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

被引：36

作者：

Becker, Laura ^{[1
]}

Steglich, Matthias ^{[2
]}

Fuchs, Stephan ^{[1
]}

Werner, Guido ^{[1
]}

Nuebel, Ulrich ^{[2
,3
]}

机构：

[1] Robert Koch Inst, Div Nosocomial Pathogens & Antibiot Resistances F, Dept Infect Dis, Wernigerode, Germany

[2] Leibniz Inst DSMZ, Braunschweig, Germany

[3] German Ctr Infect Res DZIF, Partner Site, Braunschweig, Germany

来源：

SCIENTIFIC REPORTS | 2016年 / 6卷

基金：

欧盟地平线“2020”;

关键词：

GEL-ELECTROPHORESIS PROTOCOLS; COPY-NUMBER;

D O I：

10.1038/srep28063

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

We compared commercial kits for extraction of genomic DNA from the Gram-negative bacterium Klebsiella pneumoniae for subsequent Miseq sequencing. Purification of DNA was based on matrix binding (silica or anion exchange resin) or differential precipitation (salting out), respectively. The choice of extraction kit had little effect on sequencing quality and coverage across drastically different replicons, except for an apparent depletion of small plasmids (<5 kb) during precipitation-based extractions. Sequencing coverage provided copy-number estimates for small plasmids that were consistently higher than those from quantitative real-time PCR.

引用

页数：5

共 28 条

[1] A GENERAL-METHOD FOR DETECTING AND SIZING LARGE PLASMIDS [J].

BARTON, BM ;

HARDING, GP ;

ZUCCARELLI, AJ .

ANALYTICAL BIOCHEMISTRY, 1995, 226 (02) :235-240

[2] Complete Genome Sequence of a CTX-M-15-Producing Klebsiella pneumoniae Outbreak Strain from Multilocus Sequence Type 514 [J].

Becker, Laura ;

Bunk, Boyke ;

Eller, Christoph ;

Steglich, Matthias ;

Pfeifer, Yvonne ;

Werner, Guido ;

Nuebel, Ulrich .

GENOME ANNOUNCEMENTS, 2015, 3 (04)

[3]

Budelier K., 2001, Current protocols in molecular biology

[4] Transforming clinical microbiology with bacterial genome sequencing [J].

Didelot, Xavier ;

Bowden, Rory ;

Wilson, Daniel J. ;

Peto, Tim E. A. ;

Crook, Derrick W. .

NATURE REVIEWS GENETICS, 2012, 13 (09) :601-612

[5] Prediction of Staphylococcus aureus Antimicrobial Resistance by Whole-Genome Sequencing [J].

Gordon, N. C. ;

Price, J. R. ;

Cole, K. ;

Everitt, R. ;

Morgan, M. ;

Finney, J. ;

Kearns, A. M. ;

Pichon, B. ;

Young, B. ;

Wilson, D. J. ;

Llewelyn, M. J. ;

Paul, J. ;

Peto, T. E. A. ;

Crook, D. W. ;

Walker, A. S. ;

Golubchik, T. .

JOURNAL OF CLINICAL MICROBIOLOGY, 2014, 52 (04) :1182-1191

[6] 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 [J].

Haller, Sebastian ;

Eller, Christoph ;

Hermes, Julia ;

Kaase, Martin ;

Steglich, Matthias ;

Radonic, Aleksandar ;

Dabrowski, Piotr Wojtek ;

Nitsche, Andreas ;

Pfeifer, Yvonne ;

Werner, Guido ;

Wunderle, Werner ;

Velasco, Edward ;

Abu Sin, Muna ;

Eckmanns, Tim ;

Nuebel, Ulrich .

BMJ OPEN, 2015, 5 (05)

[7] Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study [J].

Harris, Simon R. ;

Cartwright, Edward J. P. ;

Toeroek, M. Estee ;

Holden, Matthew T. G. ;

Brown, Nicholas M. ;

Ogilvy-Stuart, Amanda L. ;

Ellington, Matthew J. ;

Quail, Michael A. ;

Bentley, Stephen D. ;

Parkhill, Julian ;

Peacock, Sharon J. .

LANCET INFECTIOUS DISEASES, 2013, 13 (02) :130-136

[8] Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities [J].

Henderson, Gemma ;

Cox, Faith ;

Kittelmann, Sandra ;

Miri, Vahideh Heidarian ;

Zethof, Michael ;

Noel, Samantha J. ;

Waghorn, Garry C. ;

Janssen, Peter H. .

PLOS ONE, 2013, 8 (09)

[9] A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic [J].

Holden, Matthew T. G. ;

Hsu, Li-Yang ;

Kurt, Kevin ;

Weinert, Lucy A. ;

Mather, Alison E. ;

Harris, Simon R. ;

Strommenger, Birgit ;

Layer, Franziska ;

Witte, Wolfgang ;

de Lencastre, Herminia ;

Skov, Robert ;

Westh, Henrik ;

Zemlickova, Helena ;

Coombs, Geoffrey ;

Kearns, Angela M. ;

Hill, Robert L. R. ;

Edgeworth, Jonathan ;

Gould, Ian ;

Gant, Vanya ;

Cooke, Jonathan ;

Edwards, Giles F. ;

McAdam, Paul R. ;

Templeton, Kate E. ;

McCann, Angela ;

Zhou, Zhemin ;

Castillo-Ramirez, Santiago ;

Feil, Edward J. ;

Hudson, Lyndsey O. ;

Enright, Mark C. ;

Balloux, Francois ;

Aanensen, David M. ;

Spratt, Brian G. ;

Fitzgerald, J. Ross ;

Parkhill, Julian ;

Achtman, Mark ;

Bentley, Stephen D. ;

Nuebel, Ulrich .

GENOME RESEARCH, 2013, 23 (04) :653-664

[10] 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].

Hunter, SB ;

Vauterin, P ;

Lambert-Fair, MA ;

Van Duyne, MS ;

Kubota, K ;

Graves, L ;

Wrigley, D ;

Barrett, T ;

Ribot, E .

JOURNAL OF CLINICAL MICROBIOLOGY, 2005, 43 (03) :1045-1050

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