Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system

Neurology: Neuroimmunology and NeuroInflammation

Volumn 3, Issue 4, 2016, Pages

  Salzberg, Steven L ^a,b   Breitwieser, Florian P ^a   Kumar, Anupama ^b   Hao, Haiping ^c   Burger, Peter ^b   Rodriguez, Fausto J ^b   Lim, Michael ^c   Quiñones Hinojosa, Alfredo ^c   Gallia, Gary L ^c   Tornheim, Jeffrey A ^b   Melia, Michael T ^b   Sears, Cynthia L ^b   Pardo, Carlos A ^b  

^a Johns Hopkins University   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; BRAIN TISSUE; CASE REPORT; CLINICAL ARTICLE; CLINICAL OUTCOME; DIAGNOSIS; DNA SEQUENCING; FEMALE; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN TISSUE; MALE; MENINGEAL BIOPSY; METAGENOMICS; MICROBIOLOGY; MICROBIOME; MICROORGANISM; NONHUMAN; OUTCOME ASSESSMENT; PILOT STUDY; PIPELINE; PROSPECTIVE STUDY; RNA SEQUENCING; SPINAL CORD BIOPSY; VELOCITY;

EID: 85010620671     PISSN: None     EISSN: 23327812     Source Type: Journal    
DOI: 10.1212/NXI.0000000000000251     Document Type: Article

References (31)

1. Glaser CA, Honarmand S, Anderson LJ, et al. Beyond viruses: clinical profiles and etiologies associated with encephalitis. Clin Infect Dis 2006;43:1565–1577.
2. Barzon L, Lavezzo E, Militello V, Toppo S, Palu G. Applications of next-generation sequencing technologies to diagnostic virology. Int J Mol Sci 2011;12: 7861–7884.
3. Yin L, Liu L, Sun Y, et al. High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems. Retrovirology 2012;9:108.
4. Lecuit M, Eloit M. The human virome: new tools and concepts. Trends Microbiol 2013;21:510–515.
5. Wylie KM, Weinstock GM, Storch GA. Virome genomics: a tool for defining the human virome. Curr Opinion Microbiol 2013;16:479–484.
6. Chan BK, Wilson T, Fischer KF, Kriesel JD. Deep sequencing to identify the causes of viral encephalitis. PLoS One 2014;9:e93993.
7. Wilson MR, Shanbhag NM, Reid MJ, et al. Diagnosing balamuthia mandrillaris encephalitis with metagenomic deep sequencing. Ann Neurol 2015;78:722–730.
8. Naccache SN, Peggs KS, Mattes FM, et al. Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing. Clin Infect Dis 2015;60:919–923.
9. Brown JR, Morfopoulou S, Hubb J, et al. Astrovirus VA1/HMO-C: an increasingly recognized neurotropic pathogen in immunocompromised patients. Clin Infect Dis 2015;60:881–888.
10. Fremond ML, Perot P, Muth E, et al. Next-generation sequencing for diagnosis and tailored therapy: a case report of astrovirus-associated progressive encephalitis. J Pediatr Infect Dis Soc 2015;4:e53–e57.
11. Greninger AL, Messacar K, Dunnebacke T, et al. Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing. Genome Med 2015;7:113.
12. Tan le V, van Doorn HR, Nghia HD, et al. Identification of a new cyclovirus in cerebrospinal fluid of patients with acute central nervous system infections. MBio 2013;4: e00231–e00313.
13. Wylie KM, Blanco-Guzman M, Wylie TN, et al. High-throughput sequencing of cerebrospinal fluid for diagnosis of chronic Propionibacterium acnes meningitis in an allogeneic stem cell transplant recipient. Transpl Infect Dis 2016;18:227–233.
14. Hoffmann B, Tappe D, Hoper D, et al. A variegated squirrel bornavirus associated with fatal human encephalitis. N Engl J Med 2015;373:154–162.
15. Wilson MR, Naccache SN, Samayoa E, et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med 2014;370:2408–2417.
16. Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 2014;15:R46.
17. Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389–3402.
18. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012;9:357–359.
19. Ferenczy MW, Marshall LJ, Nelson CD, et al. Molecular biology, epidemiology, and pathogenesis of progressive multifocal leukoencephalopathy, the JC virus-induced demyelinating disease of the human brain. Clin Microbiol Rev 2012;25:471–506.
20. CDC. Outbreaks: multistate outbreak of infections caused by Elizabethkingia anophelis [online]. Available at: http://www.cdc.gov/elizabethkingia/outbreaks/index.html. Accessed May 2, 2016.
21. Pardo CA, Nabbout R, Galanopoulou AS. Mechanisms of epileptogenesis in pediatric epileptic syndromes: Rasmussen encephalitis, infantile spasms, and febrile infection-related epilepsy syndrome (FIRES). Neurotherapeutics 2014;11:297–310.
22. Maginnis MS, Atwood WJ. JC virus: an oncogenic virus in animals and humans? Semin Cancer Biol 2009;19:261–269.
23. Martelius T, Lappalainen M, Palomaki M, Anttila VJ. Clinical characteristics of patients with Epstein Barr virus in cerebrospinal fluid. BMC Infect Dis 2011;11:281.
24. Khalil M, Enzinger C, Wallner-Blazek M, et al. Epstein-Barr virus encephalitis presenting with a tumor-like lesion in an immunosuppressed transplant recipient. J Neurovirol 2008;14:574–578.
25. Ryschkewitsch CF, Jensen PN, Major EO. Multiplex qPCR assay for ultra sensitive detection of JCV DNA with simultaneous identification of genotypes that discriminates non-virulent from virulent variants. J Clin Virol 2013;57: 243–248.
26. Marshall LJ, Ferenczy MW, Daley EL, Jensen PN, Ryschkewitsch CF, Major EO. Lymphocyte gene expression and JC virus noncoding control region sequences are linked with the risk of progressive multifocal leukoencephalopathy. J Virol 2014;88:5177–5183.
27. Feierabend D, Reichart R, Romeike B, Kalff R, Walter J. Cerebral abscess due to Lactococcus lactis cremoris in a child after sinusitis. Clin Neurol Neurosurg 2013;115:614–616.
28. Inoue M, Saito A, Kon H, et al. Subdural empyema due to Lactococcus lactis cremoris: case report. Neurol Med Chir 2014;54:341–347.
29. Topcu Y, Akinci G, Bayram E, Hiz S, Turkmen M. Brain abscess caused by Lactococcus lactis cremoris in a child. Eur J Pediatr 2011;170:1603–1605.
30. Grice EA, Segre JA. The skin microbiome. Nat Rev Microbiol 2011;9:244–253.
31. Salter SJ, Cox MJ, Turek EM, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 2014;12:87.