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Test ID TBNGS Mycobacterium tuberculosis Complex, Molecular Detection of Drug Resistance Markers, Whole Genome Sequencing, Varies

Infectious


Additional Testing Requirements


If traditional broth-based phenotypic drug resistance testing is desired, add TB1LN / Antimicrobial Susceptibility, Mycobacterium tuberculosis Complex, First Line, Varies; TB2LN / Susceptibility, Mycobacterium tuberculosis Complex, Second Line, Varies; and TBPZA / Susceptibility, Mycobacterium tuberculosis Complex, Pyrazinamide, Varies.



Shipping Instructions


See Infectious Specimen Shipping Guidelines in Special Instructions



Necessary Information


1. Specimen source is required.

2. Organism identification is required; if not provided then organism identification will be reflexed to CTBID / Culture Referred for Identification, Mycobacterium and Nocardia, Varies with additional charges.

3. Method of identification is required (eg, nucleic acid hybridization probes, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry [MALDI-TOF MS], DNA sequencing, line probe assay).



Specimen Required


Supplies: Infectious Container, Large (T146)

Specimen Type: Mycobacterium tuberculosis complex isolate growing in pure culture. Isolates older than 5 weeks or not in a pure culture may require subculture for fresh, isolated growth so the turnaround time for results may be delayed.

Container/Tube: Middlebrook (7H10 or 7H11) medium slant; growth in broth medium (eg, Mycobacteria Growth Indicator Tube [7H9] broth) or on a Lowenstein-Jensen medium slant can be sent but turnaround time for results may be delayed because subculture to Middlebrook agar medium may be required. Organisms received in mixture may result in additional charges for isolation and identification.

Specimen Volume: Isolate with visible growth on solid media; if broth is sent, 3 mL or more of broth culture required.

Collection Instructions:

1. Organism must be in pure culture, actively growing. Do not submit mixed cultures.

2. Place specimen in a large infectious container and label as an etiologic agent/infectious substance.


Useful For

Molecular detection of drug resistance variants in culture isolates of the Mycobacterium tuberculosis complex

 

May provide a more rapid detection of drug resistance than phenotypic, broth-based testing

 

Aiding in the resolution of discrepant results obtained using phenotypic methods testing for M tuberculosis isolates that are not sufficiently viable to allow for culture-based testing

Testing Algorithm

Whole genome sequencing (WGS) of Mycobacterium tuberculosis complex isolates is performed followed by evaluation of selected genes of interest for the presence of well-characterized, drug resistance-conferring variants.

 

Traditional broth-based, phenotypic drug resistance testing should also be performed, since not all genes associated with resistance within the M tuberculosis complex genome have been fully elucidated or are evaluated in this test. If traditional broth-based phenotypic drug resistance testing is desired, add TB1LN / Antimicrobial Susceptibility, Mycobacterium tuberculosis Complex, First Line, Varies; TB2LN / Susceptibility, Mycobacterium tuberculosis Complex, Second Line, Varies; and TBPZA / Susceptibility, Mycobacterium tuberculosis Complex, Pyrazinamide, Varies.

Method Name

Whole Genome Sequencing

Reporting Name

Susceptibility, Mtb Complex, NGS

Specimen Type

Varies

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Ambient (preferred)
  Refrigerated 

Day(s) Performed

Tuesday, Thursday

Report Available

7 to 14 days

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Test Classification

This test was developed, and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information

81479

LOINC Code Information

Test ID Test Order Name Order LOINC Value
TBNGS Susceptibility, Mtb Complex, NGS 94053-6

 

Result ID Test Result Name Result LOINC Value
TBOR Organism Identification 9825-1
TBIS Culture isolate grown from specimen source 31208-2
602791 rpoB 94065-0
603383 rpoB Interpretation 89489-9
603384 katG 94054-4
603385 katG Interpretation 89488-1
603386 inhA 94055-1
603387 inhA Interpretation 89488-1
603388 fabG1 94056-9
603389 fabG1 Interpretation 89488-1
603390 ahpC 94057-7
603391 ahpC Interpretation 89488-1
603392 embB 94058-5
603393 embB Interpretation 89491-5
603394 pncA 94059-3
603395 pncA Interpretation 92242-7
603396 gyrA 94060-1
603397 gyrA Interpretation 89487-3
603398 gidB 94061-9
603399 gidB Interpretation 89490-7
603400 rrs 94062-7
603401 rrs Interpretation 89490-7
603402 rpsL 94063-5
603403 rpsL Interpretation 89490-7
603404 eis 94064-3
603405 eis Interpretation 89490-7
603535 Method 85069-3

Reference Values

Results are reported as variant detected or no variant detected.