61), while the OR for NGS to detect Gram-negative bacteria is 0.23 [95% CI 0.09-0.59]. UTIs are typically caused by Gram-negative bacteria like Escherichia coli and Gram-positive bacteria like Staphylococci and Streptococci. PCR and NGS are reliable, culture-free molecular diagnostic methods that, despite being expensive, are essential for UTI diagnosis and prevention due to their high sensitivity and specificity.

Antibiotics prophylaxis at the time of catheter removal after radical prostatectomy: a systematic review of the literature and meta-analysis

PURPOSE

To conduct a systematic literature review with meta-analysis to identify whether antibiotic prophylaxis after removal of the indwelling urinary catheter reduces posterior infections.

METHODS

A systematic literature review was conducted in the databases PubMed, Embase, Cochrane, Google Scholar, and Latin American and Caribbean Health Sciences Literature, using the keywords "antibiotics" AND "prostatectomy" AND "urinary catheter."

RESULTS

Three articles were identified having the scope of our review, with 1,040 patients, which were subjected to our meta-analysis revealing a marginally significant decrease in the risk of urinary infection after indwelling urinary catheter removal (odds ratio-OR = 0.51; 95% confidence interval-95%CI 0.27-0.98; p = 0.04; I2 = 0%). No difference was found regarding the presence of bacteriuria (OR = 0.39; 95%CI 0.12-1.24; p = 0.11; I2 = 73%).

CONCLUSIONS

In our meta-analysis, there was a significant decrease in urinary tract infection with antibiotic prophylaxis after indwelling urinary catheter removal following radical prostatectomy.

Urine biomarkers individually and as a consensus model show high sensitivity and specificity for detecting UTIs

BACKGROUND

Current diagnoses of urinary tract infection (UTI) by standard urine culture (SUC) has significant limitations in sensitivity, especially for fastidious organisms, and the ability to identify organisms in polymicrobial infections. The significant rate of both SUC "negative" or "mixed flora/contamination" results in UTI cases and the high prevalence of asymptomatic bacteriuria indicate the need for an accurate diagnostic test to help identify true UTI cases. This study aimed to determine if infection-associated urinary biomarkers can differentiate definitive UTI cases from non-UTI controls.

METHODS

Midstream clean-catch voided urine samples were collected from asymptomatic volunteers and symptomatic subjects ≥ 60 years old diagnosed with a UTI in a urology specialty setting. Microbial identification and density were assessed using a multiplex PCR/pooled antibiotic susceptibility test (M-PCR/P-AST) and SUC. Three biomarkers [neutrophil gelatinase-associated lipocalin (NGAL), and Interleukins 8 and 1β (IL-8, and IL-1β)] were also measured via enzyme-linked immunosorbent assay (ELISA). Definitive UTI cases were defined as symptomatic subjects with a UTI diagnosis and positive microorganism detection by SUC and M-PCR, while definitive non-UTI cases were defined as asymptomatic volunteers.

RESULTS

We observed a strong positive correlation (R2 > 0.90; p < 0.0001) between microbial density and the biomarkers NGAL, IL-8, and IL-1β for symptomatic subjects. Biomarker consensus criteria of two or more positive biomarkers had sensitivity 84.0%, specificity 91.2%, positive predictive value 93.7%, negative predictive value 78.8%, accuracy 86.9%, positive likelihood ratio of 9.58, and negative likelihood ratio of 0.17 in differentiating definitive UTI from non-UTI cases, regardless of non-zero microbial density. NGAL, IL-8, and IL-1β showed a significant elevation in symptomatic cases with positive microbe identification compared to asymptomatic cases with or without microbe identification. Biomarker consensus exhibited high accuracy in distinguishing UTI from non-UTI cases.

CONCLUSION

We demonstrated that positive infection-associated urinary biomarkers NGAL, IL-8, and IL-1β, in symptomatic subjects with positive SUC and/or M-PCR results was associated with definitive UTI cases. A consensus criterion with ≥ 2 of the biomarkers meeting the positivity thresholds showed a good balance of sensitivity (84.0%), specificity (91.2%), and accuracy (86.9%). Therefore, this biomarker consensus is an excellent supportive diagnostic tool for resolving the presence of active UTI, particularly if SUC and M-PCR results disagree.

The Prevalence and Association of Different Uropathogens Detected by M-PCR with Infection-Associated Urine Biomarkers in Urinary Tract Infections

Background

Many emerging uropathogens are currently identified by multiplex polymerase chain reaction (M-PCR) in suspected UTI cases. Standard urine culture (SUC) has significantly lower detection rates, raising questions about whether these organisms are associated with UTIs and truly cause inflammation.

Objective

To determine if microbes detected by M-PCR were likely causative of UTI by measuring inflammatory biomarkers in the urine of symptomatic patients.

Design Setting and Participants

Midstream voided urine was collected from subjects ≥60 years presenting to urology clinics with symptoms of UTI (n = 1132) between 01/2023 and 05/2023. Microbe detection was by M-PCR and inflammation-associated biomarker (neutrophil gelatinase-associated lipocalin, interleukin 8, and interleukin 1β) was by enzyme-linked immunosorbent assay. Biomarker positivity was measured against individual and groups of organisms, E. coli and non-E. coli cases, emerging uropathogens, monomicrobial and polymicrobial cases.

Outcome Measurements and Statistical Analysis

Distributions were compared using 2-sample Wilcoxon Rank Sum test with 2-tailed p-values < 0.05 considered statistically significant.

Results and Limitations

M-PCR was positive in 823 (72.7%) specimens with 28 of 30 (93%) microorganisms/groups detected. Twenty-six of twenty-eight detected microorganisms/groups (93%) had ≥2 biomarkers positive in >66% of cases. Both non-E. coli cases and E. coli cases had significant biomarker positivity (p < 0.05). Limitations were that a few organisms had low prevalence making inferences about their individual significance difficult.

Conclusion

The majority of microorganisms identified by M-PCR were associated with active inflammation measured by biomarker positivity, indicating they are likely causative of UTIs in symptomatic patients. This includes emerging uropathogens frequently not detected by standard urine culture.

Recurrent and complicated urinary tract infections in women: Utility of advanced testing to enhance care

BACKGROUND

The United States currently faces a public health crisis with regarding to antibiotic-resistant bacteria, and new urinary tract infection (UTI) diagnostics are needed. Women with recurrent UTI (rUTI) and complicated UTI (cUTI) are at particular risk given their complexity and the paucity of adequate testing modalities. The standard urine culture (SUC) is the cornerstone for diagnosis, but it has many shortcomings. These pitfalls lead to dissatisfaction and frustration among women afflicted with rUTI and cUTI, as well as overuse of antibiotics. One innovation is PCR UTI testing, which has been shown to outperform SUC among symptomatic women.

AIMS

This article discusses UTI PCR testing, as well as a possible role in clinical practice.

MATERIALS AND METHODS

Published literature was reviewed and summarized.

RESULTS

Management of rUTI and cUTI is complex, and providers should have all diagnostics available to facilitate providing optimal care. Urine PCR testing faces reimbursement issues despite fulfilling clinical indication parameters as described by insurance companies.

DISCUSSION

The role of UTI PCR testing remains unclear. Reimbursement issues have led to underuse and limited real-world outcomes reinforcing benefit.

CONCLUSION

This study proposes an algorithm for PCR testing among women with rUTI and cUTI.

Emerging and Fastidious Uropathogens Were Detected by M-PCR with Similar Prevalence and Cell Density in Catheter and Midstream Voided Urine Indicating the Importance of These Microbes in Causing UTIs

Introduction

This study compared microbial compositions of midstream and catheter urine specimens from patients with suspected complicated urinary tract infections to determine if emerging and fastidious uropathogens are infecting the bladder or are contaminants.

Methods

Urine was collected by in-and-out catheter (n = 1000) or midstream voiding (n = 1000) from 2000 adult patients (≥60 years of age) at 17 DispatchHealth sites across 11 states. The two groups were matched by age (mean 81 years), sex (62.1% female, 37.9% male), and ICD-10-CM codes. Microbial detection was performed with multiplex polymerase chain reaction (M-PCR) with a threshold for "positive detection" ≥ 10,000 cells/mL for bacteria or any detection for yeast. Results were divided by sex.

Results

In females, 28 of 30 microorganisms/groups were found by both collection methods, while in males 26 of 30 were found by both. There were significant overlaps in the detection and densities of classical uropathogens including Escherichia coli, Enterococcus faecalis, and Klebsiella pneumoniae, as well as emerging uropathogens including Actinotignum schaalii and Aerococcus urinae. In females, detection rates were slightly higher in midstream voided compared to catheter-collected (p = 0.0005) urine samples, while males showed the opposite trend (p < 0.0001). More polymicrobial infections were detected in midstream voided compared to catheter-collected samples (64.4% vs 45.7%, p < 0.0001) in females but the opposite in males (35.6% vs 47.0%, p = 0.002).

Discussion

In-and-out catheter-collected and midstream voided urine specimens shared significant similarities in microbial detections by M-PCR, with some differences found for a small subset of organisms and between sexes.

Conclusion

Non-invasive midstream voided collection of urine specimens for microbial detection and identification in cases of presumed UTI does not result in significantly more contamination compared to in-and-out catheter-collected specimens. Additionally, organisms long regarded as contaminants should be reconsidered as potential uropathogens.

Comparison Shows that Multiplex Polymerase Chain Reaction Identifies Infection-associated Urinary Biomarker-positive Urinary Tract Infections That Are Missed by Standard Urine Culture

Background

Multiplex polymerase chain reaction (M-PCR) has increased sensitivity for microbial detection compared with standard urine culture (SUC) in cases diagnosed as urinary tract infections (UTIs), leading to questions whether detected microbes are likely causative of UTIs or are incidental findings.

Objective

To compare infection-associated biomarker levels against M-PCR and SUC results in symptomatic cases with a presumptive diagnosis of a UTI by a urologist.

Design setting and participants

Participants were ≥60 yr old and presented to urology clinics between January and April 2023 with symptoms of UTIs (n = 583). Urine microbial detection was by M-PCR and SUC. Three infection-associated biomarkers (neutrophil gelatinase-associated lipocalin, interleukin-8, and interleukin-1β) were measured by enzyme-linked immunosorbent assay. Symptomatic cases with elevated biomarkers, detection of uropathogens, and a specialist clinical diagnosis of a UTI were considered definitive UTI cases.

Outcome measurements and statistical analysis

Distributions were compared using two-sample Wilcoxon rank sum test, with two-tailed p values of <0.05 considered statistically significant.

Results and limitations

In cases with M-PCR-positive/SUC-negative results (n = 80), all median biomarker levels were significantly higher (p < 0.0001) than in cases with M-PCR-negative/SUC-negative results (n = 107). Two or more biomarkers were positive in 76% of M-PCR-positive/SUC-negative specimens. Limitation was an inability to examine associations between each individual organism and inflammation.

Conclusions

A significant number of M-PCR-positive/SUC-negative cases had elevated levels of infection-related urinary biomarkers, especially when infection was caused by organisms other than Escherichia coli. This is a strong indication that microbes detected by M-PCR, which would be missed by SUC, are associated with UTIs.

Patient summary

We compared infection-associated biomarkers in patients diagnosed with urinary tract infections (UTIs) against the detection of microorganisms by standard urine culture (SUC) and multiplex polymerase chain reaction (M-PCR). We found that most patients with microorganisms detected by M-PCR, which were missed by SUC, had elevated markers of inflammation, indicating that these organisms were likely causative of UTIs.

A test combining multiplex-PCR with pooled antibiotic susceptibility testing has high correlation with expanded urine culture for detection of live bacteria in urine samples of suspected UTI patients

We evaluated whether multiplex polymerase chain reaction (M-PCR) detects viable micro-organisms by comparing micro-organism identification with standard urine culture (SUC) and expanded quantitative urine culture (EQUC). Of the 395 organisms detected by M-PCR, EQUC detected 89.1% (p = 0.10), whereas SUC detected 27.3% (p < 0.0001 vs. M-PCR and p < 0.0001 vs EQUC). M-PCR identified 260 nonfastidious bacteria, EQUC detected 96.5% (p = 0.68), whereas SUC detected 41.5% (p < 0.0001). Common nonfastidious bacteria missed by SUC included Escherichia coli (72.5% detected), Klebsiella pneumoniae (66.7% detected), Enterococcus faecalis (34.6% detected) and Enterococcus faecium (0% detected). M-PCR identified 135 fastidious bacteria and EQUC 101 (74.8%, p = 0.01), whereas SUC failed to detect any (0%, p < 0.0001). Clinical samples evaluated using EQUC and M-PCR yielded very similar findings, indicating that most microbes identified by M-PCR represented viable organisms, and validating M-PCR as a diagnostic tool for UTIs.

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

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

Patterns of Drug Resistance and Bacterial Pathogen Distribution in Patients with Urinary Tract Infections in the Jiaxing Region from 2020 to 2022

Background

Urinary tract infections (UTIs) and the antibiotic resistance of pathogenic bacteria pose severe threats to public health in the current healthcare environment.

Objective

The purpose of this study was to assess the frequency distribution of bacterial pathogens causing UTIs as well as the characteristics of antibiotic susceptibility and resistance.

Methods

The retrospective study was conducted on 32,391 samples of midstream urine culture from January 1, 2020, to December 31, 2022, in Jiaxing. Bacteria were cultivated on blood agar and identified using MALDI-TOF, and their susceptibility to different antibiotics was assessed using the Kirby-Bauer disk diffusion method and drug sensitivity reaction cards. The SPSS 22 software was used for data analysis. Bivariate logistic regression was used to analyze the risk factors for multidrug resistance.

Results

The total number of positive growth samples was 5378 (16.6%), including 3206 females (59.6%) and 2172 males (40.4%). The four most common urinary pathogens were Escherichia coli (39.2%), Enterococcus faecalis (12.4%), Klebsiella pneumoniae (7.6%), and Enterococcus faecium (7.6%). As far as antibiotic resistance was concerned, Escherichia coli had a greater than 50% resistance rate to ampicillin (76.1%), ciprofloxacin (58.6%), and levofloxacin (51.2%). The multidrug resistance rate was high (41.8%). Low levels of resistance were seen to ertapenem (0.1%), imipenem (0.7%), meropenem (0.7%), piperacillin/tazobactam (0.7%), and nitrofurantoin (1.8%). Klebsiella pneumoniae was highly sensitive to ertapenem (100%). The resistance rates to nitrofurantoin, ceftriaxone, and ciprofloxacin were 37.4%, 37.1%, and 35.1%, respectively. Up to 41% of Escherichia coli strains and 26% of Klebsiella pneumoniae strains produced extended-spectrum lactamases (ESBL). Two species of enterococci were highly sensitive to tigecycline and linezolid (100%), and a small number of norvancomycin-resistant strains (0.2%/two strains) were found.

Conclusion

Escherichia coli and Enterococcus faecium were the most common urinary pathogens in this study. The isolated pathogens showed different sensitivity patterns. Antibiotics should be selected reasonably according to the sensitivity mode of pathogenic bacteria to effectively treat and prevent urinary tract infections.

Elevated UTI Biomarkers in Symptomatic Patients with Urine Microbial Densities of 10,000 CFU/mL Indicate a Lower Threshold for Diagnosing UTIs

The literature lacks consensus on the minimum microbial density required for diagnosing urinary tract infections (UTIs). This study categorized the microbial densities of urine specimens from symptomatic UTI patients aged ≥ 60 years and correlated them with detected levels of the immune response biomarkers neutrophil gelatinase-associated lipocalin (NGAL), interleukin-8 (IL-8), and interleukin-1-beta (IL-1β). The objective was to identify the microbial densities associated with significant elevation of these biomarkers in order to determine an optimal threshold for diagnosing symptomatic UTIs. Biobanked midstream voided urine samples were analyzed for microbial identification and quantification using standard urine culture (SUC) and multiplex-polymerase chain reaction (M-PCR) testing, while NGAL, IL-8, and IL-1β levels were measured via enzyme-linked immunosorbent assay (ELISA). NGAL, IL-8, and IL-1β levels were all significantly elevated at microbial densities ≥ 10,000 cells/mL when measured via M-PCR (p < 0.0069) or equivalent colony-forming units (CFUs)/mL via SUC (p < 0.0104) compared to samples with no detectable microbes. With both PCR and SUC, a consensus of two or more elevated biomarkers correlated well with microbial densities > 10,000 cells/mL or CFU/mL, respectively. The association between ≥10,000 cells and CFU per mL with elevated biomarkers in symptomatic patients suggests that this lower threshold may be more suitable than 100,000 CFU/mL for diagnosing UTIs.

Quantitative multiplex polymerase chain reaction in copies ml-1 linearly correlates with standard urine culture in colonies ml-1 for urinary tract infection (UTI) pathogens

Standard urine culture (SUC) is the current standard method for confirmation of a urinary tract infection (UTI). SUC identifies microorganisms in urine samples and semi-quantifies these as colony-forming units (CFUs) ml-1. In contrast, quantitative multiplex polymerase chain reaction (q-MPCR) is a culture-independent assay in which the microbes are quantified by targeting genomic sequences and reported as cells ml-1, calculated from copies ml-1. Using serial dilutions within the 104-105 cells ml-1 range, the usual reporting range of SUC, this study compared the quantification results based on SUC and q-MPCR for four uropathogens with the control hemocytometer counts. The results revealed a linear relationship and a 1:1 correlation between the q-MPCR and SUC results. Additional q-MPCR quantification of 36 uropathogenic non-fastidious and fastidious bacteria and yeast indicated a reproducible linear correlation in a 1:1 manner with the control counts over a range of cell densities (103-106 cells ml-1). The results confirm that the quantifications by q-MPCR in cells ml-1 and by SUC in CFUs ml-1 are comparable and answer to the lingering question of how the results of these two methods correlate. Moreover, q-MPCR provided accurate quantification of various microorganisms over wider cell density ranges without the time required for microbial growth.

Study of antibiotic resistance and virulence genes in Escherichia coli isolated from urinary tract infection patients in Tanta University Hospitals

This study aimed to investigate the prevalence of antibiotic resistance genes CTX-M and Qnr, as well as the virulence genes HlyA, Pap, CNF1, and Afa, in uropathogenic Escherichia coli (UPEC) isolates from the Egyptian population. In this cross-sectional study, a total of 50 E. coli isolates were collected from urine samples from patients with urinary tract infections (UTIs) admitted to Tanta University Hospital from December 2020 to November 2021. The isolates were cultured, identified, and tested for antibiotic susceptibility by the disc diffusion method. The CTX-M, Qnr (QnrA, B, and S), Pap, CNF1, HlyA, and Afa genes were detected by polymerase chain reaction in UPEC isolates. The Pap, CNF1, HlyA, and Afa genes were found to be positive in 18%, 12%, 10%, and 2% of the isolates, respectively. In addition, CTX-M and QnrS were found to be positive in 44% and 8% of the isolates, while QnrA and B were not detected. Furthermore, positive Pap, CNF1, and HlyA genes were significantly associated with both upper and lower UTIs, increased frequency, urgency, and dysuria, and complicated UTIs, as well as pyuria over 100 white blood cells per high-power field. In conclusion, the prevalence of virulence and antibiotic resistance genes varies by population. At our hospital, the Pap gene is the most prevalent virulence gene and was strongly associated with complicated UTIs, while the CTX-M and QnrS genes were the most prevalent and related to antibiotic resistance. Our findings, however, should be interpreted with caution due to the small sample size.

Advantage of precision metagenomics for urinary tract infection diagnostics

Background

Urinary tract infections (UTIs) remain a diagnostic challenge and often promote antibiotic overuse. Despite urine culture being the gold standard for UTI diagnosis, some uropathogens may lead to false-negative or inconclusive results. Although PCR testing is fast and highly sensitive, its diagnostic yield is limited to targeted microorganisms. Metagenomic next-generation sequencing (mNGS) is a hypothesis-free approach with potential of deciphering the urobiome. However, clinically relevant information is often buried in the enormous amount of sequencing data.

Methods

Precision metagenomics (PM) is a hybridization capture-based method with potential of enhanced discovery power and better diagnostic yield without diluting clinically relevant information. We collected 47 urine samples of clinically suspected UTI and in parallel tested each sample by microbial culture, PCR, and PM; then, we comparatively analyzed the results. Next, we phenotypically classified the cumulative microbial population using the Explify® data analysis platform for potential pathogenicity.

Results

Results revealed 100% positive predictive agreement (PPA) with culture results, which identified only 13 different microorganisms, compared to 19 and 62 organisms identified by PCR and PM, respectively. All identified organisms were classified into phenotypic groups (0-3) with increasing pathogenic potential and clinical relevance. This PM can simultaneously quantify and phenotypically classify the organisms readily through bioinformatic platforms like Explify®, essentially providing dissected and quantitative results for timely and accurate empiric UTI treatment.

Conclusion

PM offers potential for building effective diagnostic models beyond usual care testing in complex UTI diseases. Future studies should assess the impact of PM-guided UTI management on clinical outcomes.

The Diagnosis of Urinary Tract Infections Using a Novel At-home Testing Protocol to Enhance Telemedicine: A Retrospective Analysis

OBJECTIVE

To retrospectively analyze a novel courier-based home urine collection strategy for patients with symptoms of urinary tract infections (UTIs). This model was developed to provide patient care using telehealth during the coronavirus 2019 pandemic.

METHODS

We analyzed data from 2206 patients with symptomatic UTIs to investigate the efficacy of a home urine collection protocol. The primary outcome was the impact of home versus office collection.

RESULTS

We analyzed the results of 1112 patient samples collected in-office and 1084 patient samples collected at home. There was no difference in the rate of bacterial identification between females in the office and home collection groups. However, males in the office collection group had a higher rate of bacterial identification (p = .002). The turnaround time was significantly faster in the home collection group than the office collection group (4.08 hours shorter, p < 0.0014). Antibiotic use prior to sample collection was significantly higher in the home collection group for both males (p = .0004) and females (p = .004). Changes in antibiotics were significantly higher in the home collection group than in the office collection group for both males (p = .0009) and females (p = .0006).

CONCLUSION

Our home collection protocol is a viable method to provide prompt and reliable outpatient care to urology patients suffering from UTIs. Furthermore, this approach resulted in adequate management and quicker turnaround times. Our findings demonstrate the clinical viability of a decentralized healthcare model to treat UTIs.

Within State Variability of Antimicrobial Susceptibility: Missouri as an Archetype to Assess Guidelines for Antimicrobial Prophylaxis for Transurethral Procedures

OBJECTIVE

To evaluate variability among hospitals in susceptibility of common uropathogens to antimicrobial agents frequently used in transurethral procedures in order to examine whether state-based guidelines might be more appropriate than national prophylactic guidelines.

METHODS

Hospital-level antibiograms were requested from all hospitals throughout the state of Missouri. We studied Escherichia coli, Klebsiella, and Proteus sensitivities to evaluate common guideline recommended antimicrobials including trimethoprim sulfamethoxazole (TMP-SMX), 3rd generation cephalosporins, cefazolin, penicillin combinations, gentamicin and fluoroquinolones. We evaluated variability and association between hospital characteristics and antimicrobial sensitivities.

RESULTS

Data was requested from 81 hospitals across the state and 38 provided the requested data (47% response rate). Susceptibility was highest for 3^rd generation cephalosporins for E coli (mean of 94%), Proteus (96%), and Klebsiella (96%). Gentamicin also had high susceptibility for the bacteria studied; 94% for E coli and 96% for Klebsiella. Current first line recommended agents showed more modest coverage for E coli (cefazolin 84%, TMP-SMX 78%), Proteus (cefazolin 82%, TMP-SMX 71%), and Klebsiella (cefazolin 90%, TMP-SMX 89%).

CONCLUSION

Post transurethral procedure infections are common. Rates can be limited with appropriate prophylaxis. Deciding on empirical coverage must take into account local resistance patterns. There is substantial variability among and within states in antimicrobial susceptibility for common uropathogens. When selecting antimicrobial prophylaxis, urologists should consider local- rather than state- or nation-level antibiograms, given the considerable variability. Future studies should consider the merits of very-broad spectrum prophylaxis and the potential role of molecular urinary pathogen (and pathogen-resistance) testing when selecting an optimal regimen.

A Diagnostic Test Combining Molecular Testing with Phenotypic Pooled Antibiotic Susceptibility Improved the Clinical Outcomes of Patients with Non-E. coli or Polymicrobial Complicated Urinary Tract Infections

Purpose

Complicated UTIs (cUTIs) cause significant morbidity and healthcare resource utilization and cost. Standard urine culture has limitations in detecting polymicrobial and non-E. coli infections, resulting in the under-diagnosis and under-treatment of cUTIs. In this study, patient-reported outcomes were compared between treated and untreated patients when an advanced diagnostic test combining multiplex-polymerase chain reaction (M-PCR) with a pooled antibiotic susceptibility method (P-AST) was incorporated into the patients' clinical management.

Methods

Patients who had symptoms typical of cUTI and positive M-PCR/P-AST test results were recruited from urology clinics. Symptom reduction and clinical cure rates were measured from day 0 through day 14 using the American English Acute Cystitis Symptom Score (ACSS) Questionnaire. Clinical cure was defined based on the sum of the scores of four US Food and Drug Administration (FDA) symptoms and the absence of visible blood in the urine.

Results

Of 264 patients with suspected cUTI, 146 (55.4%) had exclusively non-E. coli infections (115 treated and 31 untreated) and 190 (72%) had polymicrobial infections (162 treated and 28 untreated). Treated patients exhibited greater symptom reduction compared to untreated ones on day 14 for those with exclusively non-E. coli organisms (3.18 vs 1.64, p = 0.006) and polymicrobial infections (3.52 vs 1.41, p = 0.002), respectively. A higher percentage of treated patients than of untreated patients achieved clinical cure for polymicrobial infections on day 14 (58.7% vs 36.4%, p = 0.049).

Conclusion

Patients with cUTIs treated based on the M-PCR/P-AST diagnostic test had significantly improved symptom reduction and clinical cure rates compared to untreated patients among those with non-E. coli or polymicrobial infections.

Unmet Needs in Complicated Urinary Tract Infections: Challenges, Recommendations, and Emerging Treatment Pathways

While urinary tract infections (UTIs) are one of the most common types of infections globally, the wide variety of presentations and of severity of disease can make it difficult to manage. The definition for uncomplicated UTIs (uUTIs) is generally regarded as UTIs in healthy, non-pregnant women whereas all other UTIs are considered complicated. There is, however, a lack of consensus definition of complicated UTIs (cUTIs), leading to global differences in management. In addition, the patients who develop complicated UTIs generally have other comorbidities that warrant more urgent intervention. One of the biggest challenges in treating cUTIs is the rise of antimicrobial resistance (AMR). While there have been recent drug approvals for new antibiotic to treat these resistant organisms, a multidisciplinary approach, including regulatory frameworks, provider education and public awareness campaigns, is crucial to limiting unnecessary treatments for asymptomatic bacteriuria (ASB) and uUTIs that can ultimately lead to more severe infections.

Multiplex Polymerase Chain Reaction/Pooled Antibiotic Susceptibility Testing Was Not Associated with Increased Antibiotic Resistance in Management of Complicated Urinary Tract Infections

Objective

To compare antibiotic resistance results at different time points in patients with urinary tract infections (UTIs), who were either treated based upon a combined multiplex polymerase chain reaction (M-PCR) and pooled antibiotic susceptibility test (P-AST) or were not treated.

Methods

The M-PCR/P-AST test utilized here detects 30 UTI pathogens or group of pathogens, 32 antibiotic resistance (ABR) genes, and phenotypic susceptibility to 19 antibiotics. We compared the presence or absence of ABR genes and the number of resistant antibiotics, at baseline (Day 0) and 5-28 days (Day 5-28) after clinical management in the antibiotic-treated (n = 52) and untreated groups (n = 12).

Results

Our results demonstrated that higher percentage of patients had a reduction in ABR gene detection in the treated compared to the untreated group (38.5% reduction vs 0%, p = 0.01). Similarly, significantly more patients had reduced numbers of resistant antibiotics, as measured by the phenotypic P-AST component of the test, in the treated than in the untreated group (42.3% reduction vs 8.3%, p = 0.04).

Conclusion

Our results with both resistance gene and phenotypic antibiotic susceptibility results demonstrated that treatment based upon rapid and sensitive M-PCR/P-AST resulted in reduction rather than induction of antibiotic resistance in symptomatic patients with suspected complicated UTI (cUTI) in an urology setting, indicating this type of test is valuable in the management of these types of patients. Further studies of the causes of gene reduction, including elimination of ABR gene-carrying bacteria and loss of ABR gene(s), are warranted.

High Resistance to Antibiotics Recommended in Standard Treatment Guidelines in Ghana: A Cross-Sectional Study of Antimicrobial Resistance Patterns in Patients with Urinary Tract Infections between 2017-2021

Management of urinary tract infections is challenged by increasing antimicrobial resistance (AMR) worldwide. In this study, we describe the trends in antimicrobial resistance of uropathogens isolated from the largest private sector laboratory in Ghana over a five-year period. We reviewed positive urine cultures at the MDS Lancet Laboratories from 2017 to 2021. The proportions of uropathogens with antimicrobial resistance to oral and parenteral antimicrobials recommended by the Ghana standard treatment guidelines were determined. The proportion of multi-drug resistant isolates, ESBL and carbapenemase-producing phenotypes were determined. Of 94,134 urine specimens submitted for culture, 20,010 (22.1%) were culture positive. Enterobacterales was the most common group of organisms, E. coli (70.6%) being the most common isolate and Enterococcus spp. the most common gram-positive (1.3%) organisms. Among oral antimicrobials, the highest resistance was observed to ciprofloxacin (62.3%) and cefuroxime (60.2%) and the least resistance to fosfomycin (1.9%). The least resistance among parenteral antimicrobials was to meropenem (0.3%). The highest multi-drug resistance levels were observed among Klebsiella spp. (68.6%) and E. coli (64.0%). Extended-spectrum beta-lactamase (ESBL) positivity was highest in Klebsiella spp. (58.6%) and E. coli (50.0%). There may be a need to review the Ghana standard treatment guidelines to reflect increased resistance among uropathogens to recommended antimicrobials.

Forty Years of Molecular Diagnostics for Infectious Diseases

Nearly 40 years have elapsed since the invention of the PCR, with its extremely sensitive and specific ability to detect nucleic acids via in vitro enzyme-mediated amplification. In turn, more than 2 years have passed since the onset of the coronavirus disease 2019 (COVID-19) pandemic, during which time molecular diagnostics for infectious diseases have assumed a larger global role than ever before. In this context, we review broadly the progression of molecular techniques in clinical microbiology, to their current prominence. Notably, these methods now entail both the detection and quantification of microbial nucleic acids, along with their sequence-based characterization. Overall, we seek to provide a combined perspective on the techniques themselves, as well as how they have come to shape health care at the intersection of technologic innovation, pathophysiologic knowledge, clinical/laboratory logistics, and even financial/regulatory factors.

Molecular Diagnostic Methods Versus Conventional Urine Culture for Diagnosis and Treatment of Urinary Tract Infection: A Systematic Review and Meta-analysis

Context

Objective

Evidence acquisition

Evidence synthesis

Conclusions

Patient summary

Home urinary tract infection testing: patient experience and satisfaction with polymerase chain reaction kit

Introduction and hypothesis

We sought to evaluate patient satisfaction with a novel multiplex PCR UTI home collection kit for symptomatic UTI in a urogynecologic population. We secondarily sought to characterize reported uropathogens and resistance profiles of uropathogens in this population. We hypothesized that patients would be satisfied.

Methods

This was a cross-sectional study of women who were surveyed later about their experience undergoing evaluation for a UTI with a home UTI test at a large tertiary care urogynecology practice in 2020. Symptomatic patients were sent a home UTI kit. We assessed patient satisfaction at a later time with a 5-point Likert scale and collected baseline information. The primary outcome was patient satisfaction with this experience. Secondary outcomes included type and number of uropathogens on testing.

Results

A total of 30 patients [73% white race, mean age 71.9 (SD 12.0) years] were surveyed. Patients responded with a mean score of 4.7/5 to all satisfaction questions. Overall, 86% (26/30) of patients would choose this test again. Of those asked if they would choose this test again outside of the COVID-19 pandemic, 86% responded affirmatively. The most common symptoms reported included dysuria (53%), urgency (37%) and frequency (30%). The most common pathogens identified included Escherichia coli (70%), Enterococcus faecalis (60%) and Aerococcus urinae (43%).

Conclusions

Patients were satisfied with home UTI PCR testing and the majority would choose this option again. Home UTI PCR testing revealed common uropathogens for a population with a high proportion of recurrent UTI, but additional research comparing home versus in-office urine PCR testing is necessary.

Impact of different urinary tract infection phenotypes within the first year post-transplant on renal allograft outcomes

In this study, we investigated the clinical impact of different urinary tract infection (UTI) phenotypes occurring within the first year after renal transplantation. The population included 2368 transplantations having 2363 UTI events. Patients were categorized into four groups based on their compiled UTI events observed within the first year after transplantation: (i) no colonization or UTI (n = 1404; 59%), (ii) colonization only (n = 353; 15%), (iii) occasional UTI with 1-2 episodes (n = 456; 19%), and (iv) recurrent UTI with ≥3 episodes (n = 155; 7%). One-year mortality and graft loss rate were not different among the four groups, but patients with recurrent UTI had a 7-10 ml/min lower eGFR at year one (44 ml/min vs. 54, 53, and 51 ml/min; p < .001). UTI phenotypes had no impact on long-term patient survival (p = .33). However, patients with recurrent UTI demonstrated a 10% lower long-term death-censored allograft survival (p < .001). Furthermore, recurrent UTI was a strong and independent risk factor for reduced death-censored allograft survival in a multivariable analysis (HR 4.41, 95% CI 2.53-7.68, p < .001). We conclude that colonization and occasional UTI have no impact on pertinent outcomes, but recurrent UTI are associated with lower one-year eGFR and lower long-term death-censored allograft survival. Better strategies to prevent and treat recurrent UTI are needed.

Ratiometric PCR in a Portable Sample-to-Result Device for Broad-Based Pathogen Identification

Polymerase chain reaction (PCR)-based diagnostic testing is the gold standard method for pathogen identification (ID) with recent developments enabling automated PCR tests for point-of-care (POC) use. However, multiplexed identification of several pathogens in PCR assays typically requires optics for an equivalent number of fluorescence channels, increasing instrumentation's complexity and cost. In this study, we first developed ratiometric PCR that surpassed one target per color barrier to allow multiplexed identification while minimizing optical components for affordable POC use. We realized it by amplifying pathogenic targets with fluorescently labeled hydrolysis probes with a specific ratio of red-to-green fluorophores for each bacterial species. We then coupled ratiometric PCR and automated magnetic beads-based sample preparation within a thermoplastic cartridge and a portable droplet magnetofluidic platform. We named the integrated workflow POC-ratioPCR. We demonstrated that the POC-ratioPCR could detect one out of six bacterial targets related to urinary tract infections (UTIs) in a single reaction using only two-color channels. We further evaluated POC-ratioPCR using mock bacterial urine samples spiked with good agreement. The POC-ratioPCR presents a simple and effective method for enabling broad-based POC PCR identification of pathogens directly from crude biosamples with low optical instrumentation complexity.

Current and Future Molecular Diagnostics of Tick-Borne Diseases in Cattle

Ticks and tick-borne diseases such as babesiosis, anaplasmosis, ehrlichiosis, Lyme disease, Crimean Congo hemorrhagic fever, and Rocky Mountain spotted fever pose a significant threat to animal and human health. Tick-borne diseases cause billions of dollars of losses to livestock farmers annually. These losses are partially attributed to the lack of sensitive, robust, cost effective and efficient diagnostic approaches that could detect the infectious pathogen at the early stages of illness. The modern nucleic acid-based multiplex diagnostic approaches have been developed in human medicine but are still absent in veterinary medicine. These powerful assays can screen 384 patient samples at one time, simultaneously detect numerous infectious pathogens in each test sample and provide the diagnostic answer in a few hours. Development, commercialization, and wide use of such high throughput multiplex molecular assays in the cattle tick-borne disease surveillance will help in early detection and control of infectious pathogens in the animal reservoir before community spread and spillover to humans. Such approaches in veterinary medicine will save animal life, prevent billions of dollars of economic loss to cattle herders and reduce unwanted stress to both human and animal health care systems. This literature review provides recent updates on molecular diagnostics of tick-borne pathogens and discusses the importance of modern nucleic acid high throughput multiplex diagnostic approaches in the prevention of tick-borne infection to livestock.

Cross-sectional internet survey exploring women's knowledge, attitudes and practice regarding urinary tract infection-related symptoms in the Netherlands

OBJECTIVES

Urinary tract infections (UTIs) are the most prevalent cause for women to consult a general practitioner (GP) and are commonly treated with (broad-spectrum) empirical antibiotics, even though 50% of UTIs are self-limiting. In this study, we aim to explore women's attitudes and experiences regarding UTIs, in order to determine patients' willingness to accept delayed antibiotic prescriptions.

DESIGN

An internet-based cross-sectional survey SETTING: We recruited participants during 2 weeks of March and April in 2020 through several social media platforms.

PARTICIPANTS

We obtained 1476 responses, of which 975 were eligible for analysis.

RESULTS

We asked women about their knowledge, attitudes and practice regarding UTI-related symptoms. Participants ranked 'confirmation of diagnosis' (43.8%) as the most important reason to consult a GP with urinary symptoms, followed by 'pain relief' (32%), and 'antibiotic prescription' (14.3%). For treatment, 71% of participants reported that their GP prescribed immediate antibiotics, while only 3% received a delayed antibiotic prescription and 1% was advised pain medication. Furthermore, 50% of respondents were aware of the possible self-limiting course of UTIs and 70% would be willing to accept delayed antibiotic treatment, even if a certain diagnosis of UTI was established. Willingness to delay was lower in experienced patients compared to inexperienced patients.

CONCLUSIONS

Women are quite receptive to delayed antibiotics as an alternative to immediate antibiotics for UTIs or urinary symptoms. GPs should consider discussing delayed antibiotic treatment more often with women presenting with urinary symptoms.

Concordance Between Antibiotic Resistance Genes and Susceptibility in Symptomatic Urinary Tract Infections

PURPOSE

Studies have shown that multiple genes influence antibiotic susceptibility, but the relationship between genotypic and phenotypic antibiotic susceptibility is unclear. We sought to analyze the concordance between the presence of antibiotic resistance (ABR) genes and antibiotic susceptibility results in urine samples collected from patients with symptomatic urinary tract infection (UTI).

PATIENTS AND METHODS

Urine samples were collected from patients presenting to 37 geographically disparate urology clinics across the United States from July 2018 to February 2019. Multiplex polymerase chain reaction was used to detect 27 ABR genes. In samples containing at least one culturable organism at a concentration of ≥ 104 cells per mL, pooled antibiotic susceptibility testing (P-AST), which involves simultaneous growing all detected bacteria together in the presence of antibiotic and then measure susceptibility, was performed against 14 antibiotics. The concordance rate between the ABR genes and the P-AST results was generated for the overall group. The concordance rates for each antibiotic between monomicrobial and polymicrobial infection were compared using chi-square test.

RESULTS

Results from ABR gene detection and P-AST of urine samples from 1155 patients were included in the concordance analysis. Overall, there was a 60% concordance between the presence or absence of ABR genes and corresponding antimicrobial susceptibility with a range of 49-78% across antibiotic classes. Vancomycin, meropenem, and piperacillin/tazobactam showed significantly lower concordance rates in polymicrobial infections than in monomicrobial infections.

CONCLUSION

Given the 40% discordance rate, the detection of ABR genes alone may not provide reliable data to make informed clinical decisions in UTI management. However, when used in conjunction with susceptibility testing, ABR gene data can offer valuable clinical information for antibiotic stewardship.

Feasibility and potential significance of rapid in vitro qualitative phenotypic antimicrobial susceptibility testing of gram-negative bacilli with the ProMax system

The emergence and evolution of antibiotic resistance has been accelerated due to the widespread use of antibiotics and a lack of timely diagnostic tests that guide therapeutic treatment with adequate sensitivity, specificity, and antimicrobial susceptibility testing (AST) accuracy. Automated AST instruments are extensively used in clinical microbiology labs and provide a streamlined workflow, simplifying susceptibility testing for pathogenic bacteria isolated from clinical samples. Although currently used commercial systems such as the Vitek2 and BD Phoenix can deliver results in substantially less time than conventional methods, their dependence on traditional AST inoculum concentrations and optical detection limit their speed somewhat. Herein, we describe the GeneFluidics ProMax lab automation system intended for a rapid 3.5-hour molecular AST from clinical isolates. The detection method described utilizes a higher starting inoculum concentration and automated molecular quantification of species-specific 16S rRNA through the use of an electrochemical sensor to assess microbiological responses to antibiotic exposure. A panel of clinical isolates consisting of species of gram-negative rods from the CDC AR bank and two hospitals, New York-Presbyterian Queens and Medical College of Wisconsin, were evaluated against ciprofloxacin, gentamicin, and meropenem in a series of reproducibility and clinical studies. The categorical agreement and reproducibility for Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Klebsiella aerogenes, Klebsiella oxytoca, Klebsiella pneumoniae, and Pseudomonas aeruginosa were 100% and 100% for ciprofloxacin, 98.7% and 100% for gentamicin and 98.5% and 98.5% for meropenem, respectively.

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).

Urinary Microbiome Characteristics in Female Patients with Acute Uncomplicated Cystitis and Recurrent Cystitis

Traditionally, the diagnostic mainstay of recurrent urinary tract infection has been urinary culture. However, the causative uropathogen of recurrent cystitis has not been well established. Urine DNA next-generation sequencing (NGS) can provide additional information on these infections. Herein, we compared urine NGS results and urine cultures in patients with acute uncomplicated cystitis (AUC) and recurrent cystitis (RC), and evaluated the difference in microbiome patterns in the NGS results. Patients who underwent urine culture and NGS due to AUC or RC were retrospectively reviewed. All urine samples were collected via a transurethral catheter and studied utilizing a type of NGS called 16S ribosomal RNA gene amplification and sequencing. The sensitivity of urine NGS was significantly higher than that of conventional urine culture (69.0% vs. 16.7%, p < 0.05). The detection rate of urine NGS was slightly lower in the RC group than in the AUC group (67.7% vs. 72.7%). Microbiome diversity was significantly higher in the RC group compared to the AUC group (p = 0.007), and the microbiome composition was significantly different between the AUC and RC groups. In the urine NGS results, Pseudomonas, Acinetobacter, and Enterobacteriaceae were found in the AUC group, and Sphingomonas, Staphylococcus, Streptococcus, and Rothia spp. were detected in the RC group. Urine NGS can significantly increase the diagnostic sensitivity compared to traditional urine culture methods, especially in RC patients. AUC and RC patients had significant differences in bacterial diversity and patterns. Therefore, recurrent cystitis might be approached from a different perspective.

Capture and detection of urine bacteria using a microchannel silicon nanowire microfluidic chip coupled with MALDI-TOF MS

Fast bacterial identification in urine samples was achieved by capturing bacteria on a microchannel silicon nanowire microfluidic chip, followed by MALDI-TOF MS detection. Under the optimized conditions, bacteria with a concentration of 106 CFU mL-1 in urine samples could be identified without culture. If cultured for 4 hours, bacteria with a concentration as low as 103 CFU mL-1 were identified.

Epididymitis and its aetiologies in a central London sexual health clinic

Epididymitis is a common cause of scrotal pain presentation in sexual health clinics; however, it is unclear what fraction is attributable to transmissible infections. We, therefore, reviewed the aetiologies causing epididymitis. A retrospective data analysis of all cases of epididymitis diagnosed from January 2018 to December 2018 in three sexual health clinics was conducted, collecting demographics, results, management and symptom resolution at two weeks follow up. A total of 127 cases of epididymitis (mean age 32 years, heterosexual 97, MSM 30) were included. Among them 14 cases (11%) were caused by sexual transmitted infections (<35 years n = 9; >35 years n = 5): seven cases of chlamydia, six gonorrhoea, one syphilis and one trichomonas vaginalis. There were three cases of urinary tract infection diagnosed. All cases were treated with antibiotics recommended by the British Association for Sexual Health and HIV (BASHH). At two weeks follow up post-treatment 10 (7%) were symptomatic; 91% did not attend for follow up. Sexually transmitted infections were associated with acute epididymitis in 11% of this study cohort.

Symptoms, risk factors, diagnosis and treatment of urinary tract infections

Urinary tract infection (UTI) is a common microbial infection found in all ages and sexes which involves inflammation of the urinary tract. These infections can range from simple bladder inflammation, that is, cystitis, to severe cases of uroseptic shock. UTI ranks as the number 1 infection that leads to a prescription of antibiotics after a doctor's visit. These infections are sometimes distressing and even life threatening, and both males (12%) and females (40%) have at least one symptomatic UTI throughout their lives. Diagnostic failures in case of bacterial infections are the main contributing factor in improper use of antibiotics, delay in treatment and low survival rate in septic conditions. So, early diagnosis and appropriate therapy with antibiotics are the most significant requirements for preventing complicated UTI conditions such as urosepsis. This review article summarises the symptoms of the UTIs and the associated risk factors to it. The various conventional and recent diagnostic methods were also discussed in this review, along with treatment therapies with or without antibiotics.

Rising prevalence of multidrug-resistant uropathogenic bacteria from urinary tract infections in pregnant women

Objectives

This study aimed to determine the prevalence of urinary tract infections (UTI) in pregnant women and characterise the uropathogenic bacterial strains associated with symptomatic and asymptomatic bacteriuria in Lahore, Pakistan.

Methods

Between December 2018 and June 2019, we analysed the uropathogenic bacterial strains from midstream urine samples in 80 pregnant women. The age of the pregnant women ranged from 19 to 45 years, and they resided in urban and rural areas. We also recorded socioeconomic factors in this cohort. The isolated strains were phenotypically identified and evaluated for multiple drug resistance (MDR) patterns against recommended antimicrobial drugs.

Results

Of the 80 pregnant women, 65 had UTI, reflecting an 81% prevalence of UTI in women during pregnancy. The majority of participants aged 24–35 years, were multipara, and were in their third trimester. Results showed that 67 uropathogenic bacterial strains belonged to Escherichia (31%), Klebsiella (23%), Pseudomonas (16%), Streptococcus (4%), Enterococcus (4%), Staphylococcus (4%), and Proteus (3%) genera, as identified using biochemical characterisation. The highest overall resistance of Escherichia was seen against amoxicillin, pipemidic acid, and ampicillin; for Klebsiella against pipemidic acid, ampicillin, and cefotaxime; and for Pseudomonas against ciprofloxacin and cefotaxime. The three strains with the highest MDR were identified using 16S rRNA as Pseudomonas aeruginosa strain UA17, Escherichia coli strain UA32, and Klebsiella pneumoniae strain UA47.

Conclusion

In this study, the MDR uropathogenic strains showed the highest resistance pattern. The alarming signs of MDR uropathogenic infections are infrequently addressed and thus, urgent attention to this matter is essential.

A guide for urogynecologic patient care utilizing telemedicine during the COVID-19 pandemic: review of existing evidence

Introduction and hypothesis

The COVID-19 pandemic and the desire to “flatten the curve” of transmission have significantly affected the way providers care for patients. Female Pelvic Medicine and Reconstructive Surgeons (FPMRS) must provide high quality of care through remote access such as telemedicine. No clear guidelines exist on the use of telemedicine in FPMRS. Using expedited literature review methodology, we provide guidance regarding management of common outpatient urogynecology scenarios during the pandemic.

Methods

We grouped FPMRS conditions into those in which virtual management differs from direct in-person visits and conditions in which treatment would emphasize behavioral and conservative counseling but not deviate from current management paradigms. We conducted expedited literature review on four topics (telemedicine in FPMRS, pessary management, urinary tract infections, urinary retention) and addressed four other topics (urinary incontinence, prolapse, fecal incontinence, defecatory dysfunction) based on existing systematic reviews and guidelines. We further compiled expert consensus regarding management of FPMRS patients in the virtual setting, scenarios when in-person visits are necessary, symptoms that should alert providers, and specific considerations for FPMRS patients with suspected or confirmed COVID-19.

Results

Behavioral, medical, and conservative management will be valuable as first-line virtual treatments. Certain situations will require different treatments in the virtual setting while others will require an in-person visit despite the risks of COVID-19 transmission.

Conclusions

We have presented guidance for treating FPMRS conditions via telemedicine based on rapid literature review and expert consensus and presented it in a format that can be actively referenced.