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

Abstract

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.

Keywords

metagenomic next-generation sequencing / cerebrospinal fluid / central nervous system infection / pathogen / clinical impact

Author Contributions

C.D. planned the study and wrote the manuscript and provided graphical support; J.H., Y.Y., and R.L. provided test support; J.L. provided hospital infection control; L.L. and Q.Y. provided clinical management of the patient; C.D. and F.X. reviewed, edited, and approved the draft. All authors have read and agreed to the published version of the manuscript.

Funding

This work was partly supported by the Sanming Project of Medicine in Shenzhen (SZSM201911014) and the High-Level-Hospital Program, Health Commission of Guangdong Province, China.

Data Availability Statement

The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request.

Acknowledgments

We thank the staff at the Department of Infections and Microbiology, the University of Hong Kong—Shenzhen Hospital, for their technical support and assistance. We also like to extend our gratitude to KingMed Diagnostics (Guangzhou) for performing the mNGS detection and methodological support.

Conflicts of Interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as potential conflicts of interest.

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