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Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for the Detection of Central Nervous System Pathogens
10:08

Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for the Detection of Central Nervous System Pathogens

Published on: April 17, 2026

Prospective identification of enteroviruses involved in meningitis in 2006 through direct genotyping in cerebrospinal

Audrey Mirand1, Cécile Henquell, Christine Archimbaud

  • 1Centre de Biologie-CHRU Clermont Ferrand, Laboratoire de Virologie, 58, Rue Montalembert, 63003 Clermont-Ferrand, France. amirand@chu-clermontferrand.fr

Journal of Clinical Microbiology
|November 6, 2007
PubMed

Insights

Rapid molecular identification of enterovirus serotypes in cerebrospinal fluid (CSF) enables quick diagnosis of aseptic meningitis. This direct genotyping method in CSF provides a more complete picture of enterovirus types than traditional methods.

Area of Science:

  • Virology
  • Molecular Biology
  • Infectious Diseases

Background:

  • Enterovirus infections are a common cause of aseptic meningitis.
  • Accurate and rapid identification of enterovirus serotypes is crucial for patient management and epidemiological studies.
  • Traditional methods for enterovirus identification often rely on virus isolation, which can be time-consuming.

Purpose of the Study:

  • To develop and evaluate a rapid molecular method for identifying enterovirus serotypes directly in cerebrospinal fluid (CSF).
  • To compare the effectiveness of direct CSF genotyping with traditional virus isolate genotyping for aseptic meningitis cases.

Main Methods:

  • Two seminested PCR assays were designed to amplify VP1 and VP4/VP2 capsid protein gene sequences.
  • The method was applied to CSF samples from patients with meningitis in 2005 and 2006.
  • Genotyping of virus isolates was performed for comparison.

Main Results:

  • Direct enterovirus genotyping in CSF achieved high success rates (98% in 2005, 96% in 2006).
  • The study identified 10 frequent serotypes in 2005 and 13 human enterovirus B species and 1 human enterovirus A species serotype in 2006.
  • Direct CSF genotyping detected rare serotypes missed by indirect genotyping, revealing a different serotype pattern in 2006 compared to 2005.

Conclusions:

  • Direct molecular identification of enterovirus serotypes in CSF is feasible and efficient for diagnosing aseptic meningitis.
  • This method offers a more comprehensive understanding of circulating enterovirus serotypes, including rare ones.
  • Prospective enterovirus genotyping directly from CSF can be completed within one week in a laboratory setting.

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