Care must be taken when evaluating the claims of new laboratory tests. While new technology can be exciting and offer undeniable capabilities over conventional practices, one must consider whether the new technology meaningfully improves clinical utility and, if so, whether these improvements outweigh the downsides of the new technology.

Claims about Urine PCR

Turnaround Time

Whereas the timescale of the standard urine culture is measured in days, the timescale of urine PCR is measured in hours. However, it should be kept in mind that while the urine PCR test may only take a few hours to perform, the batch nature of urine PCR testing will somewhat diminish the final turnaround time improvement. That said, the turnaround time of urine PCR can be expected to be around 12-24 hours. In contrast, a traditional urine culture can typically provide a preliminary identification of the pathogen within 24 hours for the most common causes of UTI (e.g., E. coli, Staphylococcus, Streptococcus). For other less common microorganism, preliminary information can be provided within 24 hours (e.g., gram negative versus gram positive), and a definitive identification can typically be provided within 48 hours, along with antibiotic susceptibilities.

Sensitivity

PCR technology is capable of detecting lower microorganism concentrations in urine than can be detected by standard urine culture. The lower limit of detection for a standard urine culture is approximately 1,000 CFU/mL. In contrast, urine PCR can theoretically detect microorganisms down to 1 – 10 CFU/mL. However, the clinical utility of this improvement in sensitivity is not clear. Ordinarily, pathogenic organisms in UTIs are present at high concentrations and therefore will easily be detected by standard urine culture. Highly sensitive urine PCR tests may carry the risk of detecting non-pathogenic microorganisms present in low concentrations.

Antibiotic Resistance Genes

PCR technology allows for the detection of genes which encode antibiotic resistance. While it can be obtained quickly than antibiotic susceptibility testing in standard urine culture, this information is a poor substitute for susceptibility testing. Antibiotic resistance gene detection in current urine PCR testing only covers a fraction of relevant antibiotic resistance mechanisms, and it cannot provide information on whether the gene is expressed by the detected pathogen. In contrast, antibiotic susceptibility testing (from standard urine culture) provides the phenotypic susceptibility of the identified pathogens against a wide range of antibiotics.

Downsides of Urine PCR

No Antibiotic Susceptibility

As mentioned above, urine PCR cannot test for phenotypic antibiotic susceptibility. Testing for antibiotic resistance genes somewhat compensates for this, but it is hardly a sufficient substitute. Antibiotic susceptibility is crucial information that guides the treatment of bacterial infection and aids proper antibiotic stewardship.

Limited Test Menu

The targeted nature of urine PCR lends itself to a limited test menu of pathogens. While urine PCR panels typically test for the most common pathogenic organisms, there are a large number of less common pathogens, and current urine PCR techniques cannot test for them all. Standard urine culture, on the other hand, is not limited in this way and can detect virtually any microorganism causing a UTI.

Cost

The cost of urine PCR is dramatically higher than standard urine culture. Many major insurers, including Medicare, are dramatically limiting payment for urine PCR. As of now, this trend looks unlikely to reverse any time soon. If insurers are not paying for the test, it is more likely that the sizeable bill for urine PCR would burden the patient.

Conclusions

The clearest advantage urine PCR has over standard urine culture is a faster turnaround time. The increased sensitivity is likely of limited value in urine specimens, and while the detection of antibiotic resistance genes can be clinically useful, this is an inadequate substitute for phenotypic antibiotic susceptibility. Combine this mixed picture with the more limited test menu and much higher cost of urine PCR, and the case for urine PCR for routine UTI testing becomes much less clear. Of course, there are sure to be specialized cases in which urine PCR is called for, but standard urine culture may be the best option for routine UTI testing for the foreseeable future.