An assessment of nucleic acid amplification testing for active mycobacterial infection

Incidence of TB based on WHO estimates from 2012: high incidence = > 100 cases per 100,000 people; medium incidence = 10–100 cases per 100,000 people; low incidence = ≤ 10 cases per 100,000 people

AUC = area under curve; NAAT = nucleic acid amplification testing; SROC = summary receiver–operator characteristic; TB = tuberculosis

In summary, the sensitivity and specificity for in-house NAATs and the commercial Xpert NAAT, when compared with culture, did not differ significantly. Nevertheless, the Xpert NAAT showed a trend suggesting that it may be less sensitive than in-house NAATs, especially when testing sputum specimens (83% versus 92%; Figure 15). The summary LR values indicate that both in-house NAATs and the commercial Xpert NAAT have diagnostic value in confirming or excluding culture-positive disease. Patients with a positive commercial NAAT result were more likely to be culture-positive than those with a positive in-house NAAT result for all specimen types. Patients with a negative NAAT result in sputum specimens were more likely to be culture-negative than those with a negative Xpert NAAT result.

Meta-analysis of studies assessing the diagnostic accuracy of NAAT compared with culture in either AFB-positive or AFB-negative specimens

Among the 28 studies that reported data for AFB-positive specimens, the sensitivity was at least 94% in all but 5 studies (pooled value 99%; 95%CI 96, 100). However, the specificity was much more variable, ranging from 0% to 100% between studies (pooled value 78%; 95%CI 53, 92). Conversely, in the 39 studies that reported data for AFB-negative specimens, the sensitivity was highly variable between studies, with a pooled value of 80% (95%CI 69, 87). The specificity was at least 82% in the studies that were conducted in countries with a low or medium incidence of TB, but was highly variable (range 18–100%) in studies conducted in countries with a high incidence of TB, especially those using in-house NAAT. These observations are reflected in the 95%CIs of the pooled sensitivity and specificity values from subgroup analyses shown in Figure 19A and B.

The LR scattergram shows that the summary LR+ and LR– values for NAAT compared with culture in AFB-positive specimens were within the lower left quadrant, indicating that a negative NAAT result can confidently exclude the likelihood of an MTB infection (as determined by culture) in patients who had an AFB-positive sample (Figure 20). Unexpectedly, a positive NAAT result does not eliminate the possibility of AFB-positive patients not having a detectable MTB infection (i.e. being culture-negative). This can be explained because culture is an imperfect reference standard, which likely resulted in misclassification of many of the 22% false-positive results (1 – specificity) seen for NAAT when compared with culture in AFB-positive specimens (Figure 19). Therefore, NAAT is likely to be more effective at confirming the presence of an MTB infection in these patients than the LR scattergram suggests.

In AFB-negative specimens the overall summary LR+ and LR– values for NAAT compared with culture were in the upper right quadrant of the scattergram or within the green shaded bands, indicating that a positive NAAT result is likely to correctly confirm the presence of MTB. However, interpretation of a negative NAAT result is dependent on the type of specimen tested. In patients with AFB-negative sputum a negative NAAT indicated that the patient may not be culture-positive but it could not be ruled out (summary values are within the green shaded area; Figure 21). In patients with AFB-negative non-sputum specimens, a negative NAAT result provided no additional useful information. This is likely due to the paucibacillary nature of AFB-negative specimens. It should be noted that if few bacilli are present in the specimen, the possibility of a false-negative result would increase for all three tests.

Figure 19 Forest plot showing the pooled sensitivity and specificity values for NAAT compared with culture for AFB-positive (A) and AFB-negative (B) specimens grouped according to NAAT methodology, specimen type and incidence of TB in the country in which the study was conducted