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  • PMID: 27645539 was deleted because it is a duplicate of PMID: 27405447
Adv Exp Med Biol. 2016 Jul 13. [Epub ahead of print]

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

Author information

1
Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego St, 02-106, Warsaw, Poland.
2
Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego St, 02-106, Warsaw, Poland. karol.perlejewski@wum.edu.pl.
3
Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, Japan.
4
Department of Clinical Science, Bergen University, 5021, Bergen, Norway.
5
Department of the Medical Genetics, Warsaw Medical University, 3C Pawińskiego St, 02-106, Warsaw, Poland.
6
Municipal Hospital for Infectious Diseases, 37 Wolska St, 01-201, Warsaw, Poland.
7
Department of Laboratory Medicine and Clinical Immunology of Developmental Age, Warsaw Medical University, 24 Marszałkowska St, 00-576, Warsaw, Poland.
8
Department of Neurology, Military Institute of Medicine, 128 Szaserów St, 04-141, Warsaw, Poland.

Abstract

Next-generation sequencing (NGS) followed by metagenomic 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; Metagenomics analysis; Next-generation sequencing; Pathogens; Viruses

PMID:
27405447
DOI:
10.1007/5584_2016_42

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