Chapter

Respiratory Treatment and Prevention

Volume 944 of the series Advances in Experimental Medicine and Biology pp 53-62

Date:

Sensitivity of Next-Generation Sequencing Metagenomic Analysis for Detection of RNA and DNA Viruses in Cerebrospinal Fluid: The Confounding Effect of Background Contamination

  • Iwona Bukowska-OśkoAffiliated withDepartment of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University
  • , Karol PerlejewskiAffiliated withDepartment of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University Email author 
  • , Shota NakamuraAffiliated withDepartment of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University
  • , Daisuke MotookaAffiliated withDepartment of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University
  • , Tomasz StokowyAffiliated withDepartment of Clinical Science, Bergen University
  • , Joanna KosińskaAffiliated withDepartment of the Medical Genetics, Warsaw Medical University
  • , Marta PopielAffiliated withDepartment of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University
  • , Rafał PłoskiAffiliated withDepartment of the Medical Genetics, Warsaw Medical University
  • , Andrzej HorbanAffiliated withMunicipal Hospital for Infectious Diseases
    • , Dariusz LipowskiAffiliated withMunicipal Hospital for Infectious Diseases
    • , Kamila Caraballo CortésAffiliated withDepartment of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University
    • , Agnieszka PawełczykAffiliated withDepartment of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University
    • , Urszula DemkowAffiliated withDepartment of Laboratory Medicine and Clinical Immunology of Developmental Age, Warsaw Medical University
    • , Adam StępieńAffiliated withDepartment of Neurology, Military Institute of Medicine
    • , Marek RadkowskiAffiliated withDepartment of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University
    • , Tomasz LaskusAffiliated withDepartment of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University

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Abstract

Next-generation sequencing (NGS) followed by metagenomic analysis enables the detection and identification of known as well as novel pathogens. It could be potentially useful in the diagnosis of encephalitis, caused by a variety of microorganisms. The aim of the present study was to evaluate the sensitivity of isothermal RNA amplification (Ribo-SPIA) followed by NGS metagenomic analysis in the detection of human immunodeficiency virus (HIV) and herpes simplex virus (HSV) in cerebrospinal fluid (CSF). Moreover, we analyzed the contamination background. We detected 102 HIV copies and 103 HSV copies. The analysis of control samples (two water samples and one CSF sample from an uninfected patient) revealed the presence of human DNA in the CSF sample (91 % of all reads), while the dominating sequences in water were qualified as ‘other’, related to plants, plant viruses, and synthetic constructs, and constituted 31 % and 60 % of all reads. Bacterial sequences represented 5.9 % and 21.4 % of all reads in water samples and 2.3 % in the control CSF sample. The bacterial sequences corresponded mainly to Psychrobacter, Acinetobacter, and Corynebacterium genera. In conclusion, Ribo-SPIA amplification followed by NGS metagenomic analysis is sensitive for detection of RNA and DNA viruses. Contamination seems common and thus the results should be confirmed by other independent methods such as RT-PCR and PCR. Despite these reservations, NGS seems to be a promising method for the diagnosis of viral infections.

Keywords

Bacteria Cerebrospinal fluid DNA Encephalitis Next-generation sequencing Metagenomics analysis Pathogens Viruses