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Epic Code LAB1230037 Mycobacterium tuberculosis Complex, Molecular Detection, PCR, Varies

Additional Codes

Mayo Code: MTBRP

Reporting Name

M tuberculosis Complex PCR

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Clinical Information

Each year, Mycobacterium tuberculosis accounts for approximately 1.4 million deaths and is responsible for 9 million newly diagnosed cases of tuberculosis worldwide. M tuberculosis is spread from person-to-person via respiratory transmission, and has the potential to become resistant to many or all of the antibiotics currently used if antimycobacterial treatment is not promptly initiated. Therefore, rapid and accurate detection of M tuberculosis in patient specimens is of clinical and public health importance.

 

Conventional culture methods can generally detect M tuberculosis in 2 to 3 weeks, although up to 8 weeks of incubation may be required in some instances. Developed at Mayo Clinic, this rapid PCR assay detects M tuberculosis complex DNA directly from respiratory specimens and other specimens without waiting for growth in culture and, therefore, the results are available the same day the specimen is received in the laboratory. A mycobacterial culture should always be performed in addition to the PCR assay. The PCR assay is rapid but the culture has increased sensitivity over the PCR assay. The PCR assay targets a unique sequence within the katG gene, which is present in members of the M tuberculosis complex. In addition, the assay can detect genotypic resistance to isoniazid mediated by mutations in the katG target, when present.

Useful For

Rapid detection of Mycobacterium tuberculosis complex DNA, preferred method

 

Detection of M tuberculosis, when used in conjunction with mycobacterial culture

 

This test should not be used to determine bacteriologic cure or to monitor response to therapy.

 

This test is not intended for the detection of latent tuberculosis and must not be used as a substitute for tests intended for detection of latent tuberculosis such as the tuberculin skin test (TST/PPD) or an interferon gamma release assay (IGRA).

Specimen Type

Varies
Laboratory Test Directory Note:

Lab Central Staff: All CSF specimens to Hematology first.


Additional Testing Requirements


This test should always be performed in conjunction with mycobacterial culture.



Shipping Instructions


Specimen must arrive within 7 days of collection; specimen >7 days will be rejected.



Necessary Information


Specimen source is required.



Specimen Required


The high sensitivity of amplification by PCR requires the specimen to be processed in an environment in which contamination of the specimen by Mycobacterium tuberculosis DNA is unlikely.

 

If a single specimen is being shared between mycobacteria culture, acid-fast smear, and/or M tuberculosis PCR, a minimum volume of 2 mL for body fluid, 3 mL for respiratory specimen, or a pea-sized piece of tissue should be obtained. Specimen volumes less than indicated may decrease sensitivity of testing. If insufficient volume is submitted, test or tests will be canceled.

 

Preferred Specimens: Body fluid, cerebrospinal fluid (CSF), ocular fluid, respiratory (eg, bronchoalveolar lavage [BAL], bronchial washing, sputum), feces, fresh tissue, bone, bone marrow, or urine

 

Acceptable Specimens: If no fresh specimen is available, digested respiratory specimens treated with N-acetyl-L-cysteine/sodium hydroxide (NALC/NaOH) are acceptable (eg, BAL, bronchial washing, respiratory fluid, sputum, or tracheal secretion), as are NALC/NaOH-treated gastric washings.

 

Submit only 1 of the following specimens:

 

Specimen Type: Body fluid

Sources: Body, bone marrow aspirate, ocular, or CSF

Container/Tube: Sterile container

Specimen Volume: 1 mL

Additional Information: Only fresh, non-NALC/NaOH-digested body fluid is acceptable.

 

Specimen Type: Gastric washing

Container/Tube: Sterile container

Specimen Volume: 2 mL

Collection Instructions: Neutralize specimen within 4 hours of collection with 20 mg of sodium carbonate per 2 mL of gastric washing.

 

Specimen Type: Respiratory

Sources: BAL, bronchial washing, or sputum

Container/Tube: Sterile container

Specimen Volume: 1 mL if only PCR ordered or 3 mL if PCR ordered with smear and culture

 

Specimen Type: Feces

Container/Tube: Sterile container

Specimen Volume: 5-10 g

Additional Information: Only fresh, non-NALC/NaOH-digested fecal specimens are acceptable.

 

Specimen Type: Tissue

Sources: Fresh tissue, bone, or bone marrow biopsy

Container/Tube: Sterile container

Specimen Volume: 5-10 mm

Collection Instructions: Keep moist with sterile water or sterile saline

Additional Information: Only fresh, non-NALC/NaOH-digested tissue is acceptable.

 

Specimen Type: Urine

Container/Tube: Sterile container

Specimen Volume: 1 mL

Collection Instructions: Collect a random urine specimen.

 

Acceptable

Specimen Type: NALC/NaOH-digested respiratory specimens

Sources: Lavage fluid, bronchial washing, gastric washing, respiratory fluid, sputum, or tracheal secretion

Container/Tube: Sterile container

Specimen Volume: 2 mL

Collection Instructions:

1. Submit digested specimen treated with NALC/NaOH.

2. Clearly indicate on container and order form that specimen is a digested specimen.


Specimen Minimum Volume

Body fluid: 0.5 mL
Respiratory specimen-nondigested: 0.5 mL
Fresh tissue or bone: 5 mm
NALC-NaOH-digested specimen: 1 mL
Gastric washing: 1 mL
Stool: 5 g
Urine: 0.5 mL

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Refrigerated (preferred) 7 days
  Frozen  7 days

Reject Due To

Other Blood Specimen in anaerobe vial or viral transport medium (including but not limited to M4, M5, BD viral transport media, thioglycolate broth) Swabs Tissues in formalin fluid
 

Day(s) Performed

Monday through Sunday

Reference Values

Not applicable

Interpretation

A positive result indicates the presence of Mycobacterium tuberculosis complex DNA. Members of the M tuberculosis complex detected by this assay include M tuberculosis, M bovis, M bovis bacillus Calmette-Guerin (BCG), M africanum, M canettii, and M microti. Other species within the M tuberculosis complex (eg, M caprae, M pinnipedii, and M mungi) should, in theory, be detected using the primer and probe sequences in this assay, but they have not been tested. This assay method does not distinguish between the species of the M tuberculosis complex.

 

A negative result indicates the absence of detectable M tuberculosis complex DNA.

 

Isoniazid (INH) resistance mediated through a katG variant will be reported when observed but lack of a katG variant does not imply that the isolate is susceptible to INH. There are other genetic loci in addition to katG that can contribute to resistance for this drug.

Cautions

This rapid PCR assay detects Mycobacterium tuberculosis complex nucleic acid and, therefore, does not distinguish between viable, disease-related organisms and nucleic acid persisting from prior infection. Test results should be correlated with patient symptoms and clinical presentation before a definitive diagnosis is made.

 

A negative result does not rule out the presence of M tuberculosis complex or active disease because the organism may be present at levels below the limit of detection for this assay.

 

This test has not been studied for use with specimens from patients being treated with antituberculous agents and, therefore, should not be used to determine bacteriologic cure or to monitor response to therapy. It is not known how long the PCR assay can remain positive following treatment for M tuberculosis.

 

The sensitivity of this test with stool specimens is 80% and testing of additional stool specimens should be considered if the result from the first specimen is negative.

Clinical Reference

1. Iseman MD: A clinician’s guide to tuberculosis. Philadelphia, PA. Lippincott Williams and Wilkins, 2000

2. Centers for Disease Control and Prevention: Treatment of Tuberculosis, American Thoracic Society, CDC, and Infectious Diseases Society of America. MMWR Morb Mortal Weekly Rep 2003;52(No. RR-11):1-88

Method Name

Real-Time Polymerase Chain Reaction (PCR)

Method Description

Following specimen digestion and decontamination using N-acetyl cysteine and sodium hydroxide, genomic DNA is extracted using the MagNA Pure Compact (Roche Applied Sciences) extraction platform. The purified genomic DNA is placed on the LightCycler instrument, which amplifies and monitors, by fluorescence, the development of target nucleotide sequences after each PCR cycle. A specific target sequence from a portion of the katG gene from Mycobacterium tuberculosis complex is amplified and the resulting segment is detected by melt-curve analysis using sequence-specific fluorescence resonance energy transfer hybridization probes. The LightCycler PCR assay is a closed PCR system that greatly reduces the potential for false-positive results due to specimen cross-contamination as compared with traditional open-system PCR or other amplification methods like transcription-mediated amplification.(Unpublished Mayo method)

Report Available

1 to 3 days

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

87556-Mycobacterium tuberculosis, complex, molecular detection, PCR

87015-Mycobacteria culture, concentration (if appropriate)

LOINC Code Information

Test ID Test Order Name Order LOINC Value
MTBRP M tuberculosis Complex PCR 38379-4

 

Result ID Test Result Name Result LOINC Value
SRC62 MTB Complex PCR, Specimen Source 31208-2
56044 MTB Complex PCR, Result 38379-4

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
TBT Concentration, Mycobacteria No, ( Bill Only) No

Forms

If not ordering electronically, complete, print, and send a Microbiology Test Request (T244) with the specimen.