A closer look at urinary tract microbiome detection

Although widely used, urine culture-based methods for the detection of pathogens involved in urinary tract infections (UTIs) are cumbersome.  They require up to 30 hours of culturing time, lack sensitivity, are subjective, and have been shown to miss a significant percentage of positive cases.

Our real-time PCR solution helps enable rapid detection in under five hours and accurately detects a wider range of microbiota in a scalable, low-cost per sample format that labs can easily implement. While the advantages of molecular detection over culture-based methods have been known for some time, our solution is designed to deliver these benefits in an approachable, commercially viable format and can be tailored to your throughput needs.

More accurate than culture—over 25% increase in accuracy of urinary tract pathogen detection when compared to culture methods [1]

Fast results—end-to-end workflow allows you to process samples and get answers in five hours

Sensitive—detect slow-growing or difficult-to-culture microorganisms when traditional methods often lead to ambiguous results

Scalable—real-time PCR and our variety of assay formats enables you to run tens to hundreds of samples per day on a single instrument  

Easy to implement—analytical validation services and training available to fast-track implementation and testing menu expansion

Your qPCR instrument can help with UTI detection

More accurate than culture

Verification data demonstrates our solution is 33% more accurate when compared to traditional culture-based methods of detection. Our urinary tract microbiota assays have undergone rigorous bioinformatic analysis to help ensure maximum strain coverage while minimizing the potential for off-target cross-reactivity.



Fast results

Our real-time PCR solution is optimized to deliver results in 5 hours—much faster than traditional culture-based methods.  A complete, simple, and straightforward end-to-end solution is available to enable the processing of tens to hundreds of samples per day with minimal hands-on time.  

Detects all relevant uropathogens

Real-time PCR can detect slow-growing or difficult-to-culture microorganisms, and can be used when traditional microbiology techniques lead to ambiguous results. Utilizing real-time PCR techniques along with microorganism-specific TaqMan Assays help enable rapid and accurate detection and categorization of multiple microorganisms involved in urinary tract microbiome composition and dynamics. Housing many of these TaqMan Assays on a single panel provides a molecular approach to detecting the presence of multiple microorganisms and indicating the overall status of urinary tract microbiota. With this knowledge, appropriate courses of action can be designed.

TaqMan OpenArray Urinary Tract Microbiota Comprehensive Plate

Targets available







Acinetobacter baumannii
Citrobacter freundii
Enterobacter aerogenes
Enterobacter cloacae                                           
Enterococcus faecalis                                           
Enterococcus faecium                                             
Escherichia coli
Klebsiella oxytoca
Klebsiella pneumoniae
Morganella morganii
Proteus mirabilis
Proteus vulgaris
Providencia stuartii
Pseudomonas aeruginosa
Staphylococcus saprophyticus
Streptococcus agalactiae
Candida albicans


Human RNase P







Scalable qPCR Workflow

The QuantStudio Family of real-time PCR instruments can meet any throughput requirement. For higher throughput laboratories, leverage our OpenArray nanofluidic technology. This technology allows labs to process up to 600 urine samples per day on a single instrument.  A complete end-to-end solution is available and includes the Thermo Scientific KingFisher Flex benchtop automated DNA/RNA extraction instrument, convenient extraction and purification kits, and the OpenArray AccuFill System. Combined, these systems can automate sample prep and liquid handling to enable the processing of hundreds to thousands of samples per day.  


Whether you already own an instrument, or considering an expansion to your capabilities, your sample processing and throughput requirements can be addressed through the different formats compatible with your instrument (such as TaqMan array cards, 96- or 384-well plates, or single tube assays) with made-to-stock or custom panels.  Learn more about how OpenArray Technology can be an ideal solution for handling large numbers of samples.

Ordering information



Testing laboratories are under constant pressure to stay compliant with standards while expanding the number of molecular tests offered. When adopting a new testing method such as our real-time PCR UTM solution, we can assist in validating the workflow to ensure a successful launch.

Our analytical validation (AV) consulting services can speed up the launch process by up to 75% and cut costs by up to half. Our expert team will consult with you to develop and optimize your validation workflow, while providing data analysis support and template documentation to fully maximize your instrument and reagent investment.

Learn more ›


1. Wojno, K J et al. (2020) Multiplex PCR Based Urinary Tract Infection (UTI) Analysis Compared to Traditional Urine Culture in Identifying Significant Pathogens in Symptomatic Patients. Urology 136: 119–126. doi:10.1016/j.urology.2019.10.018

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