Enhanced Detection of DNA Viruses in the Cerebrospinal Fluid of Encephalitis Patients Using Metagenomic Next-Generation Sequencing

Manso, Carmen F.; Bibby, David F.; Mohamed, Hodan; Brown, David; Zuckerman, Mark; Mbisa, Jean L.

doi:10.3389/fmicb.2020.01879

Cited by 12 publications

(16 citation statements)

References 70 publications

(93 reference statements)

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“…Immunohistochemistry or PCR can only detect pathogens, where a specific knowledge about the presumed pathogen is present ( 20 ). In the current study, a novel non-specific viral detection technique was applied, which was already successfully used for metagenomic investigations in human CSF ( 21 – 23 ) and various veterinary samples ( 24 – 26 ): Sensitivity and specificity of NGS in human CSF sample was 95 and 96%, respectively ( 21 ).…”

Section: Discussionmentioning

confidence: 99%

Canine Meningoencephalitis of Unknown Origin—The Search for Infectious Agents in the Cerebrospinal Fluid via Deep Sequencing

Neßler

Osterhaus

et al. 2021

Front. Vet. Sci.

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Meningoencephalitis of unknown origin (MUO) describes a group of meningoencephalitides in dogs with a hitherto unknown trigger. An infectious agent has been suggested as one possible trigger of MUO but has not been proven so far. A relatively new method to screen for viral RNA or DNA is next-generation sequencing (NGS) or deep sequencing. In this study, a metagenomics analysis of the virome in a sample is analyzed and scanned for known or unknown viruses. We examined fresh-frozen CSF of 6 dogs with MUO via NGS using a modified sequence-independent, single-primer amplification protocol to detect a possible infectious trigger. Analysis of sequencing reads obtained from the six CSF samples showed no evidence of a virus infection. The inability to detect a viral trigger which could be implicated in the development of MUO in the examined population of European dogs, suggests that the current techniques are not sufficiently sensitive to identify a possible virus infection, that the virus is already eliminated at the time-point of disease outbreak, the trigger might be non-infectious or that there is no external trigger responsible for initiating MUO in dogs.

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Section: Discussionmentioning

confidence: 99%

Canine Meningoencephalitis of Unknown Origin—The Search for Infectious Agents in the Cerebrospinal Fluid via Deep Sequencing

Neßler

Osterhaus

et al. 2021

Front. Vet. Sci.

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“…Sample P3 I1 B had 2000-3000 (0.1-0.2%) sequences mapped to multiple torque teno virus (TTV) genomes. TTV has been previously identified in CSF ( Simner et al., 2018 ; Manso et al., 2020 ), but its clinical significance is unclear. Our preliminary findings from assembling the TTV reads indicate that the sample contained potentially 5 or more strains of TTV and torque teno mini virus.…”

Section: Resultsmentioning

confidence: 99%

Molecular Characterization of Microbiota in Cerebrospinal Fluid From Patients With CSF Shunt Infections Using Whole Genome Amplification Followed by Shotgun Sequencing

Hodor

Pope

Whitlock

et al. 2021

Front. Cell. Infect. Microbiol.

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Understanding the etiology of cerebrospinal fluid (CSF) shunt infections and reinfections requires detailed characterization of associated microorganisms. Traditionally, identification of bacteria present in the CSF has relied on culture methods, but recent studies have used high throughput sequencing of 16S rRNA genes. Here we evaluated the method of shotgun DNA sequencing for its potential to provide additional genomic information. CSF samples were collected from 3 patients near the beginning and end of each of 2 infection episodes. Extracted total DNA was sequenced by: (1) whole genome amplification followed by shotgun sequencing (WGA) and (2) high-throughput sequencing of the 16S rRNA V4 region (16S). Taxonomic assignments of sequences from WGA and 16S were compared with one another and with conventional microbiological cultures. While classification of bacteria was consistent among the 3 approaches, WGA provided additional insights into sample microbiological composition, such as showing relative abundances of microbial versus human DNA, identifying samples of questionable quality, and detecting significant viral load in some samples. One sample yielded sufficient non-human reads to allow assembly of a high-quality Staphylococcus epidermidis genome, denoted CLIMB1, which we characterized in terms of its MLST profile, gene complement (including putative antimicrobial resistance genes), and similarity to other annotated S. epidermidis genomes. Our results demonstrate that WGA directly applied to CSF is a valuable tool for the identification and genomic characterization of dominant microorganisms in CSF shunt infections, which can facilitate molecular approaches for the development of better diagnostic and treatment methods.

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“…Panviral group (family and genera) PCR was chosen for this study due to its sensitivity in viral discovery ( 21 , 22 ). Although next generation sequencing is ideal to identify a broad range of microorganisms, including those not yet known, the depth of sequencing may limit sensitivity and necessitate enrichment of viral nucleic acids to improve outcomes ( 48 – 52 ). However, despite the sensitivity of PCR, false negative results are still possible in this study for a number of reasons.…”

Section: Discussionmentioning

confidence: 99%

Screening for Viral Nucleic Acids in the Cerebrospinal Fluid of Dogs With Central Nervous System Inflammation

Barber

Li²,

Levine

et al. 2022

Front. Vet. Sci.

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Central nervous system (CNS) inflammation is a common cause of neurological dysfunction in dogs. Most dogs with CNS inflammation are diagnosed with presumptive autoimmune disease. A smaller number are diagnosed with an infectious etiology. Additionally, at necropsy, a subset of dogs with CNS inflammation do not fit previously described patterns of autoimmune disease and an infectious cause is not readily identifiable. Because viral infection is a common cause of meningoencephalitis in people, we hypothesize that a subset of dogs presented with CNS inflammation have an occult viral infection either as a direct cause of CNS inflammation or a trigger for autoimmunity. The goal of this research was to screen cerebrospinal fluid from a large number dogs with CNS inflammation for occult viral infection. One hundred seventy-two dogs with neurological dysfunction and cerebrospinal fluid (CSF) pleocytosis were identified. Of these, 42 had meningoencephalitis of unknown origin, six had steroid-responsive meningitis-arteritis, one had eosinophilic meningoencephalitis, five had documented infection, 21 had and undetermined diagnosis, and 97 had a diagnosis not consistent with primary inflammatory disease of the CNS (e.g., neoplasia). CSF samples were subsequently screened with broadly reactive PCR for eight viral groups: adenovirus, bunyavirus, coronavirus, enterovirus, flavivirus, herpesvirus, paramyxovirus, and parechovirus. No viral nucleic acids were detected from 168 cases screened for eight viral groups, which does not support occult viral infection as a cause of CNS inflammation in dogs. La Crosse virus (LACV) nucleic acids were detected from four cases in Georgia. Subclinical infection was supported in two of these cases but LACV could not be ruled-out as a cause of infection in the other two cases, suggesting further research is warranted to determine if LACV is an occult cause of CNS inflammation in dogs.

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Enhanced Detection of DNA Viruses in the Cerebrospinal Fluid of Encephalitis Patients Using Metagenomic Next-Generation Sequencing

Cited by 12 publications

References 70 publications

Canine Meningoencephalitis of Unknown Origin—The Search for Infectious Agents in the Cerebrospinal Fluid via Deep Sequencing

Canine Meningoencephalitis of Unknown Origin—The Search for Infectious Agents in the Cerebrospinal Fluid via Deep Sequencing

Molecular Characterization of Microbiota in Cerebrospinal Fluid From Patients With CSF Shunt Infections Using Whole Genome Amplification Followed by Shotgun Sequencing

Screening for Viral Nucleic Acids in the Cerebrospinal Fluid of Dogs With Central Nervous System Inflammation

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