Sensitivity of next-generation sequencing metagenomic analysis for detection of RNA and DNA viruses in cerebrospinal fluid: The confounding effect of background contamination

Advances in Experimental Medicine and Biology

Volumn 944, Issue , 2017, Pages 53-62

  Bukowska Ośko, Iwona ^a   Perlejewski, Karol ^a   Nakamura, Shota ^b   Motooka, Daisuke ^b   Stokowy, Tomasz ^c   Kosińska, Joanna ^a   Popiel, Marta ^a   Płoski, Rafał ^a   Horban, Andrzej ^d   Lipowski, Dariusz ^d   Caraballo Cortés, Kamila ^a   Pawełczyk, Agnieszka ^a   Demkow, Urszula ^a   Stępień, Adam ^e   Radkowski, Marek ^a   Laskus, Tomasz ^a  

^a MEDICAL UNIVERSITY OF WARSAW   (Poland)

^b OSAKA UNIVERSITY   (Japan)

^c UNIVERSITY OF BERGEN   (Norway)

^d SP ZOZ Wojewodzki Szpital Zakazny Centrum Diagnostyki i Terapii AIDS Warszawa   (Poland)

^e MILITARY INSTITUTE OF MEDICINE   (Poland)

Author keywords

Bacteria; Cerebrospinal fluid; DNA; Encephalitis; Metagenomics analysis; Next generation sequencing; Pathogens; Viruses

Indexed keywords

ACINETOBACTER; ADULT; ANALYZER; ARTICLE; BACTERIUM CONTAMINATION; CEREBROSPINAL FLUID EXAMINATION; CONTROLLED STUDY; CORYNEBACTERIUM; DIAGNOSTIC EQUIPMENT; DIAGNOSTIC VALUE; DNA DETERMINATION; DNA SEQUENCE; DNA VIRUS; FEMALE; GENE AMPLIFICATION; HERPES SIMPLEX VIRUS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; ISOTHERMAL RNA AMPLIFICATION; METAGENOMICS; NEXT GENERATION SEQUENCING; NONHUMAN; PLANT VIRUS; PRIORITY JOURNAL; PSYCHROBACTER; RNA VIRUS; SENSITIVITY ANALYSIS; VIRUS DETECTION; WATER SAMPLING;

EID: 84995484909     PISSN: 00652598     EISSN: 22148019     Source Type: Book Series    
DOI: 10.1007/5584_2016_42     Document Type: Article

References (43)

1. Barzon L, Lavezzo E, Costanzi G, Franchin E, Toppo S, Palu G (2013) Next-generation sequencing technologies in diagnostic virology. J Clin Virol 58 (2):346-350
2. Capobianchi MR, Giombini E, Rozera G (2013) Next-generation sequencing technology in clinical virology. Clin Microbiol Infect 19(1):15-22
3. Chaudhuri A, Kennedy PG (2002) Diagnosis and treatment of viral encephalitis. Postgrad Med J 78 (924):575-583
4. Cheval J, Sauvage V, Frangeul L, Dacheux L, Guigon G, Dumey N, Pariente K, Rousseaux C, Dorange F, Berthet N, Brisse S, Moszer I, Bourhy H, Manuguerra CJ, Lecuit M, Burguiere A, Caro V, Eloit M (2011) Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples. J Clin Microbiol 49(9):3268-3275
5. Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanatephenol-chloroform extraction. Anal Biochem 162 (1):156-159
6. Clement-Ziza M, Gentien D, Lyonnet S, Thiery JP, Besmond C, Decraene C (2009) Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling. BMC Genomics 10:246
7. Dickins B, Rebolledo-Jaramillo B, Su MS, Paul IM, Blankenberg D, Stoler N, Makova KD, Nekrutenko A (2014) Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach. Biotechniques 56(3):134-136, 138-141
8. Dunne WM, Westblade LF, Ford B (2012) Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur J Clin Microbiol Infect Dis 31(8):1719-1726
9. Feng H, Shuda M, Chang Y, Moore PS (2008) Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 319(5866):1096-1100
10. 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 Genomics 15:96
11. 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
12. 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
13. Granerod J, Crowcroft NS (2007) The epidemiology of acute encephalitis. Neuropsychol Rehabil 17 (4-5):406-428
14. 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) Causality in acute encephalitis: defining aetiologies. Epidemiol Infect 138(6):783-800
15. 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
16. Kircher M, Sawyer S, Meyer M (2012) Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res 40(1):e3
17. 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
18. 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
19. Lecuit M, Eloit M (2014) The diagnosis of infectious diseases by whole genome next generation sequencing: a new era is opening. Front Cell Infect Microbiol 4:25
20. 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
21. Lusk RW (2014) Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data. PLoS One 9(10):e110808
22. 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
23. Miller RR, Montoya V, Gardy JL, Patrick DM, Tang P (2013) Metagenomics for pathogen detection in public health. Genome Med 5(9):81
24. 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 comparison of secondand third-generation sequencers using a bacterial genome with two chromosomes. BMC Genomics 15:699
25. 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 nextgeneration sequencing of clinical samples. Genome Res 24(7):1180-1192
26. 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
27. 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
28. 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 arenavirus in a cluster of fatal transplant-associated diseases. N Engl J Med 358(10):991-998
29. Paradowska-Stankiewicz I, Piotrowska A (2014) Meningitis and encephalitis in Poland in 2012. Przegl Epidemiol 68(2):21-218, 333-216
30. 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) Nextgeneration sequencing (NGS) in the identification of encephalitis-causing viruses: unexpected detection of human herpesvirus 1 while searching for RNA pathogens. J Virol Methods 226:1-6
31. Quinones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA (2014) Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 61(1):9-19
32. Rasool V, Rasool S, Mushtaq S (2014) Viral encephalitis and its management through advanced molecular diagnostic methods: a review. Clin Pediatr (Phila) 53 (2):118-120
33. Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW (2014) Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 12:87
34. Shen H, Rogelj S, Kieft TL (2006) Sensitive, real-time PCR detects low-levels of contamination by Legionella pneumophila in commercial reagents. Mol Cell Probes 20(3-4):147-153
35. Silva MT (2013) Viral encephalitis. Arq Neuropsiquiatr 71(9B):703-709
36. Solomon T, Hart IJ, Beeching NJ (2007) Viral encephalitis: a clinician’s guide. Pract Neurol 7(5):288-305
37. Steiner I, Budka H, Chaudhuri A, Koskiniemi M, Sainio K, Salonen O, Kennedy PG (2005) Viral encephalitis: a review of diagnostic methods and guidelines for management. Eur J Neurol 12 (5):331-343
38. Strong MJ, Xu G, Morici L, Splinter Bon-Durant S, Baddoo M, Lin Z, Fewell C, Taylor CM, Flemington EK (2014) Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples. PLoS Pathog 10(11): e1004437
39. Tan le V, van Doorn HR, Nghia HD, Chau TT, le TP T, de Vries M, Canuti M, Deijs M, Jebbink MF, Baker S, Bryant JE, Tham NT NTBK, Boni MF, Loi TQ, Phuong le T, Verhoeven JT, Crusat M, Jeeninga RE, Schultsz C, Chau NV, Hien TT, van der Hoek L, Farrar J, de Jong MD (2013) Identification of a new cyclovirus in cerebrospinal fluid of patients with acute central nervous system infections. MBio 4(3):e00231-e00313
40. Towner JS, Sealy TK, Khristova ML, Albarino CG, Conlan S, Reeder SA, Quan PL, Lipkin WI, Downing R, Tappero JW, Okware S, Lutwama J, Bakamutumaho B, Kayiwa J, Comer JA, Rollin PE, Ksiazek TG, Nichol ST (2008) Newly discovered ebola virus associated with hemorrhagic fever outbreak in Uganda. PLoS Pathog 4(11):e1000212
41. Virgin HW, Todd JA (2011) Metagenomics and personalized medicine. Cell 147(1):44-56
42. Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, Salamat SM, Somasekar S, Federman S, Miller S, Sokolic R, Garabedian E, Candotti F, Buckley RH, Reed KD, Meyer TL, Seroogy CM, Galloway R, Henderson SL, Gern JE, DeRisi JL, Chiu CY (2014) Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med 370(25):2408-2417
43. Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, Harris E, DeRisi JL (2012) Virus identification in unknown tropical febrile illness cases using deep sequencing. PLoS Negl Trop Dis 6(2): e1485