Genotypic Testing for Resistance Markers in Mycobacteria
Test Code
AFB6
Description
Molecular assays can be performed on organisms to determine the presence of mutations associated with drug-resistance. These drug resistance markers will be tested and reported for relevant nontuberculous mycobacteria (NTM) and M. tuberculosis (MTBC) isolates. Genotypic drug marker testing can significantly shorten the time to appropriate therapy for some organisms by rapidly identifying the presence of mutations associated with antibiotic resistance.
Testing is only performed, reported and billed when appropriate for the organism identified. It is automatically included on appropriate organisms when the APPRO algorithm is ordered. It can also be ordered separately on pure isolates or clinical specimens (where it will be performed only if growth of a relevant organism is seen).
Note that a complete drug marker analysis can only be reported if a full identification has been performed. For instance, erm(41) cannot be reported without subspeciating M. abscessus. This is because erm(41) testing is not performed in the case of M. abscessus subsp. massiliense since this has a nonfunctional erm(41) and should be considered susceptible by the erm mechanism regardless of whether erm(41) is detected. On the other hand, if erm(41) is detected in the other two subspecies, mutations can cause them to be either resistant or susceptible. To get these important results, we recommend ordering full identification so that the results for all applicable resistance genes can be reported.
Collect
An identified isolate is required for testing.
- This test can be ordered on a clinical specimen that has been sent to our laboratory for isolation and identification of mycobacteria. See specimen requirements for culture of mycobacteria from a clinical specimen (AFB1, AFB3 or AFB7)
- This test can also be ordered on organisms identified elsewhere. Pure mycobacterial isolates should be sent in solid media such as a Middlebrook slant (7H10 or 7H11), Lowenstein-Jensen (LJ) slant, or in broth (7H9, MGIT, MP BACT/Alert, VersaTrek). Isolates should be pure; if contaminants are identified, an attempt will be made to isolate the AFB and an additional charge will be applied.
- Specimen Volume: visible growth of the isolate on solid media or an isolate sent in ≥ 3 mL of broth.
Unacceptable Conditions
- Cultures received with incomplete identifiers.
- Mixed cultures; Note that prior to rejection, attempts will be made to isolate organisms. A re-isolation charge will be applied in these cases.
- Cultures containing mold.
- Solid media with insufficient growth.
- Cultures submitted on agar plates.
- Liquid media with < 2 mL.
- Leaking specimens.
Storage Transport Temp
Transport or mail isolates at ambient temperature. For nontuberculous mycobacteria (NTM), follow IATA/DOT category B and for M. tuberculosis complex isolates, follow IATA/DOT category A requirements for shipping biological materials.
Stability
Specimens can be sent:
- ambient temperature if ≤3 days from collection
- refrigerate if ≤7 days from collection.
Isolates can be sent ambient on solid or liquid media.
Performed
Mon-Sat
Methodology
PCR-based methods are used. PCR/MALDI-TOF mass spectrometry assay is used as the primary method for NTM drug resistance markers; line probe assays are used as a alternative method. Line probe assays are used for MTBC isolates. See Interpretation for when various line probe assays are applied.
Turnaround Time
Resistance gene testing by line probe is typically reported within 72 hours.
Department
Infectious Disease Laboratory, Mycobacteriology
Synonyms
NTM-DR, NTMDR, line probe, resistance markers, MTB genotypic resistance
Study Offerings
RUO
CAP/CLIA
Related Tests
AFB3, AFB4, NTM3, NTM6, APPRO, NTM13, MTB2
Interpretation
| Test | Gene Markers * | Relevant organism | Explanation |
|---|---|---|---|
| NTM drug resistance markers | erm(41) | M. abscessus subsp. abscessus and M. abscessus subsp bolletii | Functional or nonfunctional erm(41) gene status will be reported. A functional erm(41) gene will encode a ribosome methylase capable of causing inducible resistance to clarithromycin in M. abscessus subspecies. A truncation, or a mutation in position 28 from a thymine to cytosine will result in a nonfunctional gene and susceptibility to clarithromycin. |
| rrs | M. abscesuss subspecies, M. chelonae, species in the M. avium complex | Detection of mutations corresponding to aminoglycoside resistance will be reported. | |
| rrl | M. abscesuss subspecies, M. chelonae, species in the M. avium complex | Detection of mutations corresponding to macrolide resistance will be reported. | |
| MTBC drug and multidrug resistance (MDR) genes | rpoB | M. tuberculosis complex | Detection of mutations corresponding to rifampin resistance will be reported. |
| katG | M. tuberculosis complex | Detection of mutations corresponding to isoniazid resistance will be reported. | |
| inhA | M. tuberculosis complex | Detection of mutations corresponding to isoniazid resistance will be reported. | |
| MTBC extensive drug resistance (XDR) genes | gyrA/ gyrB | Applied to drug/multidrug resistant MTBC | Detection of mutations corresponding to fluoroquinolone resistance will be reported. |
| eis | Applied to drug/multidrug resistant MTBC | Detection of mutations corresponding to kanamycin resistance will be reported. |
* only gene markers relevant for a particular organism will be interrogated.
CPT Code
| Test | Method | CPT code | Billing code | When is this applied? |
|---|---|---|---|---|
| NTM drug resistance genes | PCR/MALDI-TOF mass spectrometry | 87900 | MASDR (1st organism), MASR2 (2nd organism), MASR3 (3rd organism) | If appropriate organisms are recovered (see Interpretation). |
| Line probe assay | 87798 x 2 | NTMDR (1st organism), NTDR2 (2nd organism), NTDR3 (3rd organism) | If appropriate organisms are recovered (see Interpretation). Generally used as alternative method. | |
| MTBC drug and multidrug resistance (MDR) genes | Line Probe | 87798 x 2 | MTB4T | To M. tuberculosis complex |
| MTBC extensive drug resistance (XDR) genes | Line Probe | 87798 x 3 | MTB5T | If a drug or multidrug resistant MTBC is recovered. |
New York Approved
NY Validated
New York Approval Comments
The line probe assay used for drug marker analysis of NTM has been NYS approved. However, drug marker analysis for MTBC has not been NYS approved and will require a waiver for testing.
FDA
LDT