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Related Experiment Video

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Sequencing of mRNA from Whole Blood using Nanopore Sequencing
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High-throughput and Efficient Assay for Central Nervous System Infection with Targeted Nanopore Sequencing

Ye Shi1,2, Zhongdong Lin3, Zhanguo Chen4

  • 1School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China.

Infection and Drug Resistance
|October 31, 2025
PubMed
Summary

We developed targeted nanopore sequencing (tNPS), a rapid diagnostic assay for central nervous system (CNS) infections. This method enhances efficiency and pathogen detection for improved molecular diagnosis of CNS infections.

Keywords:
assay developmentcentral nervous system infectioncerebrospinal fluidmultiplex PCRnanopore sequencingtargeted sequencing

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Area of Science:

  • Infectious Diseases
  • Molecular Diagnostics
  • Genomics

Background:

  • Central nervous system (CNS) infections pose a significant global health challenge with high morbidity and mortality.
  • Current diagnostic methods for CNS infections can be time-consuming and may have limitations in pathogen detection.

Purpose of the Study:

  • To develop and validate an integrated diagnostic approach for CNS infections using high-throughput nanopore sequencing and multiplex PCR.
  • To establish a rapid, culture-independent assay for precise identification of CNS pathogens.

Main Methods:

  • Developed targeted nanopore sequencing (tNPS), combining pathogen-specific and universal primers for multiplex PCR amplification.
  • Targeted 17 prevalent CNS pathogens (bacteria, fungi, DNA viruses) and amplified 16S rRNA and ITS regions.
  • Validated tNPS using reference strains, microbial communities, and clinical cerebrospinal fluid (CSF) samples.

Main Results:

  • tNPS demonstrated analytical validation with diverse microbial samples.
  • Achieved an accelerated turnaround time of within 8 hours for clinical CSF samples.
  • Precise identification of CNS pathogens was confirmed by comparing tNPS results with CSF culture and metagenomic next-generation sequencing.

Conclusions:

  • tNPS offers enhanced efficiency, high-throughput capability, and an expanded pathogen detection spectrum for CNS infections.
  • The assay is a feasible culture-independent diagnostic tool for molecular diagnosis of CNS infections.
  • tNPS has the potential for broad implementation in clinical settings for rapid and accurate CNS infection diagnosis.