What laboratory and patient factors can cause a false‑positive Cryptococcus neoformans PCR result on cerebrospinal fluid?

Causes of False Positive Cryptococcus neoformans CSF PCR

False-positive Cryptococcus neoformans PCR results in CSF are exceedingly rare, but the more commonly used cryptococcal antigen test can yield false positives due to cross-reactivity with other organisms and autoantibodies, which clinicians must distinguish from true PCR false positives.

Key Distinction: Antigen vs PCR Testing

The available evidence primarily addresses cryptococcal antigen testing rather than PCR specifically. The IDSA/ASM guidelines note that cryptococcal antigen tests have sensitivity and specificity >90%, but false positive and false negative results may occur, for example, in patients with HIV/AIDS 1.

Documented Causes of False-Positive Cryptococcal Antigen Tests

Cross-Reactivity with Other Organisms

• Trichosporon beigelii infection can cause false-positive cryptococcal antigen reactions 1
• Stomatococcus mucilaginosis infection may produce false-positive results 1
• Cross-reactivity with other endemic fungi: Cryptococcal meningitis itself can cause false-positive antibody results for Histoplasma (35% of cases), Coccidioides (26%), and Blastomyces (4%) in CSF, suggesting bidirectional cross-reactivity may theoretically occur 2

Autoimmune Factors

• Circulating rheumatoid factor can interfere with cryptococcal antigen testing 1
• Elevated antinuclear antibody (ANA) titers in active systemic lupus erythematosus have been documented to cause false-positive CSF cryptococcal antigen results 3
• Active autoimmune disease, particularly SLE with Libman-Sacks endocarditis, has been associated with transient false-positive results that resolve on repeat testing 3

Malignancy

• Concomitant malignancy should be excluded if positive antigen is the only evidence of infection 1

PCR-Specific Considerations

For PCR testing specifically, the evidence shows:

• PCR has demonstrated high specificity (96-100%) in research studies and does not amplify other fungal DNA 4, 5
• False-positive PCR results were obtained in some bacterial meningitis studies using semi-nested PCR strategies, though the specific causes were not detailed 1
• The primary concern with PCR is false negatives rather than false positives, particularly in patients with prior antifungal exposure or low fungal burden 6

Clinical Algorithm for Suspected False Positives

When to Suspect a False Positive

• Clinical presentation inconsistent with cryptococcal meningoencephalitis despite positive test 3
• Active autoimmune disease with elevated autoantibodies (ANA, rheumatoid factor) 3
• Known infection with Trichosporon or Stomatococcus species 1
• Underlying malignancy without other evidence of cryptococcal infection 1

Confirmatory Testing Strategy

• Repeat CSF testing 2-3 days later, as false positives may resolve on repeat analysis 3
• Perform India ink microscopy with cytospin centrifugation (sensitivity 97-100%) if expertise available 6
• Order fungal culture from CSF, which remains the gold standard despite lower sensitivity 1
• Do not rely on a single positive test when clinical picture is discordant—the American Society of Transplantation guidelines emphasize that antigen positivity should be considered definitive only when consistent with clinical presentation 1

Critical Pitfall to Avoid

Never assume a positive cryptococcal test is false without thorough investigation, as cryptococcal meningitis carries high mortality if untreated. The IDSA guidelines emphasize that while false positives can occur, the test maintains >90% specificity 1. When in doubt, treat empirically while awaiting confirmatory culture results to prioritize patient survival over diagnostic certainty.