Metagenomic sequencing may be valuable for diagnosing infectious disease
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Key takeaways:
- Metagenomic sequencing detected significantly more organisms than cerebrospinal fluid culture and universal PCR combined.
- The testing demonstrated a sensitivity of 63%, specificity of 99% and accuracy of 90%.
DENVER — Metagenomic next-generation sequencing may be a reliable diagnostic tool to analyze causes of highly contagious meningitis or encephalitis in a clinical setting, according to a speaker.
“By sequencing all the DNA and RNA in clinical samples, in principle, we can diagnose any kind of infection,” Charles Chiu, MD, PhD, professor of laboratory medicine in the division of infectious diseases at the University of California, San Francisco, said during an AAN-sponsored webinar held before its annual meeting.
Chiu and colleagues attempted to analyze the performance of a metagenomic next-generation sequencing (mNGS) spinal fluid assay to diagnose causes of highly contagious meningitis and/or encephalitis when employed over a 7-year period in real-life clinical settings, compared to cerebrospinal fluid (CSF) or broad-range PCR tests.
The researchers reviewed electronic medical records from 2016 to 2023 to identify 4,849 global results of mNGS testing on CSF samples. Additional chart review was conducted to yield a subset of 968 (average age 46.4 years) individuals hospitalized at UCSF to assess demographics, infectious/noninfectious diagnoses, CSF profile including cell count and differential, glucose, protein, and other relevant laboratory and imaging results.
From the initial set, 1,231 patients had a positive mNGS result with at least one organism detected, with the remaining negative. Among the detected organisms were bacteria (44%), DNA virus (26%), RNA virus (16%), fungi (11%) and 3% of parasitic origin.
According to results, mNGS detected significantly more organisms than CSF culture and universal PCR combined. Overall, mNGS detected at least one pathogen in CSF in 25% of cases, with 192 different species represented. Additionally, mNGS testing demonstrated a sensitivity of 63%, specificity of 99% and accuracy of 90%.
“We conclude that these results justify the incorporation of cerebrospinal fluid [metagenomic next-generation sequencing] testing as part of the routine diagnostic workup in hospitalized patients who present with potential central nervous system infection,” Chiu stated.