Rapid qualitative urinary tract infection pathogen identification by SeptiFast real-time PCR

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.

Performance of an innovative culture-based digital dipstick for detection of bacteriuria

IMPORTANCE

In this study, we explore the transformative potential of UTI-lizer, an emerging technology not yet commercially available. Our manuscript shows that UTI-lizer is a promising alternative for detecting the five main pathogens that cause urinary tract infections (UTIs). The results also indicate that digital dipsticks have the potential to uniquely provide UTI diagnostic quality on par with that of gold-standard testing, with the added benefits of ease of testing, rapid test handling time, and simple test equipment. This technology can be helpful in quickly ruling out bacterial infections and reducing the unnecessary use of antibiotics, especially in primary care settings or at the point of care. Moreover, the UTI-lizer test can reduce the number of negative urine samples sent to central laboratories, thus easing the burden of UTI diagnostics on the healthcare system. We believe our study, as well as current and upcoming research based on this technology, is highly relevant for clinical microbiologists, microbiology scientists, general practitioners, and urologists.

Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology

The use of clinical molecular diagnostic methods for detecting microbial pathogens continues to expand and, in some cases, supplant conventional identification methods in various scenarios. Analytical and clinical benefits of multiplex molecular panels for the detection of respiratory pathogens have been demonstrated in various studies. The use of these panels in managing different patient populations has been incorporated into clinical guidance documents. The Association for Molecular Pathology's Infectious Diseases Multiplex Working Group conducted a review of the current benefits and challenges to using multiplex PCR for the detection of pathogens from gastrointestinal tract, central nervous system, lower respiratory tract, and joint specimens. The Working Group also discusses future directions and novel approaches to detection of pathogens in alternate specimen types, and outlines challenges associated with implementation of these multiplex PCR panels.

The Essential Role of PCR and PCR Panel Size in Comparison with Urine Culture in Identification of Polymicrobial and Fastidious Organisms in Patients with Complicated Urinary Tract Infections

Complicated urinary tract infections (cUTIs) are difficult to treat, consume substantial resources, and cause increased patient morbidity. Data suggest that cUTI may be caused by polymicrobial and fastidious organisms (PMOs and FOs, respectively); as such, urine culture (UC) may be an unreliable diagnostic tool for detecting cUTIs. We sought to determine the utility of PCR testing for patients presumed to have a cUTI and determine the impact of PCR panel size on organism detection. We reviewed 36,586 specimens from patients with presumptive cUTIs who received both UC and PCR testing. Overall positivity rate for PCR and UC was 52.3% and 33.9%, respectively (p < 0.01). PCR detected more PMO and FO than UC (PMO: 46.2% vs. 3.6%; FO: 31.3% vs. 0.7%, respectively, both p < 0.01). Line-item concordance showed that PCR detected 90.2% of organisms identified by UC whereas UC discovered 31.9% of organisms detected by PCR (p < 0.01). Organism detection increased with expansion in PCR panel size from 5-25 organisms (p < 0.01). Our data show that overall positivity rate and the detection of individual organisms, PMO and FO are significantly with PCR testing and that these advantages are ideally realized with a PCR panel size of 25 or greater.

A Multipathogen Bile Sample-based PCR Assay Can Guide Empirical Antimicrobial Strategies in Cholestatic Liver Diseases

BACKGROUND AND OBJECTIVES

Polymerase chain reaction (PCR) techniques provide rapid detection of pathogens. This pilot study evaluated the diagnostic utility and clinical impact of multiplex real-time PCR (mRT-PCR, SeptiFast) vs. conventional microbial culture (CMC) in bile samples of patients with chronic cholestatic liver diseases (cCLDs), endoscopic retrograde cholangio-pancreatography (ERCP), and peri-interventional-antimicrobial-prophylaxis (pAP).

METHODS

We prospectively collected bile samples from 26 patients for microbiological analysis by CMC and mRT-PCR. Concordance of the results of both methods was determined by Krippendorff's alpha (α) for inter-rater reliability and the Jaccard index of similarity.

RESULTS

mRT-PCR_bile and CMC_bile results were concordant for only Candida albicans (α=0.8406; Jaccard index=0.8181). mRT-PCR_bile detected pathogens in 8/8 cases (100%), CMC_bile in 7/8 (87.5%), and CMC_blood in 5/8 (62.5%) with clinical signs of infection. mRT-PCR_bile, CMC_bile, and CMC_blood had identical detection results in 3/8 (37.5%) with clinical signs of infection (two Klebsiella spp. and one Enterococcus faecium). The total pathogen count was significantly higher with mRT-PCR_bile than with CMC_bile (62 vs. 31; χ²=30.031, p<0.001). However, pathogens detected by mRT-PCR_bile were more often susceptible to pAP according to the patient infection/colonization history (PI/CH) and surveillance data for antibiotic resistance in our clinic (DARC). Pathogens identified by mRT-PCR_bile and resistant to pAP by PI/CH and DARC were likely to be clinically relevant.

CONCLUSIONS

mRT-PCR in conjunction with CMCs for bile analysis increased diagnostic sensitivity and may benefit infection management in patients with cholestatic diseases. Implementation of mRT-PCR in a bile sample-based diagnostic routine can support more rapid and targeted use of antimicrobial agents in cCLD-patients undergoing ERCP and reduce the rate/length of unnecessary administration of broad-spectrum antibiotics.

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

A review on urinary tract infections diagnostic methods: Laboratory-based and point-of-care approaches

Urinary tract infections (UTIs) are among the most common infectious diseases worldwide. This type of infections can be healthcare-associated or community-acquired and affects millions of people every year. Different diagnostic procedures are available to detect pathogens in urine and they can be divided into two main categories: laboratory-based and point-of-care (POC) detection techniques. Traditional methodologies are often time-consuming, thus, achieving a rapid and accurate identification of pathogens is a challenging feature that has been pursued by many research groups and companies operating in this area. The purpose of this review is to compare and highlight advantages and disadvantages of the traditional and currently most used detection methods, as well as the emerging POC approaches and the relevant advances in on-site detection of pathogens´ mechanisms, suitable to be adapted to UTI diagnosis. Lately, the commercially available UTI self-testing kits and devices are helping in the diagnosis of urinary infections as patients or care givers are able to perform the test, easily and comfortably at home and, upon the result, decide when to attend an appointment/Urgent Health Care Unit.

Role of 16S Ribosomal RNA Analysis in Identification of Microorganisms in Febrile Urinary Tract Infection of Infants

OBJECTIVES

To assess the role of 16S ribosomal RNA analysis in microbial identification in febrile infants under six months of age diagnosed with UTI, and compare it with the conventional culture results.

METHODS

Young infants under 6 mo of age who were suspected UTI from May 2018 to April 2019 had been enrolled. Uropathogens were analyzed by the traditional microbiologic culture system and the 16S rRNA analysis. The 16S rRNA analysis included 16S rRNA amplicon band confirmation and bacterial identification through the sequencing analysis.

RESULTS

A total of 57 infants with the febrile UTI were enrolled, and the median age was 3 mo. Uropathogens were identified in 43 patients (75.4%) in a conventional culture method: Escherichia coli in 38 patients (88.4%), Klebsiella pneumoniae in 3 (7.0%), Enterobacter cloacae in 1 (2.3%), and Pseudomonas aeruginosa in 1 (2.3%). Fifty urine samples (87.8%) had positive 16S rRNA amplicon band on electrophoresis. Among the 16S rRNA-positive urines, 40 samples were available for the sequence analysis of 16S rRNA, and the identification of bacteria were as follows: E. fergusonii in 36, K. pneumoniae in 3, and Shigella flexneri in 1. The sensitivity of 16S rRNA sequencing was 81.4% [95% confidence interval (CI), 67.4-90.3%] and the specificity was 64.3% (95% CI, 38.8-83.7%).

CONCLUSION

Uropathogen identification using 16S rRNA analysis could be applied to manage the febrile UTI in young infants clinically in combination with the conventional culture.

Applying Diagnostic Stewardship to Proactively Optimize the Management of Urinary Tract Infections

A urinary tract infection is amongst the most common bacterial infections in the community and hospital setting and accounts for an estimated 1.6 to 2.14 billion in national healthcare expenditure. Despite its financial impact, the diagnosis is challenging with urine cultures and antibiotics often inappropriately ordered for non-specific symptoms or asymptomatic bacteriuria. In an attempt to limit unnecessary laboratory testing and antibiotic overutilization, several diagnostic stewardship initiatives have been described in the literature. We conducted a systematic review with a focus on the application of molecular and microbiological diagnostics, clinical decision support, and implementation of diagnostic stewardship initiatives for urinary tract infections. The most successful strategies utilized a bundled, multidisciplinary, and multimodal approach involving nursing and physician education and feedback, indication requirements for urine culture orders, reflex urine culture programs, cascade reporting, and urinary antibiograms. Implementation of antibiotic stewardship initiatives across the various phases of laboratory testing (i.e., pre-analytic, analytic, post-analytic) can effectively decrease the rate of inappropriate ordering of urine cultures and antibiotic prescribing in patients with clinically ambiguous symptoms that are unlikely to be a urinary tract infection.

A Novel Propidium Monoazide-Based PCR Assay Can Measure Viable Uropathogenic E. coli In Vitro and In Vivo

Background

Polymerase chain reaction (PCR) is an important means by which to study the urine microbiome and is emerging as possible alternative to urine cultures to identify pathogens that cause urinary tract infection (UTI). However, PCR is limited by its inability to differentiate DNA originating from viable, metabolically active versus non-viable, inactive bacteria. This drawback has led to concerns that urobiome studies and PCR-based diagnosis of UTI are confounded by the presence of relic DNA from non-viable bacteria in urine. Propidium monoazide (PMA) dye can penetrate cells with compromised cell membranes and covalently bind to DNA, rendering it inaccessible to amplification by PCR. Although PMA has been shown to differentiate between non-viable and viable bacteria in various settings, its effectiveness in urine has not been previously studied. We sought to investigate the ability of PMA to differentiate between viable and non-viable bacteria in urine.

Methods

Varying amounts of viable or non-viable uropathogenic E. coli (UTI89) or buffer control were titrated with mouse urine. The samples were centrifuged to collect urine sediment or not centrifuged. Urine samples were incubated with PMA and DNA cross-linked using blue LED light. DNA was isolated and uidA gene-specific PCR was performed. For in vivo studies, mice were inoculated with UTI89, followed by ciprofloxacin treatment or no treatment. After the completion of ciprofloxacin treatment, an aliquot of urine was plated on non-selective LB agar and another aliquot was treated with PMA and subjected to uidA-specific PCR.

Results

PMA’s efficiency in excluding DNA signal from non-viable bacteria was significantly higher in bacterial samples in phosphate-buffered saline (PBS, dC_T=13.69) versus bacterial samples in unspun urine (dC_T=1.58). This discrepancy was diminished by spinning down urine-based bacterial samples to collect sediment and resuspending it in PBS prior to PMA treatment. In 3 of 5 replicate groups of UTI89-infected mice, no bacteria grew in culture; however, there was PCR amplification of E. coli after PMA treatment in 2 of those 3 groups.

Conclusion

We have successfully developed PMA-based PCR methods for amplifying DNA from live bacteria in urine. Our results suggest that non-PMA bound DNA from live bacteria can be present in urine, even after antibiotic treatment. This indicates that viable but non-culturable E. coli can be present following treatment of UTI, and may explain why some patients have persistent symptoms but negative urine cultures following UTI treatment.

Label-Free, Novel Electrofluidic Capacitor Biosensor for Prostaglandin E2 Detection toward Early and Rapid Urinary Tract Infection Diagnosis

Urine Prostaglandin E2 (PGE2) has been identified as an attractive diagnostic and prognostic biomarker for urinary tract infection (UTI). This work demonstrates the use of PGE2 as a biomarker for rapid and label-free testing for UTI. In this work, we have developed a novel electrofluidic capacitor-based biosensor that can used for home-based UTI management with high accuracy in less than 5 min for small volume urine samples (<60 μL). The PGE2 biosensor works on the principle of affinity capture using highly specific monoclonal PGE2 antibody and relies on non-faradaic electrical impedance spectroscopy (EIS) and Mott-Schottky (MS) for quantifying subtle variations in PGE2 levels expressed in human urine (pH 5-8). Dynamic light scattering experiments were performed to characterize surface charge properties and the impact of bulk interferents on the interfacial modulation of electrical properties due to binding and urine pH variations. Binding chemistry between the key elements of the immunosensor stack was validated using attenuated total reflectance-Fourier transform infrared spectroscopy and surface plasmon resonance studies. Linear calibration dose responses were obtained for PGE2 for both EIS and MS. The sensor reliably distinguished between UTI negative and UTI positive cases for both artificial (pH 5-8) and pooled human urine samples. The sensor was not found to cross-react with Prostaglandin D2, a structurally similar interferent, and other abundant urine interferents (urea and creatinine). Human subject studies confirmed the validity of the sensor for robust and accurate UTI diagnosis. This work can be extended to achieve easy, reliable, and rapid home-based UTI management, which can consequently help physicians with timely and appropriate administration of therapy to improve patient outcomes and treatment success.

Rapid uropathogen identification using surface enhanced Raman spectroscopy active filters

Urinary tract infection is one of the most common bacterial infections leading to increased morbidity, mortality and societal costs. Current diagnostics exacerbate this problem due to an inability to provide timely pathogen identification. Surface enhanced Raman spectroscopy (SERS) has the potential to overcome these issues by providing immediate bacterial classification. To date, achieving accurate classification has required technically complicated processes to capture pathogens, which has precluded the integration of SERS into rapid diagnostics. This work demonstrates that gold-coated membrane filters capture and aggregate bacteria, separating them from urine, while also providing Raman signal enhancement. An optimal gold coating thickness of 50 nm was demonstrated, and the diagnostic performance of the SERS-active filters was assessed using phantom urine infection samples at clinically relevant concentrations (10⁵ CFU/ml). Infected and uninfected (control) samples were identified with an accuracy of 91.1%. Amongst infected samples only, classification of three bacteria (Escherichia coli, Enterococcus faecalis, Klebsiella pneumoniae) was achieved at a rate of 91.6%.

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).

Droplet-Based Single-Cell Measurements of 16S rRNA Enable Integrated Bacteria Identification and Pheno-Molecular Antimicrobial Susceptibility Testing from Clinical Samples in 30 min

Empiric broad-spectrum antimicrobial treatments of urinary tract infections (UTIs) have contributed to widespread antimicrobial resistance. Clinical adoption of evidence-based treatments necessitates rapid diagnostic methods for pathogen identification (ID) and antimicrobial susceptibility testing (AST) with minimal sample preparation. In response, a microfluidic droplet-based platform is developed for achieving both ID and AST from urine samples within 30 min. In this platform, fluorogenic hybridization probes are utilized to detect 16S rRNA from single bacterial cells encapsulated in picoliter droplets, enabling molecular identification of uropathogenic bacteria directly from urine in as little as 16 min. Moreover, in-droplet single-bacterial measurements of 16S rRNA provide a surrogate for AST, shortening the exposure time to 10 min for gentamicin and ciprofloxacin. A fully integrated device and screening workflow were developed to test urine specimens for one of seven unique diagnostic outcomes including the presence/absence of Gram-negative bacteria, molecular ID of the bacteriaas Escherichia coli, an Enterobacterales, or other organism, and assessment of bacterial susceptibility to ciprofloxacin. In a 50-specimen clinical comparison study, the platform demonstrates excellent performance compared to clinical standard methods (areas-under-curves, AUCs >0.95), within a small fraction of the turnaround time, highlighting its clinical utility.

Role of microbiological tests and biomarkers in antibiotic stewardship

Laboratory tests are critical in the detection and timely treatment of infection. Two categories of tests are commonly used in neonatal sepsis management: those that identify the pathogen and those that detect host response to a potential pathogen. Decision-making around antibiotic choice is related to the performance of tests that directly identify pathogens. Advances in these tests hold the key to progress in antibiotic stewardship. Tests measuring host response, on the other hand, are an indirect marker of potential infection. While an important measure of the patient's clinical state, in the absence of pathogen detection these tests cannot confirm the appropriateness of antibiotic selection. The overall impact these tests then have on antibiotic utilization depends the test's specificity for bacterial infection, clinical scenario where it is being used and the decision-rule it is being integrated into for use. In this review we discuss common and emerging laboratory tests available for assisting management of neonatal infection and specifically focus on the role they play in optimizing antibiotic utilization.

Digital dipstick: miniaturized bacteria detection and digital quantification for the point-of-care

Established digital bioassay formats, digital PCR and digital ELISA, show extreme limits of detection, absolute quantification and high multiplexing capabilities. However, they often require complex instrumentation, and extensive off-chip sample preparation. In this study, we present a dipstick-format digital biosensor (digital dipstick) that detects bacteria directly from the sample liquid with a minimal number of steps: dip, culture, and count. We demonstrate the quantitative detection of Escherichia coli (E. coli) in urine in the clinically relevant range of 102-105 CFU ml-1 for urinary tract infections. Our format shows 89% sensitivity to detect E. coli in clinical urine samples (n = 28) when it is compared to plate culturing (gold standard). The significance and uniqueness of this diagnostic test format is that it allows a non-trained operator to detect urinary tract infections in the clinically relevant range in the home setting.

Differential mobility spectrometry classification of bacteria

Aim: Rapid identification of bacteria would facilitate timely initiation of therapy and improve cost–effectiveness of treatment. Traditional methods (culture, PCR) require reagents, consumables and hours to days to complete the identification. In this study, we examined whether differential mobility spectrometry could classify most common bacterial species, genera and between Gram status within minutes. Materials & methods: Cultured bacterial sample gaseous headspaces were measured with differential mobility spectrometry and data analyzed using k-nearest-neighbor and leave-one-out cross-validation. Results: Differential mobility spectrometry achieved a correct classification rate 70.7% for all bacterial species. For bacterial genera, the rate was 77.6% and between Gram status, 89.1%. Conclusion: Largest difficulties arose in distinguishing bacteria of the same genus. Future improvement of the sensor characteristics may improve the classification accuracy.

Direct identification and susceptibility testing of Gram-negative bacilli from turbid urine samples using VITEK2

INTRODUCTION:

Urinary tract infections (UTIs) are the most common infectious diseases occurring in either the community or healthcare setting. Turnaround time for urine culture is about 24 h, and antimicrobial susceptibility testing (AST) requires another 24 h. Consequently, initial antibiotic therapy is mostly empirical.

MATERIALS AND METHODS:

This study was conducted at Nizam's Institute of Medical Sciences, Hyderabad. Turbid urine samples which showed pus cells and Gram-negative (GN) bacilli of single morphotype were included. The turbidity of the urine was adjusted to 0.5 McFarland and uploaded directly in the VITEK 2 identification (ID) GN and N-280 panel for AST. The specimen was also inoculated on CHROMagar, and the ID and AST of the isolates from the agar plate were repeated on VITEK 2, and the results were compared.

RESULTS:

Out of 844 turbid urines screened, 62 met the inclusion criteria. Escherichia coli was the most common isolate (71.9%). Complete agreement for ID was 80.7%, misidentified were 12.2%, and unidentified were 7%. Complete agreement with AST was 94.3%, very major errors 0.5%, major errors 2.2%, and minor errors 3%.

CONCLUSION:

With a 94.3% agreement for AST and a reduced turnaround time by 24 h, the direct inoculation had a potential clinical benefit for initiating timely and appropriate antibiotic therapy for UTI.

Is it Time to Say Goodbye to Culture and Sensitivity? The Case for Culture-independent Urology

Next-generation sequencing has highlighted the limitations of conventional culture methods in the role of urology while discovering the intricate details of the role of microbiota in urologic health and disease. This review article explores: the utility and limitations of conventional culture methods; how culture-independent technologies are revolutionizing medicine; and how the implementation of these technologies may lead to improved patient outcomes. Finally, this article discusses the barriers to widespread adoption of culture-independent technologies, with suggestions for how these hurdles may be overcome.

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

OBJECTIVE

To evaluate whether multiplex PCR-based molecular testing is noninferior to urine culture for detection of bacterial infections in symptomatic patients.

METHODS

Retrospective record review of 582 consecutive elderly patients presenting with symptoms of lower urinary tract infection (UTI) was conducted. All patients had traditional urine cultures and PCR molecular testing run in parallel.

RESULTS

A total of 582 patients (mean age 77; range 60-95) with symptoms of lower UTI had both urine cultures and diagnostic PCR between March and July 2018. PCR detected uropathogens in 326 patients (56%, 326/582), while urine culture detected pathogens in 217 patients (37%, 217/582). PCR and culture agreed in 74% of cases (431/582): both were positive in 34% of cases (196/582) and both were negative in 40% of cases (235/582). However, PCR and culture disagreed in 26% of cases (151/582): PCR was positive while culture was negative in 22% of cases (130/582), and culture was positive while PCR was negative in 4% of cases (21/582). Polymicrobial infections were reported in 175 patients (30%, 175/582), with PCR reporting 166 and culture reporting 39. Further, polymicrobial infections were identified in 67 patients (12%, 67/582) in which culture results were negative. Agreement between PCR and urine culture for positive cultures was 90%, exceeding the noninferiority threshold of 85% (95% conflict of interest 85.7%-93.6%).

CONCLUSION

Multiplex PCR is noninferior to urine culture for detection and identification of bacteria. Further investigation may show that the accuracy and speed of PCR to diagnose UTI can significantly improve patient outcomes.

Rapid time-resolved luminescence based screening of bacteria in urine with luminescence modulating biosensing phages

Urinary tract infections (UTIs) are a common problem worldwide. The most prevalent causative pathogen of UTI is Escherichia coli, focus of this study. The current golden standard for detecting UTI is bacterial culture, creating a major workload for hospital laboratories - cost-effective and rapid mass screening of patient samples is needed. Here we present an alternative approach to screen patient samples with a single-step assay utilising time-resolved luminescence and luminescence modulating biosensing phages. Filamentous phage M13 was biopanned for binding luminescence quenching metal (copper) and further E. coli. The screening assay luminescence modulation was further enhanced by selecting right chemical environment for the functioning phage clones. Semi-specific interaction between phage, target bacteria and metal was detected by modulation in the signal of a weakly chelating, easily quenchable lanthanide complex. In the presence of the target pathogen, the phages collected quenching metal from solution to the bacterial surface changing the quenching effect on the lanthanide label and thus modulating the signal. Our method was compared with the bacterial culture data obtained from 70 patient samples. The developed proof-of-principle screening assay showed sensitivity and a specificity at the 90% mark when compared to culture method although some samples had high turbidity and even blood. The detection limit of E. coli was in the range of 1000-10 000 colony forming units/mL. Untreated urine sample was screened and time-resolved luminescence signal result was achieved within 10 min in a single incubation step.

Development of a panel of recombinase polymerase amplification assays for detection of common bacterial urinary tract infection pathogens

AIMS

To develop and evaluate the performance of a panel of isothermal real-time recombinase polymerase amplification (RPA) assays for detection of common bacterial urinary tract infection (UTI) pathogens.

METHODS AND RESULTS

The panel included RPAs for Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa and Enterococcus faecalis. All five RPAs required reaction times of under 12 min to reach their lower limit of detection of 100 genomes per reaction or less, and did not cross-react with high concentrations of nontarget bacterial genomic DNA. In a 50-sample retrospective clinical study, the five-RPA assay panel was found to have a specificity of 100% (95% CI, 78-100%) and a sensitivity of 89% (95% CI, 75-96%) for UTI detection.

CONCLUSIONS

The analytical and clinical validity of RPA for the rapid and sensitive detection of common UTI pathogens was established.

SIGNIFICANCE AND IMPACT OF THE STUDY

Rapid identification of the causative pathogens of UTIs can be valuable in preventing serious complications by helping avoid the empirical treatment necessitated by traditional urine culture's 48-72-h turnaround time. The routine and widespread use of RPA to supplement or replace culture-based methods could profoundly impact UTI management and the emergence of multidrug-resistant pathogens.

The Utility of Real-Time Quantitative Polymerase Chain Reaction Genotype Detection in the Diagnosis of Urinary Tract Infections in Children

Urinary tract infections (UTIs) are the most common serious bacterial infection in children with significant morbidity with delayed diagnosis. Polymerase chain reaction (PCR) is very accurate in detecting bacteria and widely available, but has never been evaluated to detect UTIs in children. To assess the utility of PCR as a rapid diagnostic tool, we conducted a prospective cohort study of 193 urine samples from children younger than 36 months undergoing evaluation for UTI in the emergency department over a 10-month period. A quantification cycle (Cq) threshold of 26.15 identified all Escherichia coli positive samples with sensitivity and specificity of 100% and 99.5%, respectively (95% CI = 71.5%-100% and 97.9%-99.5%, respectively). A Cq threshold of 19.03 identified E coli infections >100 000 colony forming units/mL with sensitivity and specificity of 100% (95% CI = 72.2%-100% and 98.6%-100%, respectively). PCR is very accurate in diagnosing E coli UTIs in young children and could be useful as a rapid diagnostic tool.

Diagnosis, Treatment, and Prevention of Urinary Tract Infection

UTI may involve the lower or upper urinary tract and may be uncomplicated or complicated. The emphasis of this chapter is uncomplicated UTI. The diagnosis of uncomplicated cystitis (bladder infection) and pyelonephritis (kidney infection) is usually easily made based on the clinical presentation, whereas the diagnosis in patients with complicated UTI is often more complex. Thus uncomplicated cystitis is usually manifested by dysuria, frequency and/or urgency without fever, and pyelonephritis is usually manifested by fever and back pain/costovertebral angle tenderness. However, pyuria is usually present with UTI, regardless of location, and its absence suggests that another condition may be causing the patient's symptoms. Treatment of cystitis is usually straightforward with one of several effective short-course antimicrobial regimens, although antimicrobial resistance continues to increase and can complicate treatment choices in certain areas. Likewise, antimicrobial resistance has complicated our management of uncomplicated pyelonephritis since resistance of uropathogens to the fluoroquinolone class, the mainstay of oral treatment for pyelonephritis, is increasing worldwide, and some of the other agents used for cystitis are not recommended for pyelonephritis due to low tissue levels. The goal of prevention of recurrent cystitis is to minimize the use of antimicrobials and there are several research efforts in progress to develop effective and safe antimicrobial-sparing preventive approaches for this common condition.

How to use… urine dipsticks

'Urine dipstick', the commonly used point-of-care test, is an extremely sensitive investigation. Results of this test affected by numerous factors, if not meticulously linked with detailed history and examination, can lead a well-meaning clinician down the wrong clinical pathway. The aim of this article is to provide an overview of this every day test, touching on the physiological and technological basis initially, but mainly focusing on common questions like when to request the dipstick test, the correlation of dipstick results with urine specimen collected by different method and complexities of interpretation of dipstick results in everyday clinical scenarios.

New and developing diagnostic technologies for urinary tract infections

Timely and accurate identification and determination of the antimicrobial susceptibility of uropathogens is central to the management of UTIs. Urine dipsticks are fast and amenable to point-of-care testing, but do not have adequate diagnostic accuracy or provide microbiological diagnosis. Urine culture with antimicrobial susceptibility testing takes 2-3 days and requires a clinical laboratory. The common use of empirical antibiotics has contributed to the rise of multidrug-resistant organisms, reducing treatment options and increasing costs. In addition to improved antimicrobial stewardship and the development of new antimicrobials, novel diagnostics are needed for timely microbial identification and determination of antimicrobial susceptibilities. New diagnostic platforms, including nucleic acid tests and mass spectrometry, have been approved for clinical use and have improved the speed and accuracy of pathogen identification from primary cultures. Optimization for direct urine testing would reduce the time to diagnosis, yet these technologies do not provide comprehensive information on antimicrobial susceptibility. Emerging technologies including biosensors, microfluidics, and other integrated platforms could improve UTI diagnosis via direct pathogen detection from urine samples, rapid antimicrobial susceptibility testing, and point-of-care testing. Successful development and implementation of these technologies has the potential to usher in an era of precision medicine to improve patient care and public health.

Microbial diagnosis of bloodstream infection: towards molecular diagnosis directly from blood

When a bloodstream infection (BSI) is suspected, most of the laboratory results-biochemical and haematologic-are available within the first hours after hospital admission of the patient. This is not the case for diagnostic microbiology, which generally takes a longer time because blood culture, which is to date the reference standard for the documentation of the BSI microbial agents, relies on bacterial or fungal growth. The microbial diagnosis of BSI directly from blood has been proposed to speed the determination of the etiological agent but was limited by the very low number of circulating microbes during these paucibacterial infections. Thanks to recent advances in molecular biology, including the improvement of nucleic acid extraction and amplification, several PCR-based methods for the diagnosis of BSI directly from whole blood have emerged. In the present review, we discuss the advantages and limitations of these new molecular approaches, which at best complement the culture-based diagnosis of BSI.

Multiplex PCR performed of bronchoalveolar lavage fluid increases pathogen identification rate in critically ill patients with pneumonia: a pilot study

Background

In critically ill patients with pneumonia, accurate microorganism identification allows appropriate antibiotic treatment. In patients undergoing bronchoalveolar lavage (BAL), direct examination of the fluid using Gram staining provides prompt information but pathogen identification accuracy is low. Culture of BAL fluid is actually the reference, but it is not available before 24 to 48 h. In addition, pathogen identification rate observed with direct examination and culture is decreased when antibiotic therapy has been given prior to sampling. We therefore assessed, in critically ill patients with suspected pneumonia, the performance of a multiplex PCR (MPCR) to identify pathogens in BAL fluid. This study is a prospective pilot observation.

Methods

We used a MPCR detecting 20 types of microorganisms. Direct examination, culture, and MPCR were performed on BAL fluid of critically ill patients with pneumonia suspicion. The final diagnosis of infective pneumonia was retained after the medical chart was reviewed by two experts. Pathogen identification rate of direct examination, culture, and MPCR in patients with confirmed pneumonia was compared.

Results

Among the 65 patients with pneumonia suspicion, the diagnosis of pneumonia was finally retained in 53 cases. Twenty nine (55%) were community-acquired pneumonia and 24 (45%) were hospital acquired. Pathogen identification rate with MPCR (66%) was greater than with culture (40%) and direct examination (23%) (p =0.01 and p <0.001, respectively). When considering only the microorganisms included in the MPCR panel, the pathogen identification rate provided by MPCR reached 82% and was still higher than with culture (35%, p <0.001) and direct examination (21%, p <0.001). Pathogen identification rate provided by MPCR was not modified in the case of previous antibiotic treatment (66% vs. 64%, NS) and was still better than with culture (23%, p <0.001).

Conclusions

The results of this pilot study suggest that in critically ill patients, MPCR performed on BAL fluid could provide higher identification rate of pathogens involved in pneumonia than direct examination and culture, especially in patients having received antimicrobial treatment.

A Tool to Assess the Signs and Symptoms of Catheter-Associated Urinary Tract Infection: Development and Reliability

The purpose of this pilot study was to determine the inter-rater reliability of four clinical manifestations of catheter-associated urinary tract infections (CAUTI) among hospitalized adults with short-term indwelling urinary catheters using a tool developed for this purpose: the CAUTI Assessment Profile (CAP). Study participants included 30 non-pregnant English-speaking adults, recruited from two community hospitals. Three nurses assessed each participant for fever, suprapubic tenderness, flank tenderness, and delirium using standardized techniques. Based on the generalized Kappa statistic and 95% confidence intervals, there was evidence of strong inter-rater reliability for fever (K = 1.00, 0.793-1.207), suprapubic tenderness (K = 0.39, 0.185-0.598), and delirium (K = 0.58, 0.379-0.792), but not for flank tenderness (K = 0.29, -0.036 to 0.617). This study provides preliminary evidence that the CAP can be used to consistently identify these clinical signs and symptoms of CAUTI in hospitalized adults.

Molecular diagnosis of sepsis: New aspects and recent developments

By shortening the time to pathogen identification and allowing for detection of organisms missed by blood culture, new molecular methods may provide clinical benefits for the management of patients with sepsis. While a number of reviews on the diagnosis of sepsis have recently been published we here present up-to-date new developments including multiplex PCR, mass spectrometry and array techniques. We focus on those techniques that are commercially available and for which clinical studies have been performed and published.

Usability application of multiplex polymerase chain reaction in the diagnosis of microorganisms isolated from urine of patients treated in cancer hospital

Background

The objective of this study was: i) to compare the results of urine culture with polymerase chain reaction (PCR) -based detection of microorganisms using two commercially available kits, ii) to assess antimicrobial susceptibility of urine isolates from cancer patients to chosen antimicrobial drugs and, if necessary, to update the recommendation of empirical therapy.

Materials and methods.

A one-year hospital-based prospective study has been conducted in Greater Poland Cancer Centre and Genetic Medicine Laboratory CBDNA Research Centre in 2011. Urine cultures and urine PCR assay from 72 patients were examined

Results

Urine cultures and urine PCR assay from 72 patients were examined. Urine samples were positive for 128 strains from which 95 (74%) were identical in both tests. The most frequently isolated bacteria in both culture and PCR assay were coliform organisms and Enterococcus spp. The Gram negative bacilli were most resistant to cotrimoxazol. 77.2% of these bacilli and 100% of E. faecalis and S. agalactiae were sensitive to amoxicillin-clavulanic acid. 4.7% of Gram positive cocci were resistant to nitrofurantoin.

Conclusions

The PCR method quickly finds the causative agent of urinary tract infection (UTI) and, therefore, it can help with making the choice of the proper antimicrobial therapy at an early stage. It appears to be a viable alternative to the recommendations made in general treatment guidelines, in cases where diversified sensitivity patterns of microorganisms have been found.

Pneumonia pathogen detection and microbial interactions in polymicrobial episodes

Recent reports show that microbial communities associated with respiratory infections, such as pneumonia and cystic fibrosis, are more complex than expected. Most of these communities are polymicrobial and might comprise microorganisms originating from several diverse biological and ecological sources. Moreover, unexpected bacteria in the etiology of these respiratory infections have been increasingly identified. These findings were established with the use of efficient microbiological diagnostic tools, particularly molecular tools based on common gene amplification, followed by cloning and sequencing approaches, which facilitated the identification of the polymicrobial flora. Similarly, recent investigations reported that microbial interactions might exist between species in polymicrobial communities, including typical pneumonia pathogens, such as Pseudomonas aeruginosa and Candida albicans. Here, we review recent tools for microbial diagnosis, in particular, of intensive care unit pneumonia and the reported interactions between microbial species that have primarily been identified in the etiology of these infections.

Rapid discrimination of Gram-positive and Gram-negative bacteria in liquid samples by using NaOH-sodium dodecyl sulfate solution and flow cytometry

Background

For precise diagnosis of urinary tract infections (UTI), and selection of the appropriate prescriptions for their treatment, we explored a simple and rapid method of discriminating gram-positive and gram-negative bacteria in liquid samples.

Methodology/Principal Findings

We employed the NaOH-sodium dodecyl sulfate (SDS) solution conventionally used for plasmid extraction from Escherichia coli and the automated urine particle analyzer UF-1000i (Sysmex Corporation) for our novel method. The NaOH-SDS solution was used to determine differences in the cell wall structures between gram-positive and gram-negative bacteria, since the tolerance to such chemicals reflects the thickness and structural differences of bacterial cell walls. The UF-1000i instrument was used as a quantitative bacterial counter. We found that gram-negative bacteria, including E. coli, in liquid culture could easily be lysed by direct addition of equal volumes of NaOH-SDS solution. In contrast, Enterococcus faecalis, which is a gram-positive bacterium, could not be completely lysed by the solution. We then optimized the reaction time of the NaOH-SDS treatment at room temperature by using 3 gram-positive and 4 gram-negative bacterial strains and determined that the optimum reaction time was 5 min. Finally, in order to evaluate the generalizability of this method, we treated 8 gram-positive strains and 8 gram-negative strains, or 4 gram-positive and 4 gram-negative strains incubated in voluntary urine from healthy volunteers in the same way and demonstrated that all the gram-positive bacteria were discriminated quantitatively from gram negative bacteria using this method.

Conclusions/Significance

Using our new method, we could easily discriminate gram-positive and gram-negative bacteria in liquid culture media within 10 min. This simple and rapid method may be useful for determining the treatment course of patients with UTIs, especially for those without a prior history of UTIs. The method may be easily applied in order to obtain additional information for clinical prescriptions from bacteriuria.

Bench-to-bedside review: Rapid molecular diagnostics for bloodstream infection--a new frontier?

Among critically ill patients, the diagnosis of bloodstream infection poses a major challenge. Current standard bacterial identification based on blood culture platforms is intrinsically time-consuming and slow. The continuous evolvement of molecular techniques has the potential of providing a faster, more sensitive and direct identification of causative pathogens without prior need for cultivation. This may ultimately impact clinical decision-making and antimicrobial treatment. This review summarises the currently available technologies, their strengths and limitations and the obstacles that have to be overcome in order to develop a satisfactory bedside point-of-care diagnostic tool for detection of bloodstream infection.

Rapid and sensitive detection of major uropathogens in a single-pot multiplex PCR assay

Urinary tract infection (UTI) is among the most common bacterial infections and poses a significant healthcare burden. Escherichia coli is the most common cause of UTI accounting for up to 70 % and a variable contribution from Proteus mirabilis, Pseudomonas aeruginosa and Klebsiella pneumoniae. To establish a complete diagnostic system, we have developed a single-tube multiplex PCR assay (mPCR) for the detection of the above-mentioned four major uropathogens. The sensitivity of the assay was found to be as low as 10(2) cfu/ml of cells. The mPCR evaluated on 280 clinical isolates detected 100 % of E. coli, P. aeruginosa, P. mirabilis and 95 % of K. pneumonia. The assay was performed on 50 urine samples and found to be specific and sensitive for clinical diagnosis. In addition, the mPCR was also validated on spiked urine samples using 40 clinical isolates to demonstrate its application under different strain used in this assay. In total, mPCR reported here is a rapid and simple screening tool that can compete with conventional biochemical-based screening assays that may require 2-3 days for detection.

Biosensor diagnosis of urinary tract infections: a path to better treatment?

Urinary tract infection (UTI) is among the most common bacterial infections and poses a significant healthcare burden. The standard culture-based diagnosis of UTI has a typical delay of two to three days. In the absence of definitive microbiological diagnosis at the point of care, physicians frequently initiate empirical broad-spectrum antibiotic treatment, and this has contributed to the emergence of resistant pathogens. Biosensors are emerging as a powerful diagnostic platform for infectious diseases. Paralleling how blood glucose sensors revolutionized the management of diabetes, and how pregnancy tests are now conducted in the home, biosensors are poised to improve UTI diagnosis significantly. Biosensors are amenable to integration with microfluidic technology for point-of-care (POC) applications. This review focuses on promising biosensor technology for UTI diagnosis, including pathogen identification and antimicrobial susceptibility testing, and hurdles to be surpassed in the translation of biosensor technology from bench to bedside.