Drug Markers

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).

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).
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.

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.

Reported

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

Related Tests

AFB3, AFB4, NTM3, NTM6, APPRO, NTM13, MTB2

License Comments

NY State: Waiver/single use permit required for genotypic susceptibility markers.

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.
MTBC extensive drug resistance (XDR) genes	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).
NTM drug resistance genes	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.