In meningitis/encephalitis (M/E) diagnostics, patients undergo scores of tests as clinicians try to eliminate each potential cause. Despite this, the cause of more than half of M/E cases is never identified.
Here, we speak with Steve Miller, Chief Medical Officer at Delve Bio, who was involved in a recently published study into the earlier use of comprehensive metagenomic next-generation sequencing (mNGS) for improving M/E diagnostics.
Why is M/E so difficult to diagnose quickly, even in well-resourced hospitals?
M/E sits at the intersection of infectious disease, neurology, and immunology. Patients typically present with nonspecific symptoms, and the differential includes bacterial, viral, fungal, parasitic, neoplastic, and autoimmune causes.
Most current diagnostics are hypothesis-driven. Culture, pathogen-specific PCR, and serologic testing each evaluate a limited portion of possible etiologies. If the correct cause is not suspected early, it may not be tested for. Even in well-resourced centers, more than 60 percent of cases remain without a confirmed diagnosis after comprehensive evaluation.
In a typical CNS infection workup, where do you see the biggest diagnostic delays?
Delays usually result from the stepwise nature of testing rather than any single slow assay.
Clinicians must prioritize tests from a limited cerebrospinal fluid (CSF) volume. In pediatrics, there may be only one opportunity for lumbar puncture, requiring decisions about which studies to run first: HSV PCR, a multiplex syndromic panel, cryptococcal antigen, tuberculosis, fungal studies, or autoimmune markers? If initial testing is unrevealing, additional assays are ordered sequentially, often as send-outs. Each step adds time, logistics, and cost, extending the path to diagnosis.
What did your study reveal about the earlier use of mNGS in the M/E diagnostic work-up?
Our study, published in Open Forum Infectious Diseases, evaluated what might occur if a broad mNGS assay with a 48-hour turnaround time were used earlier in the diagnostic pathway rather than as a last-line test. The cohort included patients with confirmed infectious M/E, as well as a separate group with autoimmune encephalitis.
The modeled analysis found that earlier use of the assay would reduce the number of microbiologic tests ordered per patient and shorten time to diagnosis. In patients with infectious etiologies, the projected reduction in additional microbiologic testing exceeded 60 percent. In patients ultimately diagnosed with autoimmune encephalitis, where no pathogen is identified, the reduction was greater than 90 percent.
Time to diagnosis was also shortened. In the infectious cohort, earlier mNGS testing was associated with a modeled reduction of seven days. In patients with autoimmune encephalitis, time to diagnosis was reduced by approximately 10 days by more rapidly excluding infectious causes.
Earlier clarification of etiology may influence hospital length of stay, antimicrobial use, and timing of immunotherapy. From a laboratory perspective, earlier comprehensive testing may reduce repeat lumbar punctures and downstream send-out assays.
Where does mNGS fit alongside standard testing?
mNGS does not replace initial studies. CSF cell count, glucose and protein, Gram stain, and culture remain essential for immediate management decisions.
Broad molecular testing may be considered when the differential is wide, particularly in immunocompromised patients, severe or atypical presentations, culture-negative CSF with ongoing concern for infection, suspected rare pathogens, or when CSF volume is limited. It may also be useful when rapid exclusion of infection would alter management, such as in suspected autoimmune encephalitis.
Which patients or clinical scenarios benefit most from early mNGS testing?
Although individual institutions will define their own testing criteria and stewardship protocols, several clinical scenarios are frequently discussed for early use of mNGS:
Immunocompromised patients, who are at risk for a broad range of opportunistic pathogens not fully covered by standard panels.
Severe or atypical neurologic presentations, where infectious and autoimmune causes may overlap.
Culture- or PCR-negative CSF with persistent concern for infection, when routine studies are unrevealing.
Suspected rare or travel-related infections outside the scope of conventional panels.
Limited CSF volume, particularly in pediatrics, where a single comprehensive assay may reduce the need for repeat procedures.
Earlier mNGS may also be considered when rapid exclusion of infection would alter management, such as before initiating immunosuppressive therapy.
What are the most important considerations for the interpretation of mNGS results?
Interpretation of mNGS results requires close collaboration among laboratory, neurology, and infectious disease teams. Because the assay is highly sensitive, contamination control is essential. Strict pre-analytic handling and appropriate negative controls help prevent background signals from being misinterpreted as infection.
Results must be evaluated in quantitative and clinical context. Low read counts of common commensal organisms – especially in blood-contaminated CSF – may not indicate true disease, whereas high read depth and broad genome coverage consistent with the patient’s presentation are more likely to be clinically meaningful.
Unexpected or low-abundance findings may warrant confirmation with targeted PCR, serology, or culture when management decisions depend on the result. Ultimately, mNGS interpretation extends the laboratory’s role by integrating sequencing data with clinical and microbiologic information to provide a clear, actionable report.
How can earlier mNGS results support antimicrobial stewardship?
Earlier comprehensive pathogen detection may help narrow empiric therapy when a causative organism is identified. Conversely, a negative result – interpreted within clinical context – may support de-escalation of prolonged broad-spectrum antimicrobials and consideration of noninfectious etiologies.
Looking ahead, what are the next practical steps for broader adoption?
From a systems perspective, the emphasis is shifting from analytic validity alone to practical integration of mNGS into diagnostic pathways.
First, alidation and performance data are essential, and should focus on consistent sensitivity and specificity across pathogen types and specimen conditions. Equally, standardized reporting and clinician education are critical to ensure results are interpreted accurately and within clinical context.
Integration of mNGS into the workflow requires clear ordering criteria within standard systems to support appropriate use. The workflow must ensure that
turnaround time is reliable and fast enough to inform treatment decisions.
Finally, reimbursement and utilization governance should also be considered, with institutional policies helping define when mNGS is most appropriate in patient care.
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