Are the Advantages of Urine PCR Testing Worth the Higher Costs?

Lilian White, MD
Posted on March 31, 2025

The diagnosis of urinary tract infections (UTIs) has largely been informed by urinalysis or urine culture. More recently, urine polymerase chain reaction (PCR) testing has become a more available option worth considering.

Current standard of care testing for UTIs includes point-of-care (POC) urinalysis (UA) and urine culture; both options have limitations. For instance, the presence of nitrites in urine by POC UA has a high positive predictive value in adults (male and female) and children, and the sensitivity remains high for adults; however, it is significantly reduced to 23% for children younger than 2 years. This reduction makes it less helpful for ruling out UTIs in these children. False positive results may also occur with prolonged air exposure of the test strip.

Urine culture, widely considered the preferred method of diagnosing UTI, has high negative and positive predictive values. Although urine cultures may be unnecessary to diagnose UTI in women who believe they have a UTI and do not have vaginal discharge, a urine culture with antibiotic sensitivities is currently recommended for diagnosing and managing UTI in patients in specific populations (ie, adults 65 years of age and older, men, patients with initial treatment failure, women with recurrent UTIs, patients with a history of resistant UTIs, children).

Urine PCR testing has demonstrated consistency with urine culture and is non-inferior to urine culture testing for the presence of a UTI. PCR has a high specificity and negative predictive value (100% and 94%, respectively), making it especially helpful in identifying and ruling out infections. Moreover, urine PCR testing often includes the assessment of resistance genes to guide antibiotic treatment.

Compared with POC UA, which provides results in just a couple of minutes, urine culture typically requires 24 to 48 hours for results and may take longer to report antibiotic sensitivities. PCR testing, by contrast, can yield results in less than 4 hours (plus transport time to the laboratory). This rapid turnaround may allow for more timely treatment with the most effective antibiotics narrow spectrum. Additionally, PCR testing can identify more fastidious bacteria that urine culture may miss.

The evidence for urine PCR testing in children is limited but promising. One study demonstrated a sensitivity and specificity of 100% and 99.5%, respectively, for E. coli infection specifically in children in the emergency room setting.

Additional studies are needed on potential harms, optimal testing setting (inpatient vs outpatient), cost-effectiveness, and the benefits of more timely diagnosis related to PCR testing. With the high sensitivity of PCR testing, there is a risk of overdiagnosis and overtreatment. One study found that patients with a negative urine culture and positive PCR testing tended to improve with treatment of a symptomatic infection. The cost of PCR testing varies but is substantially more expensive compared with urine culture. The median cost of urine PCR testing in 2023 was $585 for PCR and $8 for urine culture. Costs are likely to reduce with time, with some companies currently offering prices from $100 to $200. Access to PCR testing is currently limited; however, with Medicare and Medicaid covering some urine PCR testing, other insurance companies are likely to follow.

Additional reading on the diagnosis and treatment of  UTIs, including a more recent article on the effect of cranberry products on UTI prevention, may be found in the AFP by Topic collection.