Mycobacterium tuberculosis complex – Drug Susceptibility Prediction using Whole Genome Sequencing
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| WSLH Department: | CDD - Communicable Disease Division |
| WSLH Test Code: | MM00270 |
| Day(s) Performed: | Monday - Friday |
| Turn-around Time: | 1-3 weeks |
| Recommended Uses: | To identify M. tuberculosis complex (MTBC) organisms to the species level and perform molecular prediction of resistance to first line antimicrobial agents isoniazid (INH), rifampin (RIF), ethambutol (EMB), and pyrazinamide (PZA). |
| Pre-approval: | No |
| Contraindications: | |
| Additional Tests Performed: |
Phenotypic Mycobacterium tuberculosis complex susceptibility testing [MM00204] will be performed (fee-for-service) on an initial MTBC isolate from each patient. GeneXpert MTB/RIF (MM00261) will automatically be performed (fee-exempt) on all isolates submitted for 1st-line DST. Isolates predicted resistant to rifampin or two or more first-line drugs are automatically referred to CDC for second-line drug susceptibility testing (fee-exempt). The first M. tuberculosis complex isolate per patient is automatically genotyped as part of the CDC universal genotyping program (fee-exempt). |
| Preparation for Collection: | |
| Specimen Requirements: | M. tuberculosis complex isolate in broth or solid media |
| Collection Instructions: | |
| Collection Kit/Container: |
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| Requisition Form: |
(This is a reflex test, so cannot be ordered by submitter. We will perform automatically on isolates that meet our criteria) |
| Required Information: | Identification of organism as a member of the M. tuberculosis complex. Laboratory regulations require the following minimum information to be provided on the requisition form for a specimen to be accepted for testing: Patient name or unique identifier, date and time of collection, patient date of birth and sex, specimen type/site of collection, test request(s), clinician name and UPIN, and address for reporting results. Please be certain that name/identifier on the form matches that on the specimen label which is required to have a minimum of two identifiers. |
| Rejection Criteria: | This testing is only performed on pure MTBC isolates. Mixed or contaminated isolates are not acceptable for this testing. |
| Specimen Handling: | Cultures may be transported to the laboratory at ambient temperatures. Avoid temperature extremes during transport. |
| Packaging Requirements: | |
| Courier Information: | Specimens submitted for surveillance or at the request of a public health department are eligible for fee-exempt courier. Contact Purple Mountain Dispatch at 800-990-9668 for specimen pickup. |
| Specimen Receiving Hours: | Monday-Friday 6:00 AM - 4:30 PM, Saturday 8:00 AM - 12:00 PM |
| Results Include: | M. tuberculosis complex organism identification: M. tuberculosis, M. bovis, or M. bovis-BCG M. tuberculosis complex organisms: - No high-confidence mutations associated with resistance to [RIF/INH/PZA/EMB] have been detected; - Mutation(s) associated with resistance to [RIF/INH/PZA/EMB] detected; - Mutations with unknown significance to [RIF/INH/PZA/EMB] have been detected. Resistance to [RIF/INH/PZA/EMB] cannot be ruled out.; - Unable to amplify genes associated with resistance to [RIF/INH/PZA/EMB]. Resistance to [RIF/INH/PZA/EMB] cannot be ruled out; - No interpretation possible - Not performed |
| Limitations: | Test can only be performed on pure M. tuberculosis complex isolates. Mixed or contaminated cultures will extend turnaround time significantly and may prevent testing if pure M. tuberculosis complex cannot be isolated. Poorly growing isolates may not provide enough material for adequate DNA extraction. Results may be delayed or not interpretable. |
| Additional Tests Recommended: | |
| Additional Comments: | If phenotypic MTBC 1st-line susceptibility testing has already been performed on an isolate, WGS testing will not be reported for any drug for which concordant phenotypic testing has been reported. Detection of known resistance mutations that confer low-level drug resistance that is not detected by phenotypic assay may result in discordant genotypic and phenotypic susceptibility results. |
| Methodology: | Whole-genome sequencing of MTBC culture isolate DNA. |
| Includes: | Identification of MTBC species. Molecular prediction of resistance to standard 1st-line MTBC antimycobacterial agents. |
| Regulatory Compliance: |
| CPT Code: | 87153, 87900x4 |
| Price: | $320.00 |
| Fee Exempt Eligible: | Yes |
| Billing and Revenue Office: | 1-800-862-1065 arbill@slh.wisc.edu |