Yield of Metagenomics in Suspected Central Nervous System Infections with Negative Cerebrospinal Fluid Cultures

Background: Metagenomic next-generation sequencing (mNGS) represents a promising diagnostic tool for central nervous system infections, and its clinical impact on patient management when the cerebrospinal fluid is culture-negative remains inadequately explored. Methods: We conducted a retrospective cross-sectional study involving patients who underwent culture-negative cerebrospinal fluid mNGS at a tertiary hospital from March 2019 to December 2024, aiming to assess its diagnostic efficacy and clinical implications. Results: A total of 93 culture-negative cerebrospinal fluid samples from 93 patients underwent mNGS. Positive results were observed in 58.1% (54/93) of patients, with 78 microorganisms identified, and 52.6% (41/78) were clinically relevant. Clinically relevant organisms exhibited significantly higher median sequence reads compared with clinically irrelevant microbes (95 vs. 3; p < 0.0001). mNGS results positively impacted 65.6% (61/93) of patients by confirming or excluding central nervous system infections. However, among cases with negative clinical impact, 65.6% (21/32) were clinically diagnosed with central nervous system infections. Notably, 56.3% (18/32) of the positive mNGS results were considered non-pathogenic by clinicians, suggesting that mNGS alone may not be sufficient for diagnosing or ruling out central nervous system infections. Additionally, no significant differences were observed in clinical impact between immunocompromised and immunocompetent patients (68% vs. 64.7%, p = 0.802). Conclusion: mNGS demonstrates high diagnostic yield and positive clinical impact for patients with culture-negative cerebrospinal fluid. Its clinical applications should take into account factors such as patient demographics, diagnostic performance, and the interpretation of results in conjunction with conventional testing and collaboration within multidisciplinary teams.