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MDL Test Order Mycobacterium tuberculosis complex: Molecular Detection of Drug Resistance

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Test Name

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

Test Methodology	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 Criteria	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-Approval Required	Pyrosequencing is no longer offered for routine test requestions as of June 10, 2024. For molecular drug resistance detection for TB in primary specimens, or contaminated or non-viable cultures, please see: Mycobacterium tuberculosis complex: Drug Resistance Detection & Species Identification by targeted Next Generation Sequencing For molecular drug resistance detection for TB in pure culture isolates, please see: Mycobacterium tuberculosis complex: Drug Resistance Detection & Species Identification by Whole Genome Sequencing
Supplemental Information and Required Form(s)	Barcode submittal 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 Type(s)	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	Sediments: Room Temp: not acceptable. Refrigerated (2 – 8°C): up to 30 days. Frozen (≤ -70°C): up to 120 days. Cultures: 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 Department 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 CDPHTBDST@cdph.ca.gov or call the MMPDS Section at (510) 412-3929

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