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Volumn 8, Issue 1, 2018, Pages

A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; HUMAN; LIBRARY; METAGENOMICS; MICROORGANISM DETECTION; WORKFLOW; ANIMAL; BACTERIUM; CLASSIFICATION; FOOD ANALYSIS; FOOD CONTROL; GROWTH, DEVELOPMENT AND AGING; PROCEDURES;

EID: 85052713952     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/s41598-018-31496-1     Document Type: Article
Times cited : (97)

References (53)
  • 3
    • 84907867765 scopus 로고    scopus 로고
    • Emergence of Zaire Ebola virus disease in Guinea
    • Baize, S. et al. Emergence of Zaire Ebola virus disease in Guinea. N. Engl. J. Med. 371, 1418–1425 (2014)
    • (2014) N. Engl. J. Med. , vol.371 , pp. 1418-1425
    • Baize, S.1
  • 4
    • 84936768371 scopus 로고    scopus 로고
    • A Variegated squirrel bornavirus associated with fatal human encephalitis
    • PID: 26154788
    • Hoffmann, B. et al. A Variegated squirrel bornavirus associated with fatal human encephalitis. N. Engl. J. Med. 373, 154–162 (2015)
    • (2015) N. Engl. J. Med. , vol.373 , pp. 154-162
    • Hoffmann, B.1
  • 5
    • 84857594210 scopus 로고    scopus 로고
    • Novel orthobunyavirus in Cattle, Europe, 2011
    • PID: 22376991
    • Hoffmann, B. et al. Novel orthobunyavirus in Cattle, Europe, 2011. Emerg. Infect. Dis. 18, 469–472 (2012)
    • (2012) Emerg. Infect. Dis. , vol.18 , pp. 469-472
    • Hoffmann, B.1
  • 6
    • 80955168000 scopus 로고    scopus 로고
    • Epidemic profile of Shiga-toxin-producing Escherichia coli O104:H4 outbreak in Germany
    • Frank, C. et al. Epidemic profile of Shiga-toxin-producing Escherichia coli O104:H4 outbreak in Germany. N. Engl. J. Med. 365, 1771–1780 (2011)
    • (2011) N. Engl. J. Med. , vol.365 , pp. 1771-1780
    • Frank, C.1
  • 7
    • 84952984120 scopus 로고    scopus 로고
    • Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing
    • PID: 26620704
    • Greninger, A. L. et al. Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing. Genome Med. 7, 113 (2015)
    • (2015) Genome Med. , vol.7
    • Greninger, A.L.1
  • 8
    • 84976511497 scopus 로고    scopus 로고
    • Metagenomic approaches to identifying infectious agents
    • PID: 27217170
    • Höper, D., Mettenleiter, T. C. & Beer, M. Metagenomic approaches to identifying infectious agents. Rev. Sci. Tech. 35, 83–93 (2016)
    • (2016) Rev. Sci. Tech. , vol.35 , pp. 83-93
    • Höper, D.1    Mettenleiter, T.C.2    Beer, M.3
  • 9
    • 85041748407 scopus 로고    scopus 로고
    • Surveillance and foodborne pathogens: Towards diagnostic metagenomics of fecal samples
    • Andersen, S. C. & Hoorfar, J. Surveillance and foodborne pathogens: Towards diagnostic metagenomics of fecal samples. Genes 9, 14 (2018)
    • (2018) Genes , vol.9 , pp. 14
    • Andersen, S.C.1    Hoorfar, J.2
  • 10
    • 84973326052 scopus 로고    scopus 로고
    • Pathogen diagnostics for the masses
    • Koch, L. Pathogen diagnostics for the masses. Nat. Rev. Gen, 10.1038/nrg.2016.76 (2016)
    • (2016) Nat. Rev. Gen
    • Koch, L.1
  • 11
    • 85020233774 scopus 로고    scopus 로고
    • Validation of metagenomics next-generation sequencing tests for universal pathogen detection
    • PID: 28169558
    • Schlaberg, R., Chiu, C. Y., Miller, S., Procop, G. W. & Weinstock, G. Validation of metagenomics next-generation sequencing tests for universal pathogen detection. Arch. Pathol. Lab. Med. 141, 776–786 (2017)
    • (2017) Arch. Pathol. Lab. Med. , vol.141 , pp. 776-786
    • Schlaberg, R.1    Chiu, C.Y.2    Miller, S.3    Procop, G.W.4    Weinstock, G.5
  • 12
    • 85038405757 scopus 로고    scopus 로고
    • Towards a genomic-informed, real-time, global pathogen surveillance system
    • Gardy, J. L. & Loman, N. J. Towards a genomic-informed, real-time, global pathogen surveillance system. Nat. Rev. Gen. 19, 9–20 (2018)
    • (2018) Nat. Rev. Gen. , vol.19 , pp. 9-20
    • Gardy, J.L.1    Loman, N.J.2
  • 13
    • 85028946715 scopus 로고    scopus 로고
    • The First “Virus Hunters” in In Loeffler’s footsteps viral genomics in the era of high-throughput sequencing
    • (eds Beer, M. & Höper, D.)
    • Mettenleiter, T. C. The First “Virus Hunters” in In Loeffler’s footsteps viral genomics in the era of high-throughput sequencing. (eds Beer, M. & Höper, D.) Adv. Viral Res. Elsevier 99, 1–16 (2017)
    • (2017) Adv. Viral Res. Elsevier , vol.99 , pp. 1-16
    • Mettenleiter, T.C.1
  • 14
    • 79955714221 scopus 로고    scopus 로고
    • A Comprehensive Deep Sequencing Strategy for Full-Length Genomes of Influenza A
    • PID: 21559493
    • Höper, D., Hoffmann, B. & Beer, M. A Comprehensive deep sequencing strategy for full-length genomes of Influenza A. PLoS ONE 6, e19075 (2011)
    • (2011) PLoS ONE , vol.6
    • Höper, D.1    Hoffmann, B.2    Beer, M.3
  • 15
    • 84922523092 scopus 로고    scopus 로고
    • Next generation multilocus sequence typing (NGMLST) and the analytical software program MLSTEZ enable efficient, cost-effective, high-throughput, multilocus sequencing typing
    • Chen, Y. et al. Next generation multilocus sequence typing (NGMLST) and the analytical software program MLSTEZ enable efficient, cost-effective, high-throughput, multilocus sequencing typing. Fungal Gen. Biol. 75, 64–71 (2015)
    • (2015) Fungal Gen. Biol. , vol.75 , pp. 64-71
    • Chen, Y.1
  • 16
    • 84947718692 scopus 로고    scopus 로고
    • Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d’Ivoire: A proof-of-concept study
    • PID: 26391184
    • Schneeberger, P. H. H. et al. Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d’Ivoire: A proof-of-concept study. Infect. Genet. Evol. 40, 389–397 (2016)
    • (2016) Infect. Genet. Evol. , vol.40 , pp. 389-397
    • Schneeberger, P.H.H.1
  • 17
    • 85033585402 scopus 로고    scopus 로고
    • Towards standards for human fecal sample processing in metagenomic studies
    • PID: 28967887
    • Costea, P. I. et al. Towards standards for human fecal sample processing in metagenomic studies. Nat. Biotechnol. 35, 1069–1076 (2017)
    • (2017) Nat. Biotechnol. , vol.35 , pp. 1069-1076
    • Costea, P.I.1
  • 18
    • 84983591865 scopus 로고    scopus 로고
    • Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens
    • Doan, T. et al. Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens. Genome Med. 8, 106 (2016)
    • (2016) Genome Med. , vol.8
    • Doan, T.1
  • 19
    • 84961197542 scopus 로고    scopus 로고
    • Sharing Data for Global Infectious Disease Surveillance and Outbreak Detection
    • PID: 26875619
    • Aarestrup, F. M. & Koopmans, M. G. Sharing data for global infectious disease surveillance and outbreak detection. Trends Microbiol. 24, 241–245 (2016)
    • (2016) Trends Microbiol. , vol.24 , pp. 241-245
    • Aarestrup, F.M.1    Koopmans, M.G.2
  • 20
    • 85052704597 scopus 로고    scopus 로고
    • Go COMPARE! – “one serves all” next generation sequencing framework
    • Adkin, A. et al. Go COMPARE! – “one serves all” next generation sequencing framework. Euroref. 2, 58–62 (2017)
    • (2017) Euroref. , vol.2 , pp. 58-62
    • Adkin, A.1
  • 21
    • 85013758578 scopus 로고    scopus 로고
    • A novel alphaherpesvirus associated with fatal diseases in banded Penguins
    • PID: 28036249
    • Pfaff, F. et al. A novel alphaherpesvirus associated with fatal diseases in banded Penguins. J. Gen. Virol. 98, 89–95 (2017)
    • (2017) J. Gen. Virol. , vol.98 , pp. 89-95
    • Pfaff, F.1
  • 22
    • 85013391503 scopus 로고    scopus 로고
    • A novel astrovirus associated with encephalitis and ganglionitis in domestic sheep
    • PID: 28224712
    • Pfaff, F. et al. A novel astrovirus associated with encephalitis and ganglionitis in domestic sheep. Transbound. Emerg. Dis. 64, 677–682 (2017)
    • (2017) Transbound. Emerg. Dis. , vol.64 , pp. 677-682
    • Pfaff, F.1
  • 23
    • 84960398559 scopus 로고    scopus 로고
    • Detection of a novel bovine astrovirus in a cow with encephalitis
    • PID: 26948516
    • Schlottau, K. et al. Detection of a novel bovine astrovirus in a cow with encephalitis. Transbound. Emerg. Dis. 63, 253–259 (2016)
    • (2016) Transbound. Emerg. Dis. , vol.63 , pp. 253-259
    • Schlottau, K.1
  • 24
    • 85022330245 scopus 로고    scopus 로고
    • Porcine epidemic diarrhea in Europe: In-detail analyses of disease dynamics and virus evolution
    • Hanke, D. et al. Porcine epidemic diarrhea in Europe: In-detail analyses of disease dynamics and virus evolution. Viruses 9, 177 (2017)
    • (2017) Viruses , vol.9 , pp. 177
    • Hanke, D.1
  • 25
    • 85007463519 scopus 로고    scopus 로고
    • Complete coding genome sequence of putative novel bluetongue virus serotype 27
    • PID: 25767218
    • Jenckel, M. et al. Complete coding genome sequence of putative novel bluetongue virus serotype 27. Genome Announc. 3, e00016 (2015)
    • (2015) Genome Announc. , vol.3
    • Jenckel, M.1
  • 26
    • 85044753791 scopus 로고    scopus 로고
    • Depth genome analyses of viruses from vaccine-derived rabies cases and corresponding live-attenuated oral rabies vaccines
    • Pfaff, F. et al. In-depth genome analyses of viruses from vaccine-derived rabies cases and corresponding live-attenuated oral rabies vaccines. Vaccine, 10.1016/j.vaccine.2018.01.083 (2018)
    • (2018) Vaccine
    • Pfaff, F.1
  • 27
    • 84980340084 scopus 로고    scopus 로고
    • Spatio-temporal Analysis of the Genetic Diversity of Arctic Rabies Viruses and Their Reservoir Hosts in Greenland
    • PID: 27459154
    • Hanke, D. et al. Spatio-temporal analysis of the genetic diversity of Arctic Rabies viruses and their reservoir hosts in Greenland. PLoS Negl. Trop. Dis. 10, e0004779 (2016)
    • (2016) PLoS Negl. Trop. Dis. , vol.10
    • Hanke, D.1
  • 28
    • 84928732305 scopus 로고    scopus 로고
    • RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets
    • Scheuch, M., Höper, D. & Beer, M. RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets. BMC Bioinf. 16, 69 (2015)
    • (2015) BMC Bioinf. , vol.16 , pp. 69
    • Scheuch, M.1    Höper, D.2    Beer, M.3
  • 30
    • 84927910898 scopus 로고    scopus 로고
    • Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections
    • Pallen, M. J. Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections. Parasitol. 141, 1856 (2014)
    • (2014) Parasitol. , vol.141 , pp. 1856
    • Pallen, M.J.1
  • 31
    • 33646787129 scopus 로고    scopus 로고
    • Methods of mycobacterial DNA isolation from different biological material: a review
    • Hosek, J., Svastova, P., Moravkova, M., Pavlik, I. & Bartos, M. Methods of mycobacterial DNA isolation from different biological material: a review. Vet. Medicina 51, 180 (2004)
    • (2004) Vet. Medicina , vol.51 , pp. 180
    • Hosek, J.1    Svastova, P.2    Moravkova, M.3    Pavlik, I.4    Bartos, M.5
  • 33
    • 33746846140 scopus 로고    scopus 로고
    • transcriptional profiling: part I. Platforms, experimental design and standardization
    • PID: 16824028
    • Ahmed, F. E. & Microarray, R. N. A. transcriptional profiling: part I. Platforms, experimental design and standardization. Expert Rev. Mol. Diagn. 6, 535–550 (2006)
    • (2006) Expert Rev. Mol. Diagn. , vol.6 , pp. 535-550
    • Ahmed, F.E.1    Microarray, R.N.A.2
  • 34
    • 84946919159 scopus 로고    scopus 로고
    • Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis
    • PID: 26559140
    • Conceicao-Neto, N. et al. Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis. Sci. Rep. 5, 16532 (2015)
    • (2015) Sci. Rep. , vol.5
    • Conceicao-Neto, N.1
  • 35
    • 84919623528 scopus 로고    scopus 로고
    • Protocol for metagenomic virus detection in clinical specimens
    • PID: 25532973
    • Kohl, C. et al. Protocol for metagenomic virus detection in clinical specimens. Emerg. Infect. Dis. 21, 48–57 (2015)
    • (2015) Emerg. Infect. Dis. , vol.21 , pp. 48-57
    • Kohl, C.1
  • 36
    • 84962604680 scopus 로고    scopus 로고
    • Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel
    • PID: 26818672
    • Graf, E. H. et al. Unbiased detection of respiratory viruses by use of RNA sequencing-based metagenomics: a systematic comparison to a commercial PCR panel. J. Clin. Microbiol. 54, 1000–1007 (2016)
    • (2016) J. Clin. Microbiol. , vol.54 , pp. 1000-1007
    • Graf, E.H.1
  • 37
    • 33847688114 scopus 로고    scopus 로고
    • Primer-site SNPs mask mutations
    • Quinlan, A. R. & Marth, G. T. Primer-site SNPs mask mutations. Nat. Meth. 4, 192 (2007)
    • (2007) Nat. Meth. , vol.4 , pp. 192
    • Quinlan, A.R.1    Marth, G.T.2
  • 38
    • 84893522267 scopus 로고    scopus 로고
    • Library construction for next-generation sequencing: Overviews and challenges
    • PID: 24502796
    • Head, S. R. et al. Library construction for next-generation sequencing: Overviews and challenges. BioTechniques 56, 61–77 (2014)
    • (2014) BioTechniques , vol.56 , pp. 61-77
    • Head, S.R.1
  • 39
    • 84884625714 scopus 로고    scopus 로고
    • The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing
    • PID: 24086702
    • Rosseel, T. et al. The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing. PLoS One 8, e76144 (2013)
    • (2013) PLoS One , vol.8
    • Rosseel, T.1
  • 40
    • 84931271178 scopus 로고    scopus 로고
    • Evaluation of convenient pretreatment protocols for RNA virus metagenomics in serum and tissue samples
    • Rosseel, T., Ozhelvaci, O., Freimanis, G. & Van Borm, S. Evaluation of convenient pretreatment protocols for RNA virus metagenomics in serum and tissue samples. J. Virol. Meth. 222, 72–80 (2015)
    • (2015) J. Virol. Meth. , vol.222 , pp. 72-80
    • Rosseel, T.1    Ozhelvaci, O.2    Freimanis, G.3    Van Borm, S.4
  • 41
    • 84865384089 scopus 로고    scopus 로고
    • Performance of VIDISCA-454 in feces-suspensions and serum
    • PID: 23012629
    • De Vries, M. et al. Performance of VIDISCA-454 in feces-suspensions and serum. Viruses 4, 1328–1334 (2012)
    • (2012) Viruses , vol.4 , pp. 1328-1334
    • De Vries, M.1
  • 42
    • 84942807879 scopus 로고    scopus 로고
    • Challenges of the unknown: Clinical application of microbial metagenomics
    • Rose, G. et al. Challenges of the unknown: clinical application of microbial metagenomics. Int. J. Genomics 292950 (2015)
    • (2015) Int. J. Genomics
    • Rose, G.1
  • 43
    • 84920644670 scopus 로고    scopus 로고
    • Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
    • PID: 25387460
    • Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014)
    • (2014) BMC Biol. , vol.12
    • Salter, S.J.1
  • 44
    • 85052712934 scopus 로고    scopus 로고
    • Index switching causes “spreading-of-signal” among multiplexed samples in Illumina HiSeq
    • Reprint at
    • Sinha, R. et al. Index switching causes “spreading-of-signal” among multiplexed samples in Illumina HiSeq. 4000 DNA Sequencing. Reprint at https://www.biorxiv.org/content/early/2017/04/09/125724 (2017)
    • (2017) 4000 DNA Sequencing
    • Sinha, R.1
  • 46
    • 80054853710 scopus 로고    scopus 로고
    • Solving the Problem: Genome Annotation Standards before the Data Deluge
    • PID: 22180819
    • Klimke, W. et al. Solving the problem: Genome annotation standards before the data deluge. Stand. Genomic Sci. 5, 168–193 (2011)
    • (2011) Stand. Genomic Sci. , vol.5 , pp. 168-193
    • Klimke, W.1
  • 47
    • 85048278788 scopus 로고    scopus 로고
    • Genomics-based identification of microorganisms in human ocular body fluid
    • Kirstahler, P. et al. Genomics-based identification of microorganisms in human ocular body fluid. Sci. Rep. 8, 4126 (2018)
    • (2018) Sci. Rep. , vol.8 , Issue.4126
    • Kirstahler, P.1
  • 48
    • 85029629577 scopus 로고    scopus 로고
    • Loeffler 4.0: Diagnostic Metagenomics in Loeffler’s footsteps viral genomics in the era of high-throughput sequencing
    • eds Beer, M. & Höper, D
    • Höper, D., Wylezich, C. & Beer, M. Loeffler 4.0: Diagnostic Metagenomics in Loeffler’s footsteps viral genomics in the era of high-throughput sequencing. (eds Beer, M. & Höper, D.). Adv. Viral Res. Elsevier 99, 17–37 (2017)
    • (2017) Adv. Viral Res. Elsevier , vol.99 , pp. 17-37
    • Höper, D.1    Wylezich, C.2    Beer, M.3
  • 49
    • 84975475971 scopus 로고    scopus 로고
    • Characterization of tuberculous granulomas in different stages of progression and associated tertiary lymphoid tissue in goats experimentally infected with Mycobacterium avium subsp. hominissuis
    • PID: 27477506
    • Schinköthe, J., Köhler, H. & Liebler-Tenorio, E. M. Characterization of tuberculous granulomas in different stages of progression and associated tertiary lymphoid tissue in goats experimentally infected with Mycobacterium avium subsp. hominissuis. Comp. Immunol. Microbiol. Infect. Dis. 47, 41–51 (2016)
    • (2016) Comp. Immunol. Microbiol. Infect. Dis. , vol.47 , pp. 41-51
    • Schinköthe, J.1    Köhler, H.2    Liebler-Tenorio, E.M.3
  • 50
    • 70249092228 scopus 로고    scopus 로고
    • Monitoring of putative vectors of Bluetongue virus serotype 8, Germany
    • PID: 19788820
    • Hoffmann, B. et al. Monitoring of putative vectors of Bluetongue virus serotype 8, Germany. Emerg. Infect. Dis. 15, 1481–1484 (2009)
    • (2009) Emerg. Infect. Dis. , vol.15 , pp. 1481-1484
    • Hoffmann, B.1
  • 51
    • 84899891430 scopus 로고    scopus 로고
    • Schmallenberg Virus Circulation in Culicoides in Belgium in 2012: Field validation of a real time RT-PCR approach to assess virus replication and dissemination in midges
    • PID: 24466312
    • De Regge, N. et al. Schmallenberg virus circulation in Culicoides in Belgium in 2012: Field validation of a real time RT-PCR approach to assess virus replication and dissemination in midges. PLoS One 9, e87005 (2014)
    • (2014) PLoS One , vol.9
    • De Regge, N.1
  • 52
    • 36548999282 scopus 로고    scopus 로고
    • Comparison of 13 single-round and nested PCR assays targeting IS900, ISMav2, f57 and locus 255 for detection of Mycobacterium avium subsp. paratuberculosis
    • PID: 17889455
    • Möbius, P., Hotzel, H., Rassbach, A. & Köhler, H. Comparison of 13 single-round and nested PCR assays targeting IS900, ISMav2, f57 and locus 255 for detection of Mycobacterium avium subsp. paratuberculosis. Vet. Microbiol. 126, 324–333 (2008)
    • (2008) Vet. Microbiol. , vol.126 , pp. 324-333
    • Möbius, P.1    Hotzel, H.2    Rassbach, A.3    Köhler, H.4
  • 53
    • 84959440888 scopus 로고    scopus 로고
    • Genetic characterization of Arrabida virus, a novel phlebovirus isolated in South Portugal
    • PID: 26795868
    • Amaro, F. et al. Genetic characterization of Arrabida virus, a novel phlebovirus isolated in South Portugal. Virus Res. 214, 19–25 (2016)
    • (2016) Virus Res. , vol.214 , pp. 19-25
    • Amaro, F.1


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