Guest posting: Dr Ian Marr, Microbiology Registrar, Pathology NSW, Hunter

The GenXpert used in most LMIC has cartridges for detection of Mycobacterium tuberculosis (MTB) – GenXpert MTB/RIF. These contain primers and molecular beacon probes for the detection of both MTB and its resistance to the first line drug rifampicin. By looking for mutations in the rpoB gene (transcribes for RNA polymerase) it can determine if rifampicin (which inhibits RNA polymerase) will work and also if MTB is present.

What has changed?

There is a new GenXpert cartridge developed by Cepheid that has improved sensitivity for detecting Mycobacterium tuberculosis in clinical samples – MTB/RIF Ultra. While its sensitivity for detecting the rpoB mutation is approximately the same, there has been an increase in sensitivity for detecting the presence of MTB by addition of unique primers for IS6110 (an ‘insertion sequence’- basically a transposon that may have more than one copy in each genome).

Early in vitro validation reports indicated that the Ultra cartridge may be as sensitive as culture, however clinical samples while showing improved sensitivity, have not seen this. See Chakravorty et al., for further information on in vitro validation of the assay and to understand the changes in molecular primers and probes.

What does the clinical data say?

The two most interesting studies so far have been completed in CNS disease and pulmonary disease.

CNS disease

This study in Ugandan HIV positive persons was completed retrospectively on stored CSF samples. The Ultra cartridge showed a sensitivity of 70% (95% CI 47–87; 16 of 23 cases) for probable or definite tuberculous meningitis compared with 43% (23–66; 10/23) for the current cartridge. This compared to 43% (23–66; 10/23) for culture. While the study was of only small numbers it showed a significant increase from the previous GenXpert cartridge.

Pulmonary disease

This study was completed in 8 countries, analysing 1753 patients with TB symptoms found a variable sensitivity a little better than the current cartridges.

“Sensitivities of Xpert Ultra and Xpert were 63% and 46%, respectively, for the 137 participants with smear-negative and culture-positive sputum (difference of 17%, 95% CI 10 to 24); 90% and 77%, respectively, for the 115 HIV-positive participants with culture-positive sputum (13%, 6·4 to 21); and 88% and 83%, respectively, across all 462 participants with culture-positive sputum (5·4%, 3·3 to 8·0).”

Does this mean that Rifampicin resistance also has an increase in sensitivity?

Unfortunately, despite re-engineering of the rpoB sloppy molecular beacons there was little if any increase in sensitivity of the rifampicin resistance component.

Is there any change in the report generated?

A change in the method of positive MTB detection now allows for a report of how much DNA was in the specimen. This is reported as either “trace”, “very low”, “low”, “medium”, or high”. Where there is only a small amount of IS6110 found no rpoB analysis will be reported.

Interestingly a number of false positives were also found in the ‘trace’ only reports in the pulmonary study above. Some of these were in patients who previously had MTB and had completed treatment. This may be because of DNA remnants left behind in these patients.

What does all this mean?

With an increase in sensitivity it is likely that this new cartridge will take over from the current MTB cartridge, and the reports generated will be different.

References (all are free full access)

• Bahr, N. C. et al. (2018). Diagnostic accuracy of Xpert MTB/RIF Ultra for tuberculous meningitis in HIV-infected adults: a prospective cohort study. The Lancet Infectious Diseases, 18(1), 68–75.
• Chakravorty, S. et al. (2017) The New Xpert MTB/RIF Ultra: Improving Detection of Mycobacterium tuberculosis and Resistance to Rifampin in an Assay Suitable for Point-of-Care Testing,  MBio 2017.
• Dorman, S. E. et al. (2018). Xpert MTB/RIF Ultra for detection of Mycobacterium tuberculosis and rifampicin resistance: a prospective multicentre diagnostic accuracy study. The Lancet Infectious Diseases, 18(1), 76–84.  
• Khonga, M. & Nicol, M. P. (2018). Xpert MTB/RIF Ultra: a gamechanger for tuberculous meningitis? The Lancet Infectious Diseases, 18(1), 6–8.

Image credit: Wikipedia