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Volumn 10, Issue 11, 2014, Pages

Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples

Author keywords

[No Author keywords available]

Indexed keywords

ACINETOBACTER; ARTICLE; BACTERIAL GENETICS; BACTERIUM ISOLATION; DNA SEQUENCE; ENTEROBACTERIACEAE; FUSOBACTERIUM; GENE AND NUCLEIC ACID PARAMETERS; GENE EXPRESSION; GENETIC ANALYSIS; GENOME ANALYSIS; HUMAN; MICROBIAL CONTAMINATION; NEXT GENERATION SEQUENCING; NONHUMAN; PARACOCCUS DENITRIFICANS; PATHOGENESIS; PROPIONIBACTERIUM ACNES; PSEUDOMONAS; RNA SEQUENCE; TRANSCRIPTOMICS; GENETICS; HIGH THROUGHPUT SEQUENCING; INFECTION; MEDICAL DEVICE CONTAMINATION; NUCLEIC ACID DATABASE;

EID: 84912076762     PISSN: 15537366     EISSN: 15537374     Source Type: Journal    
DOI: 10.1371/journal.ppat.1004437     Document Type: Article
Times cited : (132)

References (33)
  • 1
    • 39749113080 scopus 로고    scopus 로고
    • Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma
    • Feng H, Shuda M, Chang Y, Moore PS, (2008) Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma. Science 319: 1096–1100.
    • (2008) Science , vol.319 , pp. 1096-1100
    • Feng, H.1    Shuda, M.2    Chang, Y.3    Moore, P.S.4
  • 2
    • 84856534859 scopus 로고    scopus 로고
    • Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma
    • Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, et al. (2012) Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res 22: 299–306.
    • (2012) Genome Res , vol.22 , pp. 299-306
    • Castellarin, M.1    Warren, R.L.2    Freeman, J.D.3    Dreolini, L.4    Krzywinski, M.5
  • 3
    • 84863022950 scopus 로고    scopus 로고
    • Genomic analysis identifies association of Fusobacterium with colorectal carcinoma
    • Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, et al. (2012) Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res 22: 292–298.
    • (2012) Genome Res , vol.22 , pp. 292-298
    • Kostic, A.D.1    Gevers, D.2    Pedamallu, C.S.3    Michaud, M.4    Duke, F.5
  • 4
    • 84863248011 scopus 로고    scopus 로고
    • Detection of Murine Leukemia Virus in the Epstein-Barr Virus-Positive Human B-Cell Line JY, Using a Computational RNA-Seq-Based Exogenous Agent Detection Pipeline, PARSES
    • Lin Z, Puetter A, Coco J, Xu G, Strong MJ, et al. (2012) Detection of Murine Leukemia Virus in the Epstein-Barr Virus-Positive Human B-Cell Line JY, Using a Computational RNA-Seq-Based Exogenous Agent Detection Pipeline, PARSES. J Virol 86: 2970–2977.
    • (2012) J Virol , vol.86 , pp. 2970-2977
    • Lin, Z.1    Puetter, A.2    Coco, J.3    Xu, G.4    Strong, M.J.5
  • 5
    • 84887193368 scopus 로고    scopus 로고
    • Epstein-Barr Virus and Human Herpesvirus 6 Detection in a non-Hodgkin's Diffuse Large B-Cell Lymphoma Cohort using RNA-Seq
    • Strong MJ, O'Grady T, Lin Z, Xu G, Baddoo M, et al. (2013) Epstein-Barr Virus and Human Herpesvirus 6 Detection in a non-Hodgkin's Diffuse Large B-Cell Lymphoma Cohort using RNA-Seq. J Virol 87: 13059–62.
    • (2013) J Virol , vol.87 , pp. 13059-13062
    • Strong, M.J.1    O'Grady, T.2    Lin, Z.3    Xu, G.4    Baddoo, M.5
  • 6
    • 84878510017 scopus 로고    scopus 로고
    • Differences in Gastric Carcinoma Microenvironment Stratify According to EBV Infection Intensity: Implications for Possible Immune Adjuvant Therapy
    • Strong MJ, Xu G, Coco J, Baribault C, Vinay DS, et al. (2013) Differences in Gastric Carcinoma Microenvironment Stratify According to EBV Infection Intensity: Implications for Possible Immune Adjuvant Therapy. PLoS Pathog 9: e1003341.
    • (2013) PLoS Pathog , vol.9 , pp. e1003341
    • Strong, M.J.1    Xu, G.2    Coco, J.3    Baribault, C.4    Vinay, D.S.5
  • 7
    • 84881260064 scopus 로고    scopus 로고
    • Sequence-Based Discovery of Bradyrhizobium enterica in Cord Colitis Syndrome
    • Bhatt AS, Freeman SS, Herrera AF, Pedamallu CS, Gevers D, et al. (2013) Sequence-Based Discovery of Bradyrhizobium enterica in Cord Colitis Syndrome. N Engl J Med 369: 517–528.
    • (2013) N Engl J Med , vol.369 , pp. 517-528
    • Bhatt, A.S.1    Freeman, S.S.2    Herrera, A.F.3    Pedamallu, C.S.4    Gevers, D.5
  • 8
    • 84875921666 scopus 로고    scopus 로고
    • A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of shiga-toxigenic escherichia coli o104:h4
    • Loman NJ, Constantinidou C, Christner M, et al. (2013) A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of shiga-toxigenic escherichia coli o104:h4. JAMA 309: 1502–1510.
    • (2013) JAMA , vol.309 , pp. 1502-1510
    • Loman, N.J.1    Constantinidou, C.2    Christner, M.3
  • 9
    • 84891529869 scopus 로고    scopus 로고
    • Rapid whole genome sequencing for the detection and characterization of microorganisms directly from clinical samples
    • Hasman H, Saputra D, Sicheritz-Ponten T, Lund O, Svendsen CA, et al. (2013) Rapid whole genome sequencing for the detection and characterization of microorganisms directly from clinical samples. J Clin Microbiol 52: 139–146.
    • (2013) J Clin Microbiol , vol.52 , pp. 139-146
    • Hasman, H.1    Saputra, D.2    Sicheritz-Ponten, T.3    Lund, O.4    Svendsen, C.A.5
  • 10
    • 84902602767 scopus 로고    scopus 로고
    • Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing
    • Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, et al. (2014) Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing. N Engl J Med 370: 2408–2417.
    • (2014) N Engl J Med , vol.370 , pp. 2408-2417
    • Wilson, M.R.1    Naccache, S.N.2    Samayoa, E.3    Biagtan, M.4    Bashir, H.5
  • 11
    • 84890558766 scopus 로고    scopus 로고
    • Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions
    • Fricke WF, Rasko DA, (2014) Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions. Nat Rev Genet 15: 49–55.
    • (2014) Nat Rev Genet , vol.15 , pp. 49-55
    • Fricke, W.F.1    Rasko, D.A.2
  • 12
    • 84866148001 scopus 로고    scopus 로고
    • Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology
    • Köser CU, Ellington MJ, Cartwright EJP, Gillespie SH, Brown NM, et al. (2012) Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology. PLoS Pathog 8: e1002824.
    • (2012) PLoS Pathog , vol.8 , pp. e1002824
    • Köser, C.U.1    Ellington, M.J.2    Cartwright, E.J.P.3    Gillespie, S.H.4    Brown, N.M.5
  • 13
    • 84887433583 scopus 로고    scopus 로고
    • Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories
    • t Hoen PAC, Friedlander MR, Almlof J, Sammeth M, Pulyakhina I, et al. (2013) Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat Biotech 31: 1015–1022.
    • (2013) Nat Biotech , vol.31 , pp. 1015-1022
    • t Hoen, P.A.C.1    Friedlander, M.R.2    Almlof, J.3    Sammeth, M.4    Pulyakhina, I.5
  • 14
    • 84877028141 scopus 로고    scopus 로고
    • Comprehensive molecular portraits of human breast tumours
    • Network TCGA, (2012) Comprehensive molecular portraits of human breast tumours. Nature 490: 61–70.
    • (2012) Nature , vol.490 , pp. 61-70
    • Network, T.C.G.A.1
  • 15
    • 84866894408 scopus 로고    scopus 로고
    • Comprehensive genomic characterization of squamous cell lung cancers
    • Network TCGAR, (2012) Comprehensive genomic characterization of squamous cell lung cancers. Nature 489: 519–525.
    • (2012) Nature , vol.489 , pp. 519-525
    • Network, T.C.G.A.R.1
  • 16
    • 84863922124 scopus 로고    scopus 로고
    • Comprehensive molecular characterization of human colon and rectal cancer
    • Network TCGA, (2012) Comprehensive molecular characterization of human colon and rectal cancer. Nature 487: 330–337.
    • (2012) Nature , vol.487 , pp. 330-337
    • Network, T.C.G.A.1
  • 17
    • 84896090972 scopus 로고    scopus 로고
    • RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets
    • Xu G, Strong MJ, Lacey MR, Baribault C, Flemington EK, et al. (2014) RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets. PLoS ONE 9: e89445.
    • (2014) PLoS ONE , vol.9 , pp. e89445
    • Xu, G.1    Strong, M.J.2    Lacey, M.R.3    Baribault, C.4    Flemington, E.K.5
  • 18
    • 60849117520 scopus 로고    scopus 로고
    • Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
    • Nix D, Courdy S, Boucher K, (2008) Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics 9: 523.
    • (2008) BMC Bioinformatics , vol.9 , pp. 523
    • Nix, D.1    Courdy, S.2    Boucher, K.3
  • 20
    • 84859436530 scopus 로고    scopus 로고
    • NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
    • Pruitt KD, Tatusova T, Brown GR, Maglott DR, (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 40: D130–D135.
    • (2012) Nucleic Acids Res , vol.40 , pp. D130-D135
    • Pruitt, K.D.1    Tatusova, T.2    Brown, G.R.3    Maglott, D.R.4
  • 22
    • 0016692153 scopus 로고
    • Polyadenylic acid sequences in E. coli messenger RNA
    • Nakazato H, Venkatesan S, Edmonds M, (1975) Polyadenylic acid sequences in E. coli messenger RNA. Nature 256: 144–146.
    • (1975) Nature , vol.256 , pp. 144-146
    • Nakazato, H.1    Venkatesan, S.2    Edmonds, M.3
  • 23
    • 0016752529 scopus 로고
    • Presence of polyriboadenylate sequences in pulse-labeled RNA of Escherichia coli
    • Srinivasan P, Ramanarayanan M, Rabbani E, (1975) Presence of polyriboadenylate sequences in pulse-labeled RNA of Escherichia coli. Proc Natl Acad Sci U S A 72: 2910–2914.
    • (1975) Proc Natl Acad Sci U S A , vol.72 , pp. 2910-2914
    • Srinivasan, P.1    Ramanarayanan, M.2    Rabbani, E.3
  • 24
    • 0016749578 scopus 로고
    • Poly(adenylic acid) sequences in the RNA of Caulobacter crescenus
    • Ohta N, Sanders M, Newton A, (1975) Poly(adenylic acid) sequences in the RNA of Caulobacter crescenus. Proc Natl Acad Sci U S A 72: 2343–2346.
    • (1975) Proc Natl Acad Sci U S A , vol.72 , pp. 2343-2346
    • Ohta, N.1    Sanders, M.2    Newton, A.3
  • 25
    • 0029854299 scopus 로고    scopus 로고
    • Polyadenylation of mRNA in bacteria
    • Sarkar N, (1996) Polyadenylation of mRNA in bacteria. Microbiology 142: 3125–3133.
    • (1996) Microbiology , vol.142 , pp. 3125-3133
    • Sarkar, N.1
  • 26
    • 84885645853 scopus 로고    scopus 로고
    • Transcriptome and genome sequencing uncovers functional variation in humans
    • Lappalainen T, Sammeth M, Friedlander MR, t Hoen PAC, Monlong J, et al. (2013) Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501: 506–511.
    • (2013) Nature , vol.501 , pp. 506-511
    • Lappalainen, T.1    Sammeth, M.2    Friedlander, M.R.3    t Hoen, P.A.C.4    Monlong, J.5
  • 27
    • 84901337103 scopus 로고    scopus 로고
    • Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes
    • Laurence M, Hatzis C, Brash DE, (2014) Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes. PLoS ONE 9: e97876.
    • (2014) PLoS ONE , vol.9 , pp. e97876
    • Laurence, M.1    Hatzis, C.2    Brash, D.E.3
  • 28
    • 84874420514 scopus 로고    scopus 로고
    • A Microbial Metagenome (Leucobacter sp.) in Caenorhabditis Whole Genome Sequences
    • Percudani R, (2013) A Microbial Metagenome (Leucobacter sp.) in Caenorhabditis Whole Genome Sequences. Bioinform Biol Insights 7: 55–72.
    • (2013) Bioinform Biol Insights , vol.7 , pp. 55-72
    • Percudani, R.1
  • 29
    • 84879290452 scopus 로고    scopus 로고
    • Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing
    • Xu B, Zhi N, Hu G, Wan Z, Zheng X, et al. (2013) Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing. Proc Natl Acad Sci U S A 110: 10264–10269.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 10264-10269
    • Xu, B.1    Zhi, N.2    Hu, G.3    Wan, Z.4    Zheng, X.5
  • 30
    • 84891681779 scopus 로고    scopus 로고
    • Novel Hybrid Parvovirus-Like Virus, NIH-CQV/PHV, Contaminants in Silica Column-Based Nucleic Acid Extraction Kits
    • Smuts H, Kew M, Khan A, Korsman S, (2014) Novel Hybrid Parvovirus-Like Virus, NIH-CQV/PHV, Contaminants in Silica Column-Based Nucleic Acid Extraction Kits. J Virol 88: 1398.
    • (2014) J Virol , vol.88 , pp. 1398
    • Smuts, H.1    Kew, M.2    Khan, A.3    Korsman, S.4
  • 31
    • 84886301115 scopus 로고    scopus 로고
    • The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns
    • Naccache SN, Greninger AL, Lee D, Coffey LL, Phan T, et al. (2013) The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns. J Virol 87: 11966–11977.
    • (2013) J Virol , vol.87 , pp. 11966-11977
    • Naccache, S.N.1    Greninger, A.L.2    Lee, D.3    Coffey, L.L.4    Phan, T.5
  • 32
    • 84896508411 scopus 로고    scopus 로고
    • Concerns over the origin of NIH-CQV, a novel virus discovered in Chinese patients with seronegative hepatitis
    • Naccache SN, Hackett J, Delwart EL, Chiu CY, (2014) Concerns over the origin of NIH-CQV, a novel virus discovered in Chinese patients with seronegative hepatitis. Proc Natl Acad Sci U S A 111: E976.
    • (2014) Proc Natl Acad Sci U S A , vol.111 , pp. E976
    • Naccache, S.N.1    Hackett, J.2    Delwart, E.L.3    Chiu, C.Y.4
  • 33
    • 84896500578 scopus 로고    scopus 로고
    • Reply to Naccache et al: Viral sequences of NIH-CQV virus, a contamination of DNA extraction method
    • Zhi N, Hu G, Wong S, Zhao K, Mao Q, et al. (2014) Reply to Naccache et al: Viral sequences of NIH-CQV virus, a contamination of DNA extraction method. Proc Natl Acad Sci U S A 111: E977.
    • (2014) Proc Natl Acad Sci U S A , vol.111 , pp. E977
    • Zhi, N.1    Hu, G.2    Wong, S.3    Zhao, K.4    Mao, Q.5


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