Test Catalog

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

Useful For Suggests clinical disorders or settings where the test may be helpful

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 Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

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; TB2LN / Susceptibility, Mycobacterium tuberculosis Complex, Second Line; and TBPZA / Susceptibility, Mycobacterium tuberculosis Complex, Pyrazinamide.

Clinical Information Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

An important component of disease management for patients with tuberculosis is testing of Mycobacterium tuberculosis complex isolates for resistance to first- and second-line antituberculous medications. Phenotypic culture-based drug resistance testing is often performed using broth methods since they are more rapid than the gold-standard agar proportion method. However, even the rapid broth methods require approximately 14 days culture and identification of the isolate as M tuberculosis complex before susceptibility testing can be performed.

 

This whole genome sequencing (WGS) testing provides molecular detection of well-characterized drug-resistance variants in M tuberculosis complex by sequencing M tuberculosis isolates. It is intended to aid in the detection of resistance to first- and second-line antituberculous agents including isoniazid, rifampin, ethambutol, pyrazinamide, the fluoroquinolones (moxifloxacin and ofloxacin) and the aminoglycosides (streptomycin, kanamycin, and amikacin). This testing evaluates selected genes of interest including:

 

Drug/Drug Class

Gene

Isoniazid

ahpC

fabG1

inhA

katG

Rifampin

rpoB

Ethambutol

embB

Pyrazinamide

pncA

Fluoroquinolones

gyrA

Aminoglycosides

eis

gidB

rpsL

rrs

Reference Values Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

Results are reported as variant detected or no variant detected.

Interpretation Provides information to assist in interpretation of the test results

Variants detected in the queried genes of Mycobacterium  tuberculosis complex that are highly associated with drug resistance are reported along with an indication of how often the detected gene variant correlated with phenotypic culture-based drug resistance in a verification study of the whole genome sequencing method. For example, detection of an rpoB S450L variant would be reported as "rpoB S450L" and a comment would be included on the report stating "probable rifampin resistance; in a study of 173 isolates, 35/35 (100%) of isolates with this variant were resistant to rifampin".

 

If no variants associated with drug resistance are detected in the M tuberculosis complex isolate, a "no variant detected" result is reported along with an indication of how often isolates in the verification study that displayed phenotypic culture-based drug resistance had a variant in the evaluated gene. For example, if no variant was detected in the gyrA gene, the report would indicate "No variant detected" and a comment stating "In a study of 173 isolates, 22/23 (95.7%) of fluoroquinolone resistant isolates had a variant in gyrA."

 

Genetic variants of unknown significance are not reported.

Cautions Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

The Mayo genetic variant database contains more than 380 high-confidence variants in selected genes within the Mycobacterium tuberculosis complex that are strongly associated with drug resistance. There may be other genetic variants in the queried genes, or additional genes not examined, that have an undefined correlation with resistance in M tuberculosis complex. Therefore, traditional phenotypic antimicrobial resistance testing is required to supplement the genotypic sequencing results.

 

The absence of a genetic variant in this assay does not indicate that the isolate is susceptible to an antimicrobial agent since not all genes in the M tuberculosis complex are queried and since the effect of genetic variant combinations is currently unknown.

 

The detection of a variant may not imply phenotypic resistance as the gene may not be expressed, may be expressed in low levels, or may be nonfunctional.

Clinical Reference Recommendations for in-depth reading of a clinical nature

1. Kozyreva VK, Truong C-L, Greninger AL, et al: Validation and Implementation of a Clinical Laboratory Improvements Act-Compliant Whole Genome Sequencing in the Public Health Microbiology Laboratory. J Clin Microbiol 2017;55:2502-2520

2. Shea J, Halse TA, Lapierre P, et al: Comprehensive Whole-Genome Sequencing and Reporting of Drug Resistance Profiles on Clinical Cases of Mycobacterium tuberculosis in New York State. J Clin Microbiol 2017;55:1871-1882

3. Campbell PJ, Morlock GP, Sikes RD, et al: Molecular Detection of Mutations Associated with First- and Second-Line Drug Resistance Compared with Conventional Drug Susceptibility Testing of Mycobacterium tuberculosis. Antimicrob Agents Chemother 2011;55:2032-2041

Special Instructions Library of PDFs including pertinent information and forms related to the test