Clinical impact of metagenomic next-generation sequencing testing on cerebrospinal fluid in a pediatric cohort with suspected central nervous system infections

Abstract Conflicts: M.D.T., P.B., N.B., V.S., M.O., J.S., M.H., D.I., M.W. declare no conflict of interests. A.P.W., B.O., T.B., B.M. and S.M. are employed by and own equity in Delve Bio. C.Y.C. is a founder of Delve Bio and on the scientific advisory board for Delve Bio, Flightpath Biosciences, Biomeme, Mammoth Biosciences, BiomeSense and Poppy Health. He is also an inventor on US patent 11380421, “Pathogen detection using next generation sequencing”, under which algorithms for taxonomic classification, filtering and pathogen detection are used by SURPI+ software. C.Y.C. receives research support from Delve Bio and Abbott Laboratories, Inc. Background Clinical metagenomic next-generation sequencing (mNGS) testing of cerebrospinal fluid (CSF) has been shown to improve diagnostic yield in suspected central nervous system (CNS) infections. However, real-life impact on patient care and outcomes, especially for children, remains poorly understood. Methods We retrospectively evaluated the clinical impact of mNGS testing in a cohort of 194 pediatric patients at University of California, San Francisco, reviewing cases of suspected CNS infections who underwent CSF mNGS testing from 2016 to 2023. Results Patients had a median age of 9 years [IQR 2 – 16], 43.6% females, 93.3% inpatient, 65.6% requiring an intensive care unit stay, and 31.3% immunosuppressed. Mortality at day 60 post-mNGS testing was 8.7%. Positive and clinical negative impact of CSF mNGS testing was observed in 37.6% and 0.52% of cases, respectively. Of the 23 clinically-relevant positive mNGS results, concomitant CNS infection was ruled out in 16 cases (69.6%), brain biopsy was avoided in 6 cases (26.1%), and new infectious diagnoses were identified in 5 cases (21.7%). mNGS results led to a management change in 2 cases (8.7%), whereas the results from two additional cases prompted a public health intervention. Conclusion CSF mNGS testing had a positive clinical impact in 37.6% of our pediatric cohort. Among the 62.4% of cases with no impact, more than half may have yielded actionable results with an 44.4% decrease in assay median turnaround time (from 9 to 4 days). Prioritizing strategies to reduce assay turnaround time would likely improve patient care management and enhance the clinical impact of CSF mNGS testing.