299. Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for Central Nervous System Infections: Clinical Factors Associated with Increased Diagnostic Yield
Authors: Benoit Patrick , de Lorenzi-Tognon Mikael , Brazer Noah , Kelly Emily , Servellita Venice , Oseguera Miriam , Nguyen Jenny , Tang Jack , Omura Charles , Streithorst Jessica , Hillberg Melissa , Ingebrigtsen Danielle , Jin Chengshi , Lazar Ann , Chiu Charles 
Published: January 2025

Background

Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) can improve diagnostic yields in central nervous system (CNS) infections, but the most beneficial clinical indications have yet to be defined.Table 1.Factors evaluated by univariate analysis associated with a positive CSF mNGS test*P-value in bold are considered statistically significant (P &lt; 0.05)

Methods

We analyzed CSF mNGS results and associated clinical, demographic, and laboratory metadata from a cohort of patients for whom mNGS testing was performed at University of California, San Francisco (UCSF) from 2016 to 2023. We assessed by chart-review positive CSF mNGS results that established definitive diagnoses of CNS infections in the cohort. We then used univariate and multivariate logistic regression analysis to identify clinical factors that were associated with positive mNGS results.Figure 1.Significant clinical factors associated with mNGS positivity selected by multivariate analysis.The odds ratio and associated confidence intervals are plotted for each row (clinical factors).*, P &lt; 0.05; **, P &lt; 0.01; ***, P &lt; 0.001; NS, non-significant.

Results

Of 1,164 mNGS tests, 133 were positive for CNS infection-causing pathogens. By univariate analysis (Table 1), factors including hospitalization (P = 0.009), intensive care unit (ICU) admission (P = 0.02), immunosuppressed status (P &lt; 0.0001), clinical meningitis or meningoencephalitis (P &lt; 0.0001), and abnormal CNS imaging (P = 0.004) were significantly associated with a positive mNGS result. In contrast, demographic variables, including age, sex, race, and ethnicity, were not. For CSF, early mNGS testing performed by hospital day 7 (P &lt; 0.002), elevated protein (P = 0.005), and low glucose (P = 0.001) were associated with a positive mNGS result, whereas the presence of red blood cells (P = 0.77), pleocytosis (P = 0.17), and neutrophil or lymphocyte predominance (P = 0.24) were not. Significant factors selected by multivariate analysis include ICU stay (OR = 1.8, 95%CI[1.2, 1.9]), acute abnormalities on imaging (OR = 2.3, 95%CI[1.3, 4.2]), early mNGS testing within 7 days of admission (OR = 2.8, 95%CI[1.5, 5.2]), meningitis or meningoencephalitis (OR = 10.7, 95%CI[1.4, 82.7] and OR = 14.4, 95%CI[1.9, 112.1]), and immunosuppressed status (OR = 4.3 95%CI[2.7, 7.0]) (Figure 1).

Conclusion

This study identified key factors for predicting positive CSF mNGS results that will be incorporated into a predictive scoring system to identify clinical scenarios for which testing is clinically indicated to maximize diagnostic yield. Real-time scoring metric will enhance diagnostic stewardship and optimize the cost-effectiveness of CSF mNGS testing.

Disclosures

Charles Chiu, MD, PhD, Abbott Laboratories, Inc: Grant/Research Support|Biomeme: Advisor/Consultant|Biomeme: Board Member|BiomeSense: Advisor/Consultant|BiomeSense: Board Member|Delve Bio: Advisor/Consultant|Delve Bio: Board Member|Delve Bio: Grant/Research Support|Flightpath Biosciences: Advisor/Consultant|Flightpath Biosciences: Board Member|Mammoth Biosciences: Advisor/Consultant|Mammoth Biosciences: Board Member|Pathogen detection using next generation sequencing: US patent 11380421|Poppy Health: Advisor/Consultant|Poppy Health: Board Member