Abstract Background Identification of the microorganism(s) causing infection in children with central nervous system (CNS) infection is important. Conventional cerebrospinal fluid (CSF) tests may provide limited pathogen detection. CSF metagenomic next-generation sequencing (CSF mNGS) may provide broader pathogen detection in a single assay. Methods Results of CSF mNGS testing performed at Mayo Clinic on Mayo Clinic and non-Mayo Clinic patients between January 2024 and June 2025 were retrospectively analyzed. The subcohort of children managed at Mayo Clinic was analyzed to assess test performance compared with conventional CSF diagnostics and potential clinical impact. Results 134 patients (138 CSF mNGS tests) from 22 states in the United States and two international sites were included. Overall positivity was 16%, with viruses comprising most (59%) detections. In the Mayo Clinic subcohort (n=15), test positivity was 27%; organisms detected included Streptococcus mitis group, human immunodeficiency virus type 1, and Epstein-Barr virus (2), all confirmed by conventional tests. Positive results were associated with CSF pleocytosis (P=0.026). Higher yield was observed in subjects whose care was overseen by pediatric infectious diseases (PID) specialists (P=0.026), and when a specimen hold strategy was applied (P=0.033). Most results (87%) did not alter antimicrobial therapy, with two negative results contributing to antimicrobial de-escalation. Conclusions CSF mNGS demonstrated higher diagnostic yield in patients whose specimens showed CSF pleocytosis and in those who had PID consultation. Diagnostic stewardship strategies, including specimen hold approaches and PID consultation were applied.
Li et al. (Wed,) studied this question.
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