What can cause a positive Tuberculosis (TB) Polymerase Chain Reaction (PCR) result other than actual TB infection?

Causes of Positive TB PCR Other Than Active TB Infection

A positive TB PCR result without active TB infection is most commonly caused by nontuberculous mycobacteria (NTM) infection, laboratory cross-contamination, or detection of non-viable Mycobacterium tuberculosis DNA from prior treated or latent infection.

Primary Causes of False-Positive TB PCR

Nontuberculous Mycobacteria (NTM)

• NTM species are the leading cause of positive molecular tests in patients without active TB, particularly M. avium, M. intracellulare, M. kansasii, M. abscessus, M. massiliense, and M. fortuitum 1
• NTM infections present with similar clinical symptoms to TB but require different antimicrobial treatment strategies 1
• In one study, among patients with positive acid-fast bacilli cultures but negative T-SPOT.TB results, 4 were confirmed as NTM and 2 were suspected NTM 2
• Cross-reactivity occurs because some PCR primers may amplify DNA sequences shared between MTB complex and NTM species 1

Laboratory Cross-Contamination

• Cross-contamination during simultaneous processing of multiple specimens is a well-documented cause of false-positive results 3
• The three most critical factors causing laboratory false-positives are: inappropriate technician function, contamination of reagents, and aerosol production 3
• False-positives most commonly occur in cases with only one positive culture but negative direct smear 3
• Contamination can occur at any step from specimen collection through PCR amplification 4

Detection of Non-Viable or Residual MTB DNA

• PCR detects DNA from both viable and non-viable organisms, meaning it can remain positive after successful treatment or in latent infection 4
• Positive PCR results in asymptomatic patients may represent PCR-amplifiable MTB DNA without clinical relevance 4
• In a prospective study, 16 of 54 presumably non-TB patients showed amplifiable MTB DNA (specificity 0.7), suggesting PCR positivity does not necessarily reflect active infection 4

Clinical Context and Interpretation

When to Suspect False-Positive Results

• Single positive PCR with negative AFB smear and negative culture should raise suspicion for false-positive 3
• Discordance between PCR results and clinical presentation (absence of TB symptoms, normal chest X-ray) 4
• Positive PCR in immunocompromised patients over 70 years old with lymphocytopenia may represent either NTM or false-positive 2

Confirmatory Testing Strategy

• Use of two MTB-specific primer pairs is essential for diagnostic applications to improve specificity 4
• Culture remains the gold standard and should be performed in parallel with PCR 3, 4
• Whole-genome sequencing or genotyping of all positive samples can identify false-positives and distinguish MTB from NTM 3
• Species-specific molecular testing can identify the six dominant NTM species in three-quarters of NTM-positive cases 1

Common Pitfalls to Avoid

• Never rely on a single positive PCR result alone without clinical correlation and confirmatory testing 4
• Do not assume all positive PCR results represent active TB requiring full treatment 4
• Failure to use contamination controls parallel to all PCR steps compromises validity of results 4
• Ignoring the possibility of NTM in elderly or immunocompromised patients with positive molecular tests 2
• Not considering prior TB treatment history—PCR may remain positive long after successful treatment 4

Practical Diagnostic Algorithm

1. Obtain AFB smear, culture, and PCR simultaneously from clinical specimens 3, 4
2. If PCR positive but smear negative: high suspicion for false-positive, NTM, or non-viable DNA 3, 4
3. If culture grows mycobacteria, perform species identification to distinguish MTB from NTM 1, 2
4. If PCR positive but culture negative after adequate incubation: likely false-positive or non-viable DNA 4
5. Use molecular epidemiological surveillance and genotyping to confirm true positives in questionable cases 3