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August 22, 2022

The Current Status of Next-Generation Sequencing for Diagnosis of Central Nervous System Infections

Author Affiliations
  • 1Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco
  • 2Neuroinfectious Disease Program, Department of Neurology, University of Colorado School of Medicine, Aurora
  • 3Department of Immunology-Microbiology, University of Colorado School of Medicine, Aurora
JAMA Neurol. 2022;79(11):1095-1096. doi:10.1001/jamaneurol.2022.2287

The prime directive in diagnosing neuroinfectious disease is to answer 3 deceptively simple questions: (1) Is the patient infected? (2) If so, with what? (3) How do we treat the infection? Our ability to answer the first 2 questions has been substantially improved by the emergence of multiplex approaches to diagnosis of central nervous system (CNS) infections, as exemplified by metagenomic next-generation sequencing (mNGS). Eight years ago, the first publications of proof-of-concept case reports were just appearing, establishing that mNGS could lead to actionable diagnosis with clear treatment implications, as in a case involving neuroleptospirosis in an immunocompromised child.1 The passage of time has enabled a more mature assessment of the role and limitations of mNGS in neurodiagnostics. The prospective Precision Diagnosis of Acute Infectious Diseases (PDAID) Study2 enrolled 204 patients with idiopathic encephalitis (64%), meningitis (34%), or myelitis (2%) from 8 hospitals. Of the 58 CNS infections ultimately diagnosed, 13 (22%) were only diagnosed using mNGS, including cases of St Louis encephalitis virus, hepatitis E virus, and Streptococcus agalactiae; 8 of these diagnoses affected clinical care. Overall, mNGS was highly concordant with other cerebrospinal fluid (CSF) direct detection tests (ie, pathogen-specific polymerase chain reaction [PCR], culture, and antigen testing); nevertheless, 26 additional infections (45%) diagnosed with conventional testing were missed by mNGS.

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