False Positive Rate for Neisseria Gonorrhoeae PCR Testing for Anal Swabs

Understanding False Positives in N. gonorrhoeae PCR Testing

The specificity of nucleic acid amplification tests (NAATs) for N. gonorrhoeae, including PCR tests, is generally high at 97-99%, which translates to a false positive rate of 1-3% 2
Despite this high specificity, false positive results can account for a significant proportion of all positive test results, particularly in low-prevalence populations 3

In high-prevalence populations (≥15%), the positive predictive value (PPV) of testing remains high (around 88%), meaning most positive results are true positives 4
In low-prevalence populations (<5%), the PPV drops dramatically (as low as 44%), meaning more than half of positive results could be false positives 4
For example, when using a test with 98% specificity and 80% sensitivity in a population with 2% prevalence, 36 out of 1000 tests will be positive, but only 16 will be true positives (PPV = 44%) 3

The CDC recommends verifying positive screening test results with a supplemental test if a false-positive result is likely to have adverse medical, social, or psychological consequences 5
Verification should be routine in low-prevalence patient populations but might be selective in high-prevalence populations 5
Methods suitable for verifying positive results include culture confirmation, a second NAAT that identifies a different target than the screening test, or use of "blocking" antibody or "competitive" probe verification methods 5

Relying on a single positive PCR result without confirmatory testing, especially in low-prevalence populations 1
Failing to consider the population prevalence when interpreting positive test results 1

Anal swabs may contain higher levels of commensal bacteria that could potentially cross-react with N. gonorrhoeae tests 3
The CDC recommends that clinicians be aware of the potential for false positives and consider verification testing, particularly in low-prevalence populations 3