Evaluation of the Performance of CSF Pyrosequencing in the Diagnosis of TB Meningitis

Background: We evaluated the performance of pyrosequencing, a rapid genotypic test which detects TB and resistance to isoniazid, rifampicin, aminoglycosides and fluoroquinolones within 6 h, directly on CSF samples in the diagnosis of TB meningitis. Methods and materials: This retrospective study was conducted in a tertiary care centre of Mumbai, India from May 2017 to May 2019. One hundred and seven consecutive patients with suspected TB meningitis for whom CSF pyrosequencing was requested were studied. Seven patients with incomplete data were excluded. Lancet consensus case definition criteria were used to classify patients into following categories: definite, probable, possible and alternative diagnosis. Those with definite TB meningitis were considered to have the disease and those with alternative diagnosis were considered to not have the disease. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of pyrosequencing was determined. Sensitivity of pyrosequencing was compared to MGIT culture and Xpert MTB Rif using chi square test. Results were interpreted at 5% significance. Mutations obtained on pyrosequencing and subsequent concordance rate with MGIT culture DST and Xpert MTB Rif were analysed. Results: Study cohort comprised of 100 patients [definite (n = 33), probable (n = 20), possible (n = 30) and alternative (n = 17)] with 50% males [median age: 38 years (range, 2–87 years)]. Sensitivity, specificity, PPV and NPV of CSF pyrosequencing to diagnose TB meningitis was 96.7%, 100%, 100% and 94.4% respectively. It was more sensitive (not statistically significant) than Xpert MTB Rif (96.7% vs 69.6%, p = 0.12) and MGIT culture (96.7% vs 72%, p = 0.16). This test was positive in all patients with probable TB meningitis, 95% (n = 19/20) of whom showed good clinical response to treatment. Mutational analysis revealed the following patterns on pyrosequencing: wild strain [50.9% (n = 27/53)], MDR [26.4% (n = 14/53)], INH mono-resistance [11.3% (n = 6/53)], MDR+ quinolone/aminoglycoside resistance [9.4% (n = 5/53)] and XDR [2% (1/53)]. Susceptibility concordance rate of pyrosequencing with MGIT culture DST (n = 21/23) was 91.3% and with Xpert MTB Rif (n = 22/23) was 95.6%. Conclusion: CSF pyrosequencing is more sensitive than Xpert MTB Rif and MGIT culture and may facilitate early therapeutic decisions in TB meningtis. This is especially useful in Probable TB meningitis, when both Xpert MTB Rif and MGIT culture are negative.