Dunne WM, Westblade LF, Ford B (2012) Next-
generation and whole-genome sequencing in the diag-
nostic clinical microbiology laboratory. Eur J Clin
Microbiol Infect Dis 31(8):1719–1726
Feng H, Shuda M, Chang Y, Moore PS (2008) Clonal
integration of a polyomavirus in human Merkel cell
carcinoma. Science 319(5866):1096–1100
Frey KG, Herrera-Galeano JE, Redden CL, Luu TV,
Servetas SL, Mateczun AJ, Mokashi VP, Bishop-
Lilly KA (2014) Comparison of three next-generation
sequencing platforms for metagenomic sequencing
and identification of pathogens in blood. BMC Geno-
mics 15:96
Glaser CA, Gilliam S, Schnurr D, Forghani B,
Honarmand S, Khetsuriani N, Fischer M, Cossen
CK, Anderson LJ, California Encephalitis (2003) In
search of encephalitis etiologies: diagnostic
challenges in the California Encephalitis Project,
1998–2000. Clin Infect Dis 36(6):731–742
Glaser CA, Honarmand S, Anderson LJ, Schnurr DP,
Forghani B, Cossen CK, Schuster FL, Christie LJ,
Tureen JH (2006) Beyond viruses: clinical profiles
and etiologies associated with encephalitis. Clin Infect
Dis 43(12):1565–1577
Granerod J, Crowcroft NS (2007) The epidemiology of
acute encephalitis. Neuropsychol Rehabil 17
(4–5):406–428
Granerod J, Cunningham R, Zuckerman M, Mutton K,
Davies NW, Walsh AL, Ward KN, Hilton DA,
Ambrose HE, Clewley JP, Morgan D, Lunn MP,
Solomon T, Brown DW, Crowcroft NS (2010a) Cau-
sality in acute encephalitis: defining aetiologies.
Epidemiol Infect 138(6):783–800
Granerod J, Tam CC, Crowcroft NS, Davies NW,
Borchert M, Thomas SL (2010b) Challenge of the
unknown. A systematic review of acute encephalitis
in non-outbreak situations. Neurology 75
(10):924–932
Kircher M, Sawyer S, Meyer M (2012) Double indexing
overcomes inaccuracies in multiplex sequencing on
the Illumina platform. Nucleic Acids Res 40(1):e3
Kurn N, Chen P, Heath JD, Kopf-Sill A, Stephens KM,
Wang S (2005) Novel isothermal, linear nucleic acid
amplification systems for highly multiplexed
applications. Clin Chem 51(10):1973–1981
Laurence M, Hatzis C, Brash DE (2014) Common
contaminants in next-generation sequencing that hin-
der discovery of low-abundance microbes. PLoS One
9(5):e97876
Lecuit M, Eloit M (2014) The diagnosis of infectious
diseases by whole genome next generation sequenc-
ing: a new era is opening. Front Cell Infect Microbiol
4:25
Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B,
Johnson WE, Geman D, Baggerly K, Irizarry RA
(2010) Tackling the widespread and critical impact
of batch effects in high-throughput data. Nat Rev
Genet 11(10):733–739
Lusk RW (2014) Diverse and widespread contamination
evident in the unmapped depths of high throughput
sequencing data. PLoS One 9(10):e110808
Malboeuf CM, Yang X, Charlebois P, Qu J, Berlin AM,
Casali M, Pesko KN, Boutwell CL, DeVincenzo JP,
Ebel GD, Allen TM, Zody MC, Henn MR, Levin JZ
(2013) Complete viral RNA genome sequencing of
ultra-low copy samples by sequence-independent
amplification. Nucleic Acids Res 41(1):e13
Miller RR, Montoya V, Gardy JL, Patrick DM, Tang P
(2013) Metagenomics for pathogen detection in public
health. Genome Med 5(9):81
Miyamoto M, Motooka D, Gotoh K, Imai T, Yoshitake K,
Goto N, Iida T, Yasunaga T, Horii T, Arakawa K,
Kasahara M, Nakamura S (2014) Performance com-
parison of second- and third-generation sequencers
using a bacterial genome with two chromosomes.
BMC Genomics 15:699
Naccache SN, Federman S, Veeraraghavan N,
Zaharia M, Lee D, Samayoa E, Bouquet J, Greninger
AL, Luk KC, Enge B, Wadford DA, Messenger SL,
Genrich GL, Pellegrino K, Grard G, Leroy E,
Schneider BS, Fair JN, Martinez MA, Isa P, Crump
JA, DeRisi JL, Sittler T, Hackett J, Miller S, Chiu CY
(2014) A cloud-compatible bioinformatics pipeline
for ultrarapid pathogen identification from next-
generation sequencing of clinical samples. Genome
Res 24(7):1180–1192
Nakamura S, Yang CS, Sakon N, Ueda M, Tougan T,
Yamashita A, Goto N, Takahashi K, Yasunaga T,
Ikuta K, Mizutani T, Okamoto Y, Tagami M,
Morita R, Maeda N, Kawai J, Hayashizaki Y,
Nagai Y, Horii T, Iida T, Nakaya T (2009) Direct
metagenomic detection of viral pathogens in nasal
and fecal specimens using an unbiased high-
throughput sequencing approach. PLoS One 4(1),
e4219
Newsome T, Li BJ, Zou N, Lo SC (2004) Presence of
bacterial phage-like DNA sequences in commercial
Taq DNA polymerase reagents. J Clin Microbiol 42
(5):2264–2267
Palacios G, Druce J, Du L, Tran T, Birch C, Briese T,
Conlan S, Quan PL, Hui J, Marshall J, Simons JF,
Egholm M, Paddock CD, Shieh WJ, Goldsmith CS,
Zaki SR, Catton M, Lipkin WI (2008) A new arenavi-
rus in a cluster of fatal transplant-associated diseases.
N Engl J Med 358(10):991–998
Paradowska-Stankiewicz I, Piotrowska A (2014) Menin-
gitis and encephalitis in Poland in 2012. Przegl
Epidemiol 68(2):21–218, 333–216
Perlejewski K, Popiel M, Laskus T, Nakamura S,
Motooka D, Stokowy T, Lipowski D, Pollak A,
Lechowicz U, Caraballo Cortes K, Stepien A,
Radkowski M, Bukowska-Osko I (2015) Next-
generation sequencing (NGS) in the identification of
encephalitis-causing viruses: unexpected detection of
human herpesvirus 1 while searching for RNA
pathogens. J Virol Methods 226:1–6Sensitivity of Next-Generation Sequencing Metagenomic Analysis for Detection... 61