Evaluate the concordance and additional diagnostic yield of metagenomic-next generation sequencing (mNGS) with a syndromic multiplex-PCR panel using a cohort of remnant cerebrospinal fluid (CSF) samples.

mNGS enables the simultaneous detection of bacteria, fungi, viruses, and parasites. The Delve Detect CSF mNGS assay is a laboratory developed test (LDT) for use in suspected central nervous system (CNS) infections. A retrospective cohort of CSF samples previously characterized by the BioFire FilmArray Meningitis/Encephalitis Panel (BFMEP) was selected to evaluate the concordance and diagnostic yield of mNGS.

122 specimens were tested (47 BFMEP-positive and 75 BFMEP-negative). The 47 positive samples spanned the 14 BFMEP targets (Cryptococcus neoformans/gattii, Escherichia coli K1, Haemophilus influenzae, Listeria monocytogenes, Neisseria meningitidis, Streptococcus agalactiae, Streptococcus pneumoniae, Cytomegalovirus, Enterovirus, HSV 1, HSV 2, Human herpesvirus 6, Human parechovirus, and VZV). Where possible, discrepancy testing will be performed with orthogonal targeted PCR testing.

All 47 BFMEP-positive samples were positive for a single BFMEP target, with mNGS demonstrating concordance in 77%. mNGS identified 14 additional organisms, of which 5 were BFMEP targets. Of the 75 BFMEP-negative samples, mNGS was concordant in 95%; 26 additional organisms were detected by mNGS, 5 of which were BFMEP targets. Co-detections by mNGS were seen in 10% of samples (9 samples with 2 organisms, and 1 sample each with 3, 4, or 5 organisms).

mNGS can complement existing standard clinical assays such as the BFMEP by providing higher organism yield and broader detection. mNGS identified additional pathogens in both BFMEP-positive and BFMEP-negative samples, with co-detection of multiple organisms in 10% of samples. These results support the value of mNGS in diagnostically challenging CNS infections. Future studies will examine the clinical utility and optimal utilization of mNGS in routine practice.