Molecular Assay for the Identification of Clinically Relevant Mycobacterial Species from Patient Specimens

Overview

Non-tuberculous mycobacteria (NTM) are free-living, ubiquitous organisms. Over 200 species of NTM have been identified using molecular techniques. Their pathogenic potential varies, making accurate species-level identification critical for assessing clinical relevance and guiding patient care.

The GenoType CMdirect assay is a molecular test that detects both:

• Mycobacterium tuberculosis complex
• Clinically relevant NTM species

This test is used directly on patient specimens and serves as an adjunct to mycobacterial culture, especially when:

• Acid-fast bacilli (AFB) microscopy is positive, but
• TB PCR is negative

GenoType CMdirect Assay – Organisms Detected

M. tuberculosis complex

• Identity confirmed by TB PCR
• Genotypic susceptibility testing performed if possible

NTM species identified and reported

M. avium complex
M. fortuitum group
M. gordonae
M. malmoense
M. interjectum
M. szulgai
M. kansasii
M. xenopi

If clinically significant, submit a specimen for mycobacterial culture to enable susceptibility testing.

M. chelonae
M. abscessus complex

If clinically relevant, culture confirmation and susceptibility testing are recommended.

M. scrofulaceum / M. intracellulare
M. marinum / M. ulcerans

These pairs cannot be distinguished by the assay. Submit a culture if clinical confirmation is required.

Unclassified Mycobacterial species

Detected when no specific banding pattern is identified. Mycobacteria are present but untyped. Culture recommended if relevant.

Test Information

Specimen types accepted:

• Sputum
• Endotracheal aspirate
• Bronchoalveolar lavage (BAL)
• Tissue
• Bone marrow
• Pus
• Fluids

Turnaround time: 72 hours

Mnemonic: MOTTPCR

Test Performance

Sensitivity:

• AFB smear positive: 100%
• AFB smear negative: 63.6%–75%

Specificity (AFB smear negative):

• 93.7%–98.9%

(Compared to culture and/or sequencing)

Clinical Relevance of NTM Detection

As environmental organisms, NTM may represent either colonisation, contamination, or true infection. The significance of NTM detection must be evaluated in the context of:

• Clinical and radiological presentation
• Patient’s immune status
• Risk factors for NTM disease
• Repeated detection from sterile sites

Recommendations

• Use Mycobacterial culture to:
  • Confirm identification
  • Perform susceptibility testing