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Test Name 

Mycobacterium tuberculosis complex: Molecular Detection of Drug Resistance by Pyrosequencing Assay

Test ​​​​​M​​​e​th​o​​​d​​​olog​y​​​

​​Pyrosequencing (PSQ) is the method used to identify mutations associated with drug resistance.

The following molecular targets associated with drug resistance are detected:

First-line drug resistance (default):
Isoniazid:  katG, inhA promoter, ahpC promoter, and fabG1
Rifampin:  rpoB
Second-line drug resistance (reflex or special request):
Quinolones:  gyrA
Injectable drugs (kanamycin, amikacin, capreomycin):  rrs (upon request)  

Please contact the laboratory for more information on pyrosequencing method.​

Reflex Testing

​If mutations associated with resistance are detected in the first-line targets, the second-line PSQ panel testing will be performed automatically. Alternatively, second-line PSQ testing can be performed in parallel or alone upon submitter request.

Pre-A​pproval Required​
​​Pre-approval is not required except when requesting testing for the following:

  • AFB-negative specimen
  • Sterile body fluids/specimens 
  • Duplicate submission, i.e., samples from the same patient collected within 2 months from prior collection date.​​​
Supp​lemental Information and Required Form(s)​
​Barcode subm​ittal form 444 “Mycobacteriology-Drug Susceptibility Testing of MTBC (CA only)”  or instructions for using the MDL Lab Web Portal (ETOR) can be found at:  MDL Submission Instructions and Forms​.
​Indicate submitter’s test results on the submittal form.​

Required Specimen/Sample

​Sediments or cultures are acceptable.

Processed sediment. Concentrated specimens from pulmonary and extra-pulmonary sources, including sputum, bronchial alveolar lavage, pleural fluid, CSF, abscess, gastric aspirate, urine, and tissues are acceptable.

Unprocessed clinical specimens should not be submitted. Submission of specimens from sterile body sites requires pre-approval.

Sediment should be confirmed to be AFB-positive (at least 1+); smear-negative specimens need approval prior to submission.

Culture on solid or in liquid media.

Minimum Volume Required

Sediments: 0.5mL; 1.0 mL is preferred.

Culture in broth: 0.5 mL; 1.0 mL is preferred.

Culture on solid media: visible growth is desired.

Specimen Stability

Room Temp: not acceptable.
Refrigerated (2 – 8°C): up to 30 days.
Frozen (≤ -70°C): up to 120 days.

Room Temp: up to 30 days.
Refrigerated: 2 – 8°C: up to 6 months.
Frozen: Subculture prior to submission.
If culture age exceeds the age mentioned above, subculture prior to submission and submit fresh culture.

Rejection Criteria

  • ​​​Specimens with insufficient or conflicting labelling
  • ​​Leaking specimens
  • Specimens with insufficient quantities
  • Specimens that are too old
  • Specimens improperly stored or transported
  • Formalin fixed tissue and other specimen/sample types not meeting acceptance criteria
  • Duplicate submission, i.e., samples from the same patient collected within 2 months from prior collection date, if no prior approval was received.
Storage/Transport Conditions

​​​Sediment: Refrigerated or frozen.

Cultures: Grow isolate under appropriate conditions. Isolates may be stored under refrigeration or ambient temperature prior to shipping.

Transport Medium,​
if applicable​​

​Not Applicable
Specimen Labeling

​Two identifiers, including patient full name, and at least one other identifier (specimen accession number, date of birth, medical record number).​​
Shipping Instructions and Specimen Handling Requirements

​​​​Ship diagnostic specimen with cold packs (do not freeze). Ship cultures at ambient temperature (do not freeze).

Follow the appropriate DOT/IATA approved shipping procedures. All the suspected MTBC human specimens should be shipped as a Biological Substance, Category B (UN3373).

Suspected or confirmed MTBC cultures should be shipped as a Category A Infectious Substance, Affecting Humans (UN2814).

​Ensure that culture isolates are sent in media flask or tubes containing a screw-top cap that is additionally sealed with parafilm or tape for additional protection against leaking.

Ship to:

California Depart​ment of Public Health​
Microbial Diseases Laboratory ​
ATTN:  TB Drug Susceptibility Testing Unit ​​
850 Marina Bay Parkway, Specimen Receiving Room B106
Richmond, CA  94804

Specimen Collection Instructions, if applicable

​​Not Applicable
Turnaround Time

​3 days​
Interferences & Limitations

​​Inhibitory substances in the specimen may prevent successful DNA amplification and pyrosequencing.

Reference Range
​Not Applicable
Additional Information
​​The assay is indicated for the patients suspected of having drug-resistant tuberculosis and patients who are especially susceptible to treatment failure. The test can be performed on cultures of M. tuberculosis complex mixed with non-TB mycobacteria or other bacteria.

​​The samples will be forwarded to CDC if further characterization is needed. 

MDL Point of Contact
​For questions regarding submissions, please email or call the MMPDS Section at (510) 412-3929​​


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