A COMPREHENSIVE 7-year analysis from the University of California, San Francisco (UCSF) reveals that metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) is a highly effective tool for identifying central nervous system (CNS) infections.
The study reviewed 4,828 CSF samples processed between June 2016–April 2023, finding that mNGS testing identified infectious organisms in 697 samples, or 14.4% of cases. Among the 797 organisms detected, DNA viruses were the most common (45.5%), followed by RNA viruses (26.4%), bacteria (16.6%), fungi (8.5%), and parasites (2.9%). For a subset of 1,164 samples from 1,053 patients, mNGS testing yielded unique insights, providing exclusive diagnoses in 21.8% of the cases (48 out of 220) that were not identified by other testing methods.
In terms of diagnostic performance, mNGS testing demonstrated a sensitivity of 63.1%, specificity of 99.6%, and overall accuracy of 92.9%. Notably, mNGS outperformed other testing methods: its sensitivity was higher than indirect serologic testing (28.8%), CSF direct detection testing (45.9%), and non-CSF direct detection testing (15.0%), with statistical significance (P<0.001 for each comparison). For cases where diagnoses were made solely by direct CSF testing, mNGS sensitivity rose to 86%, highlighting its robust performance for detecting CNS infections.
The UCSF study advocates for the routine use of mNGS testing in hospitalised patients suspected of CNS infection, given its diagnostic advantages over conventional methods. The findings suggest that mNGS testing provides a valuable, broad-based approach for the early and accurate diagnosis of complex CNS infections.
Reference
Benoit P et al. Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections. Nat Med. 2024; DOI:10.1038/s41591-024-03275-1.
