Tuberculosis Information for Laboratorians

M. Tuberculosis Nucleic Acid Amplification Testing (NAAT) Frequently Asked Questions

What is the advantage of the Tuberculosis Nucleic Acid Amplification Test (TB NAAT)?

Conventional culture methods may take up to six weeks to detect growth of M.tuberculosis, whereas NAAT can be performed directly on sputum and other respiratory specimens and results can be provided to the clinician within 24-48 hours of specimen receipt.  In January 2009 CDC published Updated Guidelines for the Use of Nucleic Acid Amplification Tests in the Diagnosis of Tuberculosis.

When should TB NAAT be ordered?

The Centers for Disease Control and Prevention (CDC) recommends in its 2009 guidance that NAAT be performed on at least one respiratory specimen from each patient with signs and symptoms of pulmonary TB for whom a diagnosis of TB is being considered but has not yet been established, and for whom the test result would alter case management or TB control activities.  TB NAAT should only be ordered on patients when the clinician’s index of suspicion for pulmonary TB is moderate to high (more).

When is it NOT appropriate to order a TB NAAT?

The test should not be ordered when the clinician has a low index of suspicion for pulmonary TB in the patient, as the positive predictive value of the test falls to <50% if ordered under this circumstance (1)  

What types of specimens are accepted for NAAT?

The Rhode Island State Health Laboratory accepts only the following respiratory specimens for TB NAAT:  sputum, bronchoalveolar lavage (BAL), bronchial washing, bronchial lavage, lung washing, thoracentesis fluid, and pleural fluid.  Our NAAT PCR method has been verified on these specimens in an extensive in-house study.

Why can’t NAAT be ordered on other types of specimens?

To date there is limited information regarding TB NAAT performance on non-respiratory specimens or specimens from patients under treatment. (1)  

What testing method is used at the Rhode Island State Health Laboratory to perform TB NAAT?

The State Health Laboratory performs TB NAAT by real time PCR.  The test was developed “in-house” and is a modification of the PCR method developed, validated and currently used by the New York State Wadsworth Center. The test is not FDA approved, but has been validated and verified in accordance with applicable Clinical Laboratory Improvement Amendments (CLIA) regulations.

If a TB NAAT is ordered on a specimen, do I still need to order an AFB smear and culture?

Yes, AFB smear and culture should always be ordered on specimens submitted for NAAT.  The result of the NAAT is always interpreted in conjunction with the AFB smear result and AFB culture remains the “gold standard” for the laboratory confirmation of TB and is required in order to conduct drug susceptibility testing and genotyping.  When a specimen is sent to our laboratory for a TB NAAT, an AFB smear and a culture will also be ordered and performed.

What if AFB smear and culture is performed by my hospital laboratory; will another smear and culture be performed by the State Health Laboratory if a NAAT is ordered?

The Rhode Island State Health Laboratory will require an additional unprocessed specimen be submitted to our laboratory for NAAT. This same specimen will also have an AFB smear and culture done at our laboratory.  The method verification that took place in our laboratory was done on specimens that had been through the specimen decontamination process used in our laboratory, so it has not been verified for use on specimens that have been decontaminated by other methods.

If a hospital laboratory wishes to send the remaining sediment from a specimen that they have all ready decontaminated, along with the additional unprocessed specimen, we would encourage them to do so.  This will allow our laboratory to do additional verification studies to see if other decontamination methods are compatible with our NAAT PCR method.

How do I order a TB NAAT at the Rhode Island State Health Laboratory?

Complete both a Rhode Island State Health Laboratory Test Requisition Form and a TB NAAT Request Form. Both forms are available in all hospital microbiology and send out laboratories and can also be requested by contacting the Rhode Island State Health Laboratory Mycobacteriology Lab at 222-5587/222-5586. 

If the State Health Laboratory finds that a specimen is AFB smear positive, how do I order a TB NAAT?

The Mycobacteriology section of the Special Pathogens Lab processes approximately 2,000 specimens a year for AFB smear and culture. If we determine that a specimen (acceptable for NAAT) is AFB smear positive, we will automatically order a TB NAAT provided:

• Patient has not been previously diagnosed with tuberculosis
• Patient has not been laboratory diagnosed by our laboratory with a respiratory infection/colonization with non-tuberculosis mycobacteria (NTM) within the previous 12-month period.
• Patient has not had a previous positive TB NAAT result. Exception: an additional specimen from a patient with an initial specimen that was smear negative/NAAT positive (refer to NAAT interpretation guidelines)
• Patient has not had a total of 3 NAAT tests (negative, inconclusive or indeterminate results) performed on specimens collected during the previous three month period.

What is the expected turn around time for receiving TB NAAT results?

Our goal is to have NAAT results available within two working days of specimen receipt.  Specimens should be sent to the State Health Laboratory as soon as possible after collection.

How will I be notified of the NAAT result?

All positive TB NAAT results will be considered a critical test value and will be immediately phoned to the ordering provider, the laboratory that submitted the specimen, the Health Department Tuberculosis Control Program, and the RISE TB Clinic.  NAAT results will be routinely reported through our laboratory information system to submitters in the same manner they receive other reports from our laboratory.

Is a negative NAAT result enough to rule out tuberculosis?

No, a single negative NAAT should not be used as a definitive result to exclude TB (refer to NAAT Interpretation Guidelines) especially in a patient where the clinical suspicion of TB is moderate to high. If the clinician is not experienced with the interpretation of NAAT or the diagnosis of TB, consultation with the expert TB clinicians at the RISE TB Clinic is highly recommended (401) 793-2427/2433. (1)

I have a patient in respiratory isolation; can this test help me to decide if my patient can be removed from isolation?

A negative NAAT and two independent AFB smear-negative sputum samples (taken at least 8 hours apart, with at least one being an early morning specimen) may be used to determine whether patients may be removed from respiratory isolation, provided that (a) clinical suspicion for infectious TB is low and (b) if the patient has been started on multidrug treatment, there is clinical improvement. (1)