Metagenomic sequencing (unknown etiology)
Metagenomic / unknown etiology
Last reviewed 2026-08-13
Public health significance
The assay you want when the differential is 'we do not know.' Bioinformatics is part of the quality system.
Specimen types
As validated (CSF, plasma, tissue, stool)
Method
Metagenomic NGS
CLIA / validation
LDT. Validate wet lab and bioinformatics as one method. Version the pipeline.
Interpretation
Organism identified / none identified. Specific organisms get SNOMED when called. Pipeline notes belong in NTE.
Reflex / referral
Orthogonal confirmation of unexpected high-consequence organisms.
Quality control
Internal controls, no-template controls, and a characterized positive. Reproducibility of the informatics matter.
Reportability
Report identified reportable organisms. A negative metagenomic run is not a negative for every pathogen.
HL7 / ELR
Evolving LOINC coverage (e.g. 94187-4 family). Prefer coded organism findings plus narrative.
Sources
CDC/APHL genomic epidemiology; local validation records.