Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Suspected Cryptococcal Meningitis : A Single-Center Clinical Study

Cryptococcal meningitis (CM) is one of the most common fungal meningitides with high misdiagnosis rates and mortality. Therefore, rapid, accurate, and early diagnosis of CM is essential for successful treatment. In the present study, cerebrospinal fluid (CSF) samples from 69 suspected CM patients who received both conventional microbiological tests (CMTs) and metagenomic next-generation sequencing (mNGS) were ultimately collected for in-depth differentiation analysis according to the strict inclusion and exclusion criteria. The results showed that CSF pressure (p=0.004), use of antibiotics before mNGS (p=0.012), adjustment of antibiotics after mNGS (p=0.006), hospital stays (p=0.002) and 90-day discharge rates (p=0.020) differed significantly between mNGS-positive and mNGS-negative patients. mNGS had a better detection rate for fungi (34 vs 11, p=0.009) and viruses (13 vs 1, p=0.007) than CMTs, especially for Cryptococcus neoformans (32 vs 8, p=0.003). The sensitivity and specificity of mNGS was 97.06% and 100.00% in identification of fungi, and 92.31% and 80.00% in detection of viruses. Our results indicate that mNGS is effective in the pathogenic detection of CM, especially in fungi and viruses, which may serve as an alternative and promising method in the diagnosis of suspected CM