Mycobacterium tuberculosis complex PCR

Which test do we use?

For pulmonary specimens, CSF, and extra-pulmonary specimens with strong suspicion of rifampicine-resistant TB: Xpert MTB/RIF.


  • The World Health Organization recommends the test as a primary diagnostic tool for (i) all cases suspected of multi-drug resistant TB, (ii) all HIV-positive cases suspected for TB and (iii) all cases suspected of TB meningitis (WHO/HTM/TB/2013.16),
  • At ITM the test has been validated for pulmonary specimens.


For extra-pulmonary specimens other than CSF without suspicion of rifampicin-resistant TB: DNA extraction followed by in-house PCR based on the gene coding for 16S rRNA with primers specific for the genus Mycobacterium and primers specific for M. tuberculosis-complex.


  • Non-tuberculous mycobacteria (NTM) are identified to the species level by sequencing of the positive ‘Mycobacterium’ amplicron.


In case of suspicion for M. lepae or M. ulcerans infection: specific in-house (q)PCR.

Sampling instructions

Possible on sputum, broncial lavage, bronchial aspirate, cerebrospinal fluid, biopsy, purulence, gastric fluid, urine, sperm, aspirates.


A minimum volume of 1 ml is required.


PCR analyses are not performed on formamide-treated samples.

Storage conditions

The samples must be kept in the refrigerator at 2-8°C.
The samples can be sent at room temperature.


Samples can be stored and shipped without additives, or in the presence of sterile physiological water.

Important advice

Attention: Xpert MTB/RIF does not allow for detection of non-tuberculous mycobacteria (NTM): analysis for such cases should be mentioned explicitly on the request form to intiiate the in-house PCR. Standard Xpert MTB/RIF analysis leaves insufficient sample to perform additional analyses.


Suspicion of M. leprae or M. ulcerans should be mentioned explicitly on the request form.


Detection limit:

  • Xpert MTB/RIF: 131 CFU/ml (spiked sputum studies) or 10-100 CFU/mL(concentrated specimens)
  • in-house PCR: 100 bacilli/20µl sample.


Please indicate whether art. 24bis is applicable.


If this analysis is not conform the above requirements, it will only be performed if sufficiently motivated.


If you also request a culture, the samples should not be older than 7 days.


Additional culture can only be realized if sufficient sample has been provided.


  • Xpert MTB/RIF: daily
  • In-house PCR: Once a week (DNA extraction is initiated on Monday morning)

Reference values


Delivery time of the result

  • Xpert MTB/RIF: within 2 working days
  • In-house PCR:
    • When delivered on Friday (or Thursday if Friday is a holiday): approximately 4 working days.
    • When delivered on any other day: approximately 7 working days.


Attention: Sequence analysis for identifciation of NTM, will take approximately 5 extra working days.


Xpert MTB/RIF: yes

in-house 16S PCR: yes

ISO 15189 – Belac 147-MED

M. leprae and M. ulcerans PCR: no

Laatste wijziging op: 23/01/2020