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Adv Exp Med Biol. 2016;935:89-98. doi: 10.1007/5584_2016_25.

Metagenomic Analysis of Cerebrospinal Fluid from Patients with Multiple Sclerosis.

Author information

1
Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego Street, Warsaw, 02-106, Poland.
2
Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego Street, Warsaw, 02-106, Poland. ibukowska@wum.edu.pl.
3
Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Osaka, Japan.
4
Department of Clinical Science, University of Bergen, Bergen, 5021, Norway.
5
Department of the Medical Genetics, Warsaw Medical University, 3C Pawińskiego Street, Warsaw, 02-106, Poland.
6
Department of Neurology, Warsaw Medical University, 1A Banacha, Warsaw, 02-097, Poland.
7
Department of Laboratory Medicine and Clinical Immunology of Developmental Age, Medical University of Warsaw, 24 Marszałkowska Street, Warsaw, 00-576, Poland.
8
Department of Neurology, Military Institute of Medicine, 128 Szaserów Street, Warsaw, 04-141, Poland.

Abstract

Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of central nervous system of unknown etiology. However, some infectious agents have been suggested to play a significant role in its pathogenesis. Next-generation sequencing (NGS) and metagenomics can be employed to characterize microbiome of MS patients and to identify potential causative pathogens. In this study, 12 patients with idiopathic inflammatory demyelinating disorders (IIDD) of the central nervous system were studied: one patient had clinically isolated syndrome, one patient had recurrent optic neuritis, and ten patients had multiple sclerosis (MS). In addition, there was one patient with other non-inflammatory neurological disease. Cerebrospinal fluid (CSF) was sampled from all patients. RNA was extracted from CSF and subjected to a single-primer isothermal amplification followed by NGS and comprehensive data analysis. Altogether 441,608,474 reads were obtained and mapped using blastn. In a CSF sample from the patient with clinically isolated syndrome, 11 varicella-zoster virus reads were found. Other than that similar bacterial, fungal, parasitic, and protozoan reads were identified in all samples, indicating a common presence of contamination in metagenomics. In conclusion, we identified varicella zoster virus sequences in one out of the 12 patients with IIDD, which suggests that this virus could be occasionally related to the MS pathogenesis. A widespread bacterial contamination seems inherent to NGS and complicates the interpretation of results.

KEYWORDS:

Cerebrospinal fluid; Idiopathic inflammatory demyelinating disorder; Metagenomics; Multiple sclerosis; Next-generation sequencing

PMID:
27311319
DOI:
10.1007/5584_2016_25
[Indexed for MEDLINE]

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