Diagnostic accuracy of quantitative PCR (Xpert MTB/RIF) for tuberculous meningitis in a high burden setting: a prospective study

Abstract

Background: Tuberculous meningitis (TBM) is difficult to diagnose promptly. The utility of the Xpert MTB/RIF test for the diagnosis of TBM remains unclear, and the effect of host- and sample-related factors on test performance is unknown. This study sought to evaluate the sensitivity and specificity of Xpert MTB/RIF for the diagnosis of TBM.

Methods and findings: 235 South-African patients with a meningeal-like illness were categorised as having definite (culture or Amplicor PCR positive), probable (anti-TBM treatment initiated but microbiological confirmation lacking), or non-TBM. Xpert MTB/RIF accuracy was evaluated using 1 ml of uncentrifuged and, when available, 3 ml of centrifuged cerebrospinal fluid (CSF). To evaluate the incremental value of MTB/RIF over a clinically based diagnosis, test accuracy was compared to a clinical score (CS) derived using basic clinical and laboratory information. Of 204 evaluable patients (of whom 87% were HIV-infected), 59 had definite TBM, 64 probable TBM, and 81 non-TBM. Overall sensitivity and specificity (95% CI) were 62% (48%-75%) and 95% (87%-99%), respectively. The sensitivity of Xpert MTB/RIF was significantly better than that of smear microscopy (62% versus 12%; p = 0.001) and significantly better than that of the CS (62% versus 30%; p = 0.001; C statistic 85% [79%-92%]). Xpert MTB/RIF sensitivity was higher when centrifuged versus uncentrifuged samples were used (82% [62%-94%] versus 47% [31%-61%]; p = 0.004). The combination of CS and Xpert MTB/RIF (Xpert MTB/RIF performed if CS<8) performed as well as Xpert MTB/RIF alone but with a ∼10% reduction in test usage. This overall pattern of results remained unchanged when the definite and probable TBM groups were combined. Xpert MTB/RIF was not useful in identifying TBM among HIV-uninfected individuals, although the sample was small. There was no evidence of PCR inhibition, and the limit of detection was ∼80 colony forming units per millilitre. Study limitations included a predominantly HIV-infected cohort and the limited number of culture-positive CSF samples.

Conclusions: Xpert MTB/RIF may be a good rule-in test for the diagnosis of TBM in HIV-infected individuals from a tuberculosis-endemic setting, particularly when a centrifuged CSF pellet is used. Further studies are required to confirm these findings in different settings. Please see later in the article for the Editors' Summary.

Figure 1. Summary flow chart of patient recruitment and diagnostic testing performed.

MGIT, Bactec MGIT 960; ND, not done; +ve, positive; −ve, negative. * These patients could not be clearly categorised as definite TBM, probable TBM, or non-TBM (e.g., reference negative and lost to follow-up, and without initiation of TB treatment). † Note that the uncentrifuged and centrifuged Xpert MTB/RIF groups include 12 patients who had both processes done, i.e., paired samples.

Figure 2. Level of detection of CSF Xpert MTB/RIF for M. tuberculosis using serial dilutions (500, 250, 100, 80, and 10 colony forming units per millilitre) of H37Rv.

CFU, colony forming units.

Figure 3. Correlation of CSF Xpert MTB/RIF cycle threshold (C _T) and Bactec MGIT 960 time to positive culture in all samples (both centrifuged and uncentrifuged).

Figure 4. Comparison of PCR inhibition using the comparative internal positive control C _T values in CSF and sputum (all HIV-infected patients).

CSF IPC: median (IQR) C _T value is 27.2 (range: 27.83–35.4), n = 82. Sputa IPC: median (IQR) C _T value is 29.85 (range: 31.9–40.5), n = 238. Comparison between C _T values for CSF and sputum, p≤0.001.