Metagenomic Next-Generation Sequencing Identifies Pathogens Causing CNS Infections

Metagenomic next-generation sequencing (mNGS) is a shotgun sequencing method where all the nucleic acid (DNA and RNA) in a clinical sample is sequenced at a very high depth, 10-20 million sequences per sample. This technique is applicable to various clinical samples, including cerebrospinal fluid, plasma, respiratory secretions, urine, stool, or tissue. A single mNGS test can detect sequences from all pathogens—viruses, bacteria, fungi, and parasites—thereby aiding in identifying the potential cause of a patient’s infection. Now, data from a new study underscores the effectiveness and diagnostic capabilities of mNGS in diagnosing infectious diseases such as meningitis, encephalitis, and myelitis in both adults and children.

mNGS technology, originally developed at the University of California, San Francisco (UCSF, San Francisco, CA, USA) and exclusively licensed to Delve Bio (Boston, MA, USA), has been hailed as the future of infectious disease diagnostics, enabling physicians to avoid frustrating cycles of testing for patients battling serious neurological infections. The study analyzed over 4,800 patients who underwent cerebrospinal fluid (CSF) mNGS testing from 2016 to 2023. The results revealed that mNGS identified 797 organisms from 697 out of 4,828 samples (14.4%), encompassing 440 unique pathogenic species. The detection covered DNA and RNA viruses in nearly three-quarters of the cases, along with a wide range of bacteria, fungi, and parasites.

Image: Clinical laboratory workflow for mNGS (Photo courtesy of UCSF)

Further analysis and clinical review of more than 1,000 patients treated at UCSF indicated that 21.8% (48 out of 220) of infections were exclusively detected by mNGS. The sensitivity and specificity of CSF mNGS testing in clinically diagnosed infections were 63.1% and 99.6%, respectively, with a positive predictive value (PPV) of 97.1%, and a negative predictive value (NPV) of 92.3%. Comparatively, CSF mNGS demonstrated a higher diagnostic yield (63.1%) than all other forms of direct detection testing from CSF (45.9%), direct detection from non-CSF samples (15.0%), and indirect serologic testing (28.8%).

“Our experience over the seven years at UCSF covered in these studies shows that mNGS delivers the single most conclusive, unbiased and actionable tool for the diagnosis of infectious diseases,” said Charles Chiu, M.D., Ph.D., Delve Bio co-founder and UCSF Professor of Laboratory Medicine and Infectious Diseases and Director of the Clinical Microbiology Laboratory. “These data offer a compelling look at our real-world experience of using mNGS to uncover the cause of difficult-to-diagnose central nervous system infections to guide timely management and treatment for these life-threatening conditions.”

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