Metagenomic Analysis of Cerebrospinal Fluid from Patients with Multiple Sclerosis

Perlejewski, Karol; Bukowska-Ośko, Iwona; Nakamura, Shota; Motooka, Daisuke; Stokowy, Tomasz; Płoski, Rafał; Rydzanicz, Małgorzata; Zakrzewska-Pniewska, Beata; Podlecka-Piętowska, Aleksandra; Nojszewska, Monika; Gogol, Anna; Cortés, Kamila Caraballo; Demkow, Urszula; Stępień, Adam; Laskus, Tomasz; Radkowski, Marek

doi:10.1007/5584_2016_25

Cited by 29 publications

(26 citation statements)

References 35 publications

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“…Case-control studies offer opportunities, but also require care and caution, especially when selecting subjects, particularly controls. 125 A common principle is that controls should be selected from the same source ("at risk") population as cases.…”

Section: Study Design and Sample Collectionmentioning

confidence: 99%

The gut microbiome in human neurological disease: A review

Tremlett

Bauer

Appel‐Cresswell

et al. 2017

Annals of Neurology

437

292

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Almost half the cells and 1% of the unique genes found in our bodies are human, the rest are from microbes, predominantly bacteria, archaea, fungi, and viruses. These microorganisms collectively form the human microbiota, with most colonizing the gut. Recent technological advances, open access data libraries, and application of high-throughput sequencing have allowed these microbes to be identified and their contribution to neurological health to be examined. Emerging evidence links perturbations in the gut microbiota to neurological disease, including disease risk, activity, and progression. This review provides an overview of the recent advances in microbiome research in relation to neuro(auto)immune and neurodegenerative conditions affecting humans, such as multiple sclerosis, neuromyelitis optica spectrum disorders, Parkinson disease, Alzheimer disease, Huntington disease, and amyotrophic lateral sclerosis. Study design and terminology used in this rapidly evolving, highly multidisciplinary field are summarized to empower and engage the neurology community in this "newly discovered organ." Ann Neurol 2017;81:369-382.

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Section: Study Design and Sample Collectionmentioning

confidence: 99%

The gut microbiome in human neurological disease: A review

Tremlett

Bauer

Appel‐Cresswell

et al. 2017

Annals of Neurology

437

292

View full text Add to dashboard Cite

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“…During previous studies, we encountered the problem of contaminating DNA complicating the analysis of sequencing results (26), which is emerging as a common problem encountered when attempting to do metagenomic analysis of clinical samples (3,(27)(28)(29). Here, we evaluated three commercially available WGA kits to characterize the relative amount and composition of contaminating DNA associated with the use of each of them to inform selection of the appropriate WGA kit for further metagenomics studies of PJI.…”

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confidence: 99%

Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis

et al. 2017

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Whole-genome amplification (WGA) is a useful tool for amplification of very small quantities of DNA for many uses, including metagenomic shotgun sequencing for infection diagnosis. Depending on the application, background DNA from WGA kits can be problematic. Three WGA kits were tested for their utility in a metagenomics approach to identify the pathogens in sonicate fluid comprised of biofilms and other materials dislodged from the surfaces of explanted prosthetic joints using sonication. The Illustra V2 Genomiphi, Illustra single cell Genomiphi, and Qiagen REPLI-g single cell kits were used to test identical sonicate fluid samples. Variations in the number of background reads, the genera identified in the background, and the number of reads from known pathogens known to be present in the samples were observed between kits. These results were then compared to those obtained with a library preparation without prior WGA using an NEBNext Ultra II paired-end kit, which requires a very small amount of input DNA. This approach also resulted in the presence of contaminant bacterial DNA and yielded fewer reads from the known pathogens. These findings highlight the impact that WGA kit selection can have on metagenomic analysis of low-biomass samples and the importance of the careful selection and consideration of the implications of using these tools.KEYWORDS metagenomics, prosthetic joint infection, whole-genome amplification M etagenomic shotgun sequencing is a rapidly developing powerful tool to examine microbial communities. It is also gaining interest in the field of clinical microbiology as a way to identify pathogens in normally sterile specimens (1-7). Not only does this approach allow for pathogen identification, but the gene content information can also be used for other analyses, such as antibiotic resistance prediction (8, 9), typing for tracking of outbreaks or epidemiological studies (10), or assessment for other relevant genes, such as those encoding virulence factors (11,12).One significant barrier to metagenomic shotgun sequencing approaches is the amount of genetic material necessary to perform these experiments. This is not an obstacle in settings such as fecal microbiome studies, where abundant organisms are present, but in other scenarios (e.g., in scenarios with low-biomass environmental samples and uncultured bacteria or in single cell analysis), the number of cells and the amount of genetic material can be limited (13)(14)(15)(16)(17). It is in these situations that whole-genome amplification (WGA) has the potential to play an important role in pathogen detection. Citation Thoendel M, Jeraldo P, GreenwoodQuaintance KE, Yao J, Chia N, Hanssen AD, Abdel MP, Patel R. 2017. Impact of contaminating DNA in whole-genome amplification kits used for metagenomic shotgun sequencing for infection diagnosis. J

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“…VZV, another Herpesviridae was detected in one MS patient. VZV DNA was reported to be commonly present in CSF during MS relapses [ 46 ] and in our previous study we detected it in a patient with clinically isolated syndrome (CIS) which is considered to represent the earliest stage of MS demyelination [ 16 , 47 ].…”

Section: Discussionmentioning

confidence: 99%

“…Only a few metagenomic studies were conducted so far on viral populations in MS patients which resulted in finding of GB virus-C (GBV-C) in the brain of one MS patient [ 14 ] and a very limited number of NGS reads mapping to EBV, CMV, and parvovirus in cerebrospinal fluid (CSF) [ 15 ]. In our previous small study shotgun metagenomic analysis of CSF detected VZV-DNA in a patient with Central Nervous System Idiopathic Inflammatory Demyelinating Disorder (IIDD); [ 16 ]. This finding encouraged us to conduct a more comprehensive search for viral agents in CSF of MS patients using both RT-PCR/PCR testing for the most common neurotropic viruses and shotgun DNA/RNA-based metagenomics.…”

Section: Introductionmentioning

confidence: 99%

Search for viral agents in cerebrospinal fluid in patients with multiple sclerosis using real-time PCR and metagenomics

et al. 2020

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Multiple sclerosis (MS) is a chronic, immune-mediated demyelinating disease of the central nervous system of unclear etiology, but there is some evidence that viral infections could be responsible for triggering autoimmune mechanisms against myelin. We searched for viral RNA and DNA in cerebrospinal fluid (CSF) of 34 MS patients and 13 controls using RT-PCR/PCR against common neurotropic viruses. In addition, shotgun DNA- and RNA-based metagenomics were done in 13 MS patients and 4 controls. Specific quantitative real-time RT-PCR/PCR testing revealed the presence of viral nucleic acid in seven (20.59%) MS patients and in one (7.69%) control patient. In MS patients the most frequently detected was human herpesvirus type 6 (HHV-6; 3 cases; 8.82%); followed by Epstein-Barr virus (EBV; 2 cases; 5.88%), varicella zoster virus (VZV; 1 case; 2.94%) and Enterovirus (EV; 1 case; 2.94%). The single identified virus among controls was EBV (7.69%). DNA and RNA metagenomic assays did not identify any known eukaryotic viruses even though three of the analyzed samples were low-level positive by specific quantitative real-time PCR. In conclusion, we detected the presence of Herpesviridae and occasionally Enteroviridae in CSF from patients with MS but their prevalence was not significantly higher than among controls. Metagenomic analysis seems to be less sensitive than real-time RT-PCR/PCR and it did not detect any potential viral pathogens.

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Metagenomic Analysis of Cerebrospinal Fluid from Patients with Multiple Sclerosis

Cited by 29 publications

References 35 publications

The gut microbiome in human neurological disease: A review

The gut microbiome in human neurological disease: A review

Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis

Search for viral agents in cerebrospinal fluid in patients with multiple sclerosis using real-time PCR and metagenomics

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