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Volumn 6, Issue , 2016, Pages

Comparison of six commercial kits to extract bacterial chromosome and plasmid DNA for MiSeq sequencing

Author keywords

[No Author keywords available]

Indexed keywords

ANION EXCHANGE RESIN; BACTERIAL DNA; SILICON DIOXIDE;

EID: 84975498126     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep28063     Document Type: Article
Times cited : (41)

References (29)
  • 2
    • 84865231395 scopus 로고    scopus 로고
    • Transforming clinical microbiology with bacterial genome sequencing
    • Didelot, X., Bowden, R., Wilson, D. J., Peto, T. E. & Crook, D. W. Transforming clinical microbiology with bacterial genome sequencing. Nature reviews. Genetics 13, 601-612, doi: 10.1038/nrg3226 (2012).
    • (2012) Nature Reviews. Genetics , vol.13 , pp. 601-612
    • Didelot, X.1    Bowden, R.2    Wilson, D.J.3    Peto, T.E.4    Crook, D.W.5
  • 3
    • 84920861234 scopus 로고    scopus 로고
    • Microbial sequencing to improve individual and population health
    • Peacock, S. J. & Weinstock, G. M. Microbial sequencing to improve individual and population health. Genome Med 6, 103, doi: 10.1186/s13073-014-0103-5 (2014).
    • (2014) Genome Med , vol.6 , pp. 103
    • Peacock, S.J.1    Weinstock, G.M.2
  • 4
    • 84930226040 scopus 로고    scopus 로고
    • What caused the outbreak of ESBL-producing klebsiella pneumoniae in a neonatal intensive care unit, Germany 2009 to 2012? Reconstructing transmission with epidemiological analysis and whole-genome sequencing
    • Haller, S. et al. What caused the outbreak of ESBL-producing Klebsiella pneumoniae in a neonatal intensive care unit, Germany 2009 to 2012? Reconstructing transmission with epidemiological analysis and whole-genome sequencing. BMJ Open 5, e007397, doi: 10.1136/bmjopen-2014-007397 (2015).
    • (2015) BMJ Open , vol.5 , pp. e007397
    • Haller, S.1
  • 5
    • 84872515273 scopus 로고    scopus 로고
    • Whole-genome sequencing for analysis of an outbreak of meticillin-resistant staphylococcus aureus: A descriptive study
    • Harris, S. R. et al. Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. The Lancet. Infectious diseases 13, 130-136, doi: 10.1016/S1473-3099(12)70268-2 (2013).
    • (2013) The Lancet. Infectious Diseases , vol.13 , pp. 130-136
    • Harris, S.R.1
  • 6
    • 84897134429 scopus 로고    scopus 로고
    • Prediction of staphylococcus aureus antimicrobial resistance by whole-genome sequencing
    • Gordon, N. C. et al. Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing. J Clin Microbiol 52, 1182-1191, doi: 10.1128/JCM.03117-13 (2014).
    • (2014) J Clin Microbiol , vol.52 , pp. 1182-1191
    • Gordon, N.C.1
  • 7
    • 84875741847 scopus 로고    scopus 로고
    • A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant staphylococcus aureus pandemic
    • Holden, M. T. et al. A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic. Genome research 23, 653-664, doi: 10.1101/gr.147710.112 (2013).
    • (2013) Genome Research , vol.23 , pp. 653-664
    • Holden, M.T.1
  • 8
    • 84875265483 scopus 로고    scopus 로고
    • Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing
    • Zankari, E. et al. Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother 68, 771-777, doi: 10.1093/jac/dks496 (2013).
    • (2013) J Antimicrob Chemother , vol.68 , pp. 771-777
    • Zankari, E.1
  • 9
    • 73449135108 scopus 로고    scopus 로고
    • DNA, RNA, and protein extraction: The past and the present
    • Tan, S. C. & Yiap, B. C. DNA, RNA, and protein extraction: the past and the present. Journal of biomedicine & biotechnology 2009, 574398, doi: 10.1155/2009/574398 (2009).
    • (2009) Journal of Biomedicine & Biotechnology , vol.2009 , pp. 574398
    • Tan, S.C.1    Yiap, B.C.2
  • 10
    • 84887756987 scopus 로고    scopus 로고
    • Improved workflows for high throughput library preparation using the transposome-based nextera system
    • Lamble, S. et al. Improved workflows for high throughput library preparation using the transposome-based Nextera system. BMC Biotechnol 13, 104, doi: 10.1186/1472-6750-13-104 (2013).
    • (2013) BMC Biotechnol , vol.13 , pp. 104
    • Lamble, S.1
  • 11
    • 84876670514 scopus 로고    scopus 로고
    • Systematic biases in DNA copy number originate from isolation procedures
    • van Heesch, S. et al. Systematic biases in DNA copy number originate from isolation procedures. Genome biology 14, R33, doi: 10.1186/gb-2013-14-4-r33 (2013).
    • (2013) Genome Biology , vol.14 , pp. R33
    • Van Heesch, S.1
  • 14
    • 84889102325 scopus 로고    scopus 로고
    • Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by illumina sequencing of 16S rRNA tags
    • Peng, X. et al. Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags. J Microbiol Methods 95, 455-462, doi: 10.1016/j.mimet.2013.07.015 (2013).
    • (2013) J Microbiol Methods , vol.95 , pp. 455-462
    • Peng, X.1
  • 15
    • 84896089558 scopus 로고    scopus 로고
    • The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing
    • Kennedy, N. A. et al. The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing. PLos One 9, e88982, doi: 10.1371/journal.pone.0088982 (2014).
    • (2014) PLos One , vol.9 , pp. e88982
    • Kennedy, N.A.1
  • 16
    • 84893848394 scopus 로고    scopus 로고
    • Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities
    • Henderson, G. et al. Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities. PLos One 8, e74787, doi: 10.1371/journal.pone.0074787 (2013).
    • (2013) PLos One , vol.8 , pp. e74787
    • Henderson, G.1
  • 17
    • 84965173148 scopus 로고    scopus 로고
    • Estimates of soil bacterial ribosome content and diversity are significantly affected by the nucleic acid extraction method employed
    • Wüst, P. K. et al. Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed. Appl Environ Microbiol 82, 2595-2607, doi: 10.1128/AEM.00019-16 (2016).
    • (2016) Appl Environ Microbiol , vol.82 , pp. 2595-2607
    • Wüst, P.K.1
  • 18
    • 84921532911 scopus 로고    scopus 로고
    • Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis
    • Wesolowska-Andersen, A. et al. Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis. Microbiome 2, 19, doi: 10.1186/2049-2618-2-19 (2014).
    • (2014) Microbiome , vol.2 , pp. 19
    • Wesolowska-Andersen, A.1
  • 19
    • 85008429799 scopus 로고    scopus 로고
    • Complete genome sequence of a CTX-M-15-producing klebsiella pneumoniae outbreak strain from multilocus sequence type 514
    • Becker, L. et al. Complete Genome Sequence of a CTX-M-15-Producing Klebsiella pneumoniae Outbreak Strain from Multilocus Sequence Type 514. Genome Announc 3, doi: 10.1128/genomeA.00742-15 (2015).
    • (2015) Genome Announc , vol.3
    • Becker, L.1
  • 21
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with burrows-wheeler transform
    • Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760, doi: 10.1093/bioinformatics/btp324 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 22
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and SAM tools
    • Li, H. et al. The Sequence Alignment/Map format and SAM tools. Bioinformatics 25, 2078-2079, doi: 10.1093/bioinformatics/btp352 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 24
    • 84863507534 scopus 로고    scopus 로고
    • Geneious basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
    • Kearse, M. et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647-1649, doi: 10.1093/bioinformatics/bts199 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 1647-1649
    • Kearse, M.1
  • 25
    • 42449157617 scopus 로고    scopus 로고
    • Improved determination of plasmid copy number using quantitative real-time PCR for monitoring fermentation processes
    • Skulj, M. et al. Improved determination of plasmid copy number using quantitative real-time PCR for monitoring fermentation processes. Microb Cell Fact 7, 6, doi: 10.1186/1475-2859-7-6 (2008).
    • (2008) Microb Cell Fact , vol.7 , pp. 6
    • Skulj, M.1
  • 26
    • 33646340437 scopus 로고    scopus 로고
    • The copy-number of plasmids and other genetic elements can be determined by SYBR-green-based quantitative real-time PCR
    • Providenti, M. A., O'Brien, J. M., Ewing, R. J., Paterson, E. S. & Smith, M. L. The copy-number of plasmids and other genetic elements can be determined by SYBR-Green-based quantitative real-time PCR. J Microbiol Methods 65, 476-487, doi: 10.1016/j. mimet.2005.09.007 (2006).
    • (2006) J Microbiol Methods , vol.65 , pp. 476-487
    • Providenti, M.A.1    O'Brien, J.M.2    Ewing, R.J.3    Paterson, E.S.4    Smith, M.L.5
  • 27
    • 14944355089 scopus 로고    scopus 로고
    • Establishment of a universal size standard strain for use with the pulsenet standardized pulsed-field gel electrophoresis protocols: Converting the national databases to the new size standard
    • Hunter, S. B. et al. Establishment of a universal size standard strain for use with the PulseNet standardized pulsed-field gel electrophoresis protocols: converting the national databases to the new size standard. J Clin Microbiol 43, 1045-1050, doi: 10.1128/JCM.43.3.1045-1050.2005 (2005).
    • (2005) J Clin Microbiol , vol.43 , pp. 1045-1050
    • Hunter, S.B.1
  • 28
    • 33645707707 scopus 로고    scopus 로고
    • Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, salmonella, and shigella for pulsenet
    • Ribot, E. M. et al. Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet. Foodborne pathogens and disease 3, 59-67, doi: 10.1089/fpd.2006.3.59 (2006).
    • (2006) Foodborne Pathogens and Disease , vol.3 , pp. 59-67
    • Ribot, E.M.1
  • 29
    • 0028924342 scopus 로고
    • A general method for detecting and sizing large plasmids
    • Barton, B. M., Harding, G. P. & Zuccarelli, A. J. A general method for detecting and sizing large plasmids. Anal Biochem 226, 235-240, doi: 10.1006/abio.1995.1220 (1995).
    • (1995) Anal Biochem , vol.226 , pp. 235-240
    • Barton, B.M.1    Harding, G.P.2    Zuccarelli, A.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.