Diagnostic yield and clinical–mNGS discordance in adults with suspected central nervous system infection: a prospective single-centre study

Central nervous system (CNS) infections are diagnostically challenging because clinical syndromes overlap and conventional microbiological tests have pathogen- and specimen-specific limitations. Metagenomic next-generation sequencing (mNGS) provides agnostic detection of microbial nucleic acids and may complement routine investigations, particularly in diagnostically challenging cases. We conducted a prospective observational study of adults with suspected CNS infection evaluated at a tertiary-care centre in Central India from January 2023 to January 2024. Cerebrospinal fluid (CSF) was investigated using routine microbiological and molecular methods according to clinical indication, together with mNGS. The prespecified descriptive objective of the present analysis was to characterize mNGS pathogen detection and discordance between the initial clinical diagnosis and mNGS findings. Because an independent reference standard was not established in the original analysis, mNGS results were not treated as a definitive reference diagnosis. Of 197 enrolled patients, all had an available mNGS result. A reportable microbial finding was identified in 80/197 (40.6%; 95% CI 34.0–47.6%), comprising 52 bacterial, 25 Mycobacterium tuberculosis-associated, 2 viral, and 1 fungal finding. No reportable microbial finding was identified in 117/197 (59.4%). Clinical follow-up was available for 160 patients (81.2%); 63 were recorded as improved, 70 had treatment ongoing, and 27 had expired, while 37 were lost to follow-up (Section "Study design and participants"). Clinical–mNGS differences were interpreted descriptively because no independent reference standard was established. In this prospective single-centre cohort, CSF mNGS identified reportable microbial findings in 40.6% of patients with suspected CNS infection. Bacterial and Mycobacterium tuberculosis-associated findings predominated. The observed differences between initial clinical diagnoses and mNGS findings support the complementary diagnostic role of mNGS but do not establish superior diagnostic accuracy, treatment benefit, or improved outcomes.