Allcock OM, Guo C, Uhlemann AC, Whittier S, Chauhan LV, Garcia J, Price A, Morse SS, Mishra N, Briese T, Lipkin WI (2018) BacCapSeq: a platform for diagnosis and characterization of bacterial infections. mBio 9(5):e02007–18
Allcock RJN, Jennison AV, Warrilow D (2017) Towards a universal molecular microbiological test. J Clin Microbiol 55(11):3175–3182. https://doi.org/10.1128/JCM.01155-17
Article PubMed PubMed Central CAS Google Scholar
Briese T, Kapoor A, Mishra N, Jain K, Kumar A, Jabado OJ, Lipkin WI (2015) Virome capture sequencing enables sensitive viral diagnosis and comprehensive virome analysis. mBio 6(5):e01491–15
Glaser CA, Honarmand S, Anderson LJ et al (2006) Beyond viruses: clinical profiles and etiologies associated with encephalitis. Clin Infect Dis 43:1565–1577
Article PubMed CAS Google Scholar
Granerod J, Ambrose HE, Davies NW et al (2010) Causes of encephalitis and differences in their clinical presentations in England: a multicentre, population-based prospective study. Lancet Infect Dis 10:835–844
Gu W, Miller S, Chiu CY (2019) Clinical metagenomic next-generation sequencing for pathogen detection. Annu Rev Pathol 14:319–338. https://doi.org/10.1146/annurev-pathmechdis-012418-012751
Article PubMed CAS Google Scholar
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359. Published 2012 Mar 4. https://doi.org/10.1038/nmeth.1923
Laurence M, Hatzis C, Brash DE (2014) Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes. PLoS One 9(5):e97876. https://doi.org/10.1371/journal.pone.0097876
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17(1):10–12. https://doi.org/10.14806/ej.17.1.200
Miller S, Naccache SN, Samayoa E et al (2019) Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid. Genome Res 29(5):831–842. https://doi.org/10.1101/gr.238170.118
Article PubMed PubMed Central CAS Google Scholar
Naccache SN, Federman S, Veeraraghavan N et al (2014) A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res 24(7):1180–1192. https://doi.org/10.1101/gr.171934.113
Article PubMed PubMed Central CAS Google Scholar
Quail MA, Swerdlow H, Turner DJ (2009) Improved protocols for the Illumina genome analyzer sequencing system. Curr Protoc Hum Genet 18. https://doi.org/10.1002/0471142905.hg1802s62
Ramachandran PS, Wilson MR (2020) Metagenomics for neurological infections — expanding our imagination. Nat Rev Neurol 16:547–556. https://doi.org/10.1038/s41582-020-0374-y
Article PubMed PubMed Central Google Scholar
Salter SJ, Cox MJ, Turek EM et al (2014) Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 12:87. Published 2014 Nov 12. https://doi.org/10.1186/s12915-014-0087-z
Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27(6):863–864. https://doi.org/10.1093/bioinformatics/btr026
Article PubMed PubMed Central CAS Google Scholar
Sejvar JJ, Kohl KS, Bilynsky R et al (2007) Encephalitis, myelitis, and acute disseminated encephalomyelitis (ADEM): case definitions and guidelines for collection, analysis, and presentation of immunization safety data. Vaccine 25:5771–92
Strong MJ, Xu G, Morici L et al (2014) Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples. PLoS Pathog 10(11):e1004437. Published 2014 Nov 20. https://doi.org/10.1371/journal.ppat.1004437
Wilson MR, O’Donovan BD, Gelfand JM et al (2018) Chronic meningitis investigated via metagenomic next-generation sequencing. JAMA Neurol 75:947–955
Wilson MR, Sample HA, Zorn KC et al (2019) Clinical metagenomic sequencing for diagnosis of meningitis and encephalitis. N Engl J Med 380:2327–2340
Article PubMed PubMed Central CAS Google Scholar
Zinter MS, Mayday MY, Ryckman KK et al (2019) Towards precision quantification of contamination in metagenomic sequencing experiments. Microbiome 7:62. https://doi.org/10.1186/s40168-019-0678-6
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