Comparison of mNGS with conventional methods for diagnosis of cryptococcal meningitis: a retrospective study

Abstract

The application of metagenomic next-generation sequencing (mNGS) in the diagnosis of cryptococcal meningitis is relatively under characterized. Here, we retrospectively evaluated data from cryptococcal meningitis patients who were tested using mNGS and/or routine testing, including fungal culture, India ink staining, and cryptococcal antigen (CrAg) testing. The performance of mNGS was then assessed. Initial cerebrospinal fluid (CSF) samples were collected from 65 patients with suspected central nervous system (CNS) infection and tested using conventional tests and/or mNGS. mNGS offers a culture-independent approach, facilitating a rapid and unbiased detection of a broad spectrum of pathogens. Patients with bacterial tuberculous or viral meningitis were used as mNGS-positive controls and one autoimmune encephalitis patient was used as an mNGS-negative control. In the 45 patients diagnosed with cryptococcal meningitis, the sensitivity, specificity, positive predictive value, negative predictive value, and concordance rate of mNGS were 92%, 100%, 100%, 90.9%, and 95.6%, respectively. Compared to conventional methods, the sensitivity of mNGS was slightly lower than CrAg tests (96.7%) but higher than India ink (79.5%) and culturing (63.4%). Of the two negative mNGS cases (2/25, 8.0%), one was positive by India ink staining, culture, and CrAg testing, while the other was positive only by CrAg testing. A combination of mNGS and conventional methods enhanced the detection rate to 100%. Our study demonstrates that both CrAg and mNGS offer excellent diagnostic accuracy for cryptococcal meningitis, and utilizing both tests can enhance clinical assessment and patient management.

Keywords: Cerebrospinal fluid; Conventional method; Cryptococcal meningitis; Diagnosis; Metagenomic next-generation sequence.

Fig. 1

Venn diagram of conventional cryptococcal testing and metagenomic next-generation sequencing (mNGS) results in 45 patients with central nervous system cryptococcal infections. The number of cases tested by India ink stain, culture, cryptococcal antigen (CrAg) testing and mNGS was 44, 41, 30 and 25, respectively, and the number of positive cases was 35, 26, 29 and 23, respectively.

Fig. 2

Overview of patients enrolled, final diagnosis and number of patients tested by each method. A total of 65 patients were enrolled. Of these patients, 45 were diagnosed with CNS cryptococcal infection. As controls, 1 patient with purulent meningitis, 17 patients with tuberculous meningitis, 1 patient with viral encephalitis, and 1 patient with autoimmune encephalitis were enrolled.