An assessment of nucleic acid amplification testing for active mycobacterial infection

Clinical need

The use of NAAT in the diagnosis and management of active TB infection is proposed to be an addition to the current clinical algorithm and does not substitute for any current test.

Both the Australian National Tuberculosis Advisory Committee (National Tuberculosis Advisory Committee 2006) and the Association of Public Health Laboratories in the USA (Association of Public Health Laboratories 2013) strongly recommend that all specimens received for NAAT also undergo both AFB microscopy (where possible) and culture and drug susceptibility testing (DST). This would occur regardless of the NAAT result confirming the presence or absence of MTB.

The rationale for this recommendation relates to the view that knowledge of the AFB microscopy result, in conjunction with a NAAT result, can better inform clinical decisions. For example, a NAAT-negative, AFB-positive specimen in conjunction with patient history and clinical presentation could contribute to ruling out MTB infection, and may suggest an NTM infection. Patients with HIV and pulmonary TB have a higher likelihood of being AFB microscopy negative (de Albuquerque et al. 2014; Scherer et al. 2011), so a NAAT-positive result could be useful for managing TB in these patients.

Culturing the organism is still important, as a negative NAAT does not exclude the possibility of a positive culture. Additionally, a positive NAAT does not differentiate among the species of MTB or determine the presence of other Mycobacterium species (Association of Public Health Laboratories 2013).

As the Xpert assay only determines the presence or absence of rifampicin resistance, all MTB isolates should receive additional DST using culture-based methods to determine the susceptibility patterns of other first- and second-line drugs used to treat TB (Association of Public Health Laboratories 2013).

The applicant has proposed that patient outcomes will differ according to the pre-test probability of a patient having TB. Given the public health implications of active pulmonary TB, patients with a high pre-test probability of having TB (approximately 20% of those tested, of whom 50–70% will actually have TB) commence antibiotic treatment immediately. Of the remaining 80% of patients with a low pre-test probability of having TB and in whom treatment is delayed until culture results are available, only 5–10% will actually have TB. In this population the applicant has suggested that the use of NAAT is non-inferior to current practice.

When rifampicin-resistant MTB is detected by NAAT in patients who have already started treatment, clinicians are provided with information on whether the patient’s treatment is likely to be effective within a few days, and this can lead to a change in case management. There are theoretical public health benefits associated with reducing the infectiousness of the patient earlier. Currently, a change in the antibiotic regimen would be due to ongoing AFB tests (where they can be collected), indicating that a patient is either not responding to treatment or is waiting for the result of the culture and DST in 6–8 weeks. In this situation the applicant has suggested that the use of NAAT may be superior to current practice.

For patients whose pre-test probability of TB is low, the applicant has suggested that positive NAAT results would result in immediate treatment that would not normally have been indicated, given the patient’s TB risk assessment.

In patients suspected of having an NTM infection, NAAT is expected to be an additional test to those currently performed to diagnose NTM.

Existing tests for diagnosing Mycobacterium species

NAAT for mycobacteria is currently not listed on the MBS. However, some Australian diagnostic laboratories, such as Alfred Health⁵ and PathWest Pathology Services⁶, offer in-house NAAT (MTB PCR) for screening specimens from patients with suspected TB.

Currently, most testing for MTB occurs using both AFB smear microscopy and culture tests. Although they are two separate tests, they are usually performed at the same time using the same specimen. The results for these two tests are delivered at different times; AFB microscopy results are reported within 24–48 hours, whereas culture results are reported at 6–8 weeks.

AFB smear microscopy involves spreading a suitable specimen thinly onto a glass slide, treating it with an acid-fast stain (Ziehl-Neelsen (ZN), Kinyoun stain or auramine-rhodamine stain) and examining the stained slide under a microscope (Lab Tests Online 2012). Results are typically available between several hours and 1 day after a sample is collected. AFB microscopy is ordered when:

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  the patient has symptoms that suggest pulmonary or extrapulmonary TB
  
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  the patient has a positive TB screening test and is at increased risk for active disease and/or has characteristic lung involvement as shown by X-ray
  
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  an individual has been in close contact with a person who has been diagnosed with TB and has either symptoms or a condition that increases their risk of contracting the disease
  
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  for monitoring purposes during treatment for TB
  
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  an immunosuppressed patient is systemically unwell and they are screened for unusual infections such as mycobacteria and fungi.
  

Cultures are used to diagnose active MTB and NTB infections, to help determine whether the TB is confined to the lungs or has spread to other organs, to monitor the effectiveness of treatment, and to help determine when a patient is no longer infectious (Lab Tests Online 2012). Traditionally, cultures have used semi-solid agar-based media and require 4–8 weeks for sufficient growth to obtain a diagnosis. However, newer liquid culture systems are approximately 10% more sensitive for detection of mycobacteria than semi-solid media, and can obtain results in days rather than weeks (WHO 2007). One drawback is that liquid culture is more prone to contamination with other microorganisms (WHO 2007).

DST is usually conducted in conjunction with a culture to determine the most effective antibiotics to treat the infection. The mycobacteria are grown in the presence of anti-TB drugs, either in liquid or semi-solid media, and compared with growth when the drug is absent. If growth of the MTB is detected in the presence of the anti-TB drug, it indicates drug resistance (TBFacts.org). Liquid culture systems can reduce the delay for results to as little as 10 days instead of several weeks (WHO 2007).