The 60 Percent Diagnostic Gap in M/E
What earlier mNGS testing could mean for labs and clinicians
By
Jessica Allerton
March 12, 2026
Clinical Scorecard: The 60 Percent Diagnostic Gap in M/E
At a Glance
Category Detail
Condition Meningitis/Encephalitis (M/E)
Key Mechanisms Complex interplay of infectious disease, neurology, and immunology; diagnostic challenges due to nonspecific symptoms and limited testing capacity.
Target Population Patients with suspected meningitis or encephalitis, particularly immunocompromised individuals and those with atypical presentations.
Care Setting Well-resourced hospitals and clinical settings with access to advanced diagnostic tools.
Key Highlights
Over 60% of M/E cases remain undiagnosed after comprehensive evaluation. Traditional diagnostics are hypothesis-driven and limited in scope. Early use of comprehensive metagenomic next-generation sequencing (mNGS) can reduce diagnostic time and additional testing. mNGS testing can decrease microbiologic tests ordered by over 60% in infectious cases. Collaboration among laboratory, neurology, and infectious disease teams is crucial for mNGS result interpretation.
Guideline-Based Recommendations
Diagnosis
Consider mNGS for patients with severe or atypical neurologic presentations. Use mNGS when culture-negative CSF persists with concern for infection.
Management
Integrate mNGS into the diagnostic pathway to inform treatment decisions. Narrow empiric therapy based on identified pathogens from mNGS results.
Monitoring & Follow-up
Evaluate mNGS results in clinical context to guide ongoing management.
Risks
Contamination control is essential due to the high sensitivity of mNGS.
Patient & Prescribing Data
Patients with suspected infectious or autoimmune causes of meningitis/encephalitis.
Earlier mNGS testing may influence hospital length of stay and timing of immunotherapy.
Clinical Best Practices
Maintain strict pre-analytic handling and appropriate negative controls for mNGS. Ensure standardized reporting and clinician education for accurate result interpretation. Develop clear ordering criteria for mNGS within diagnostic workflows.
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