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

Highlights

This assay may provide results within 1 week as opposed to phenotypic broth-based or agar-based assays that can take, on average, 14 days to produce results. Additionally, this assay can be useful as an aid in the resolution of discrepant phenotypic results or in instances when the isolate does not grow sufficiently well to allow for phenotypic 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, Varies; TB2LN / Susceptibility, Mycobacterium tuberculosis Complex, Second Line, Varies; and TBPZA / Susceptibility, Mycobacterium tuberculosis Complex, Pyrazinamide, Varies.

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

Method Name
A short description of the method used to perform the test

Whole Genome Sequencing

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

Yes

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

Susceptibility, Mtb Complex, NGS

Aliases
Lists additional common names for a test, as an aid in searching

Next Gen Sequencing Test

Mycobacterium tuberculosis Drug Susceptibility Test

Whole Genome Sequencing Test

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

Specimen Type
Describes the specimen type validated for testing

Varies

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).

ORDER QUESTIONS AND ANSWERS

Question ID Description Answers
TBOR Organism Identification
TBIS Culture isolate grown from specimen source
TIDM Identification method

Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing

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.

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

Forms

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

Agar plate
Mixed culture
Reject

Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included

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

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

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 Clinic 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, Crandall J, Mukhopadhyay R, Chaturvedi V: Validation and implementation of a Clinical Laboratory Improvements Act-Compliant Whole Genome Sequencing in the Public Health Microbiology Laboratory. J Clin Microbiol. 2017 Aug;55(8):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 Jun;55(6):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 May;55(5):2032-2041

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

Method Description
Describes how the test is performed and provides a method-specific reference

Mycobacterium tuberculosis complex isolates are lysed and genomic nucleic acid is purified and quantified. Library preparation for whole genome sequencing is performed using 50 to 100 ng of the purified M tuberculosis complex DNA and the Illumina TruSeq Nano DNA Library Preparation Kit. Following library preparation, samples are quantitated and pooled on an Illumina sequencer for multiplexed, paired-end whole genome sequencing. Sequences obtained are compared to the M tuberculosis reference genome (strain H37Rv) to identify variants. Variant review and interpretation is completed by comparing the any variants detected with the Mayo Experience Database and any matching variants are reported. A minimum of 40X position coverage, 20X variant coverage, and 15% variant frequency compared to the H37Rv reference genome is required before reporting a variant. Variants of unknown significance are not reported.(Unpublished Mayo method)

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

No

Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.

Tuesday, Thursday

Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.

7 to 14 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

1 Year

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

Fees
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.

  • Authorized users can sign in to Test Prices for detailed fee information.
  • Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
  • Prospective clients should contact their Regional Manager. For assistance, contact Customer Service.

Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.

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
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.

CPT codes are provided by the performing laboratory.

81479

LOINC® Information
Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the order and results codes of this test. LOINC values are provided by the performing laboratory.

Test Id Test Order Name Order LOINC Value
TBNGS Susceptibility, Mtb Complex, NGS 94053-6
Result Id Test Result Name Result LOINC Value
Applies only to results expressed in units of measure originally reported by the performing laboratory. These values do not apply to results that are converted to other units of measure.
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

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Pdf

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports

Test Update Resources

Change Type Effective Date
Test Status - Test Down 2022-02-10