Performance of metagenomic next-generation sequencing for the diagnosis of viral meningoencephalitis in a resource limited setting

Background
Meningoencephalitis is a devastating disease worldwide. Current diagnosis fails to establish the cause in ≥50% of patients. Metagenomic next-generation sequencing (mNGS) has emerged as pan-pathogen assays for infectious-diseases diagnosis, but few studies have been conducted in resource-limited settings.

Methods
We assessed the performance of mNGS on cerebrospinal fluid (CSF) of 66 consecutively treated adults with meningoencephalitis in a tertiary referral hospital for infectious diseases in Vietnam, a resource-limited setting. All mNGS results were confirmed by viral specific PCRs. As a complementary analysis, six viral-PCR positive samples were analyzed using MinION-based metagenomics.

Results
Routine diagnosis could identify a virus in 15 (22.7%) patients, including HSV (n=7) and VZV (n=1) by PCR, and mumps virus (n=4), DENV (n=2) and JEV (n=1) by serological diagnosis. mNGS detected HSV, VZV and mumps virus in 5/7, 1/1 and 1/4 of the CSF positive by routine assays, respectively, but DENV and JEV in none of the positive CSF. Additionally, mNGS detected enteroviruses in seven patients of unknown cause. Metagenomic MinION-nanopore sequencing could detect a virus in 5/6 PCR positive CSF samples, including HSV in one CSF negative by mNGS, suggesting that the sensitivity of MinION is comparable with that of mNGS/PCR.

Discussion
In a single assay, metagenomics could accurately detect a wide spectrum of neurotropic viruses in CSF of meningoencephalitis patients. The study needed is to determine the value that real-time sequencing may contribute to the diagnosis and management of meningoencephalitis patients, especially in resource-limited settings where pathogen-specific assays are limited in number.