Lab Update 11 – Molecular Assay for the Identification of Clinically Relevant Mycobacterial Species from Patient Specimens

November 2019
Ampath | ampath.co.za

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

Contributors:
Dr. Kathy-Anne Strydom – Microbiologist
Dr. Pieter Ekermans – Clinical Pathologist

Edition No. 11

📌 For clinical support or additional information, please contact your local Ampath pathologist.