Literature DB >> 25878343

Optimized Protocol for Simple Extraction of High-Quality Genomic DNA from Clostridium difficile for Whole-Genome Sequencing.

James Heng Chiak Sim1, Victoria Anikst1, Akshar Lohith2, Nader Pourmand2, Niaz Banaei3.   

Abstract

Successful sequencing of the Clostridium difficile genome requires high-quality genomic DNA (gDNA) as the starting material. gDNA extraction using conventional methods is laborious. We describe here an optimized method for the simple extraction of C. difficile gDNA using the QIAamp DNA minikit, which yielded high-quality sequence reads on the Illumina MiSeq platform.
Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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Year:  2015        PMID： 25878343      PMCID： PMC4473243          DOI： 10.1128/JCM.00956-15

Source DB:  PubMed          Journal:  J Clin Microbiol        ISSN： 0095-1137            Impact factor:   5.948


  9 in total

Review 1.  Three-stage quality control strategies for DNA re-sequencing data.

Authors:  Yan Guo; Fei Ye; Quanghu Sheng; Travis Clark; David C Samuels
Journal:  Brief Bioinform       Date:  2013-09-24       Impact factor: 11.622

2.  Genetic manipulation of Clostridium difficile.

Authors:  Laurent Bouillaut; Shonna M McBride; Joseph A Sorg
Journal:  Curr Protoc Microbiol       Date:  2011-02

3.  Emergence of a ribotype 244 strain of Clostridium difficile associated with severe disease and related to the epidemic ribotype 027 strain.

Authors:  Sze K Lim; Rhonda L Stuart; Kate E Mackin; Glen P Carter; Despina Kotsanas; Michelle J Francis; Marion Easton; Karolina Dimovski; Briony Elliott; Thomas V Riley; Geoff Hogg; Eldho Paul; Tony M Korman; Torsten Seemann; Timothy P Stinear; Dena Lyras; Grant A Jenkin
Journal:  Clin Infect Dis       Date:  2014-04-04       Impact factor: 9.079

4.  AdapterRemoval: easy cleaning of next-generation sequencing reads.

Authors:  Stinus Lindgreen
Journal:  BMC Res Notes       Date:  2012-07-02

5.  The genome of Clostridium difficile 5.3.

Authors:  Aaron E Darling; Paul Worden; Toni A Chapman; Piklu Roy Chowdhury; Ian G Charles; Steven P Djordjevic
Journal:  Gut Pathog       Date:  2014-02-24       Impact factor: 4.181

6.  Diverse sources of C. difficile infection identified on whole-genome sequencing.

Authors:  Derrick W Crook; Mark H Wilcox; Tim E A Peto; A Sarah Walker; David W Eyre; Madeleine L Cule; Daniel J Wilson; David Griffiths; Alison Vaughan; Lily O'Connor; Camilla L C Ip; Tanya Golubchik; Elizabeth M Batty; John M Finney; David H Wyllie; Xavier Didelot; Paolo Piazza; Rory Bowden; Kate E Dingle; Rosalind M Harding
Journal:  N Engl J Med       Date:  2013-09-26       Impact factor: 91.245

7.  Asymptomatic Clostridium difficile colonisation and onward transmission.

Authors:  David W Eyre; David Griffiths; Alison Vaughan; Tanya Golubchik; Milind Acharya; Lily O'Connor; Derrick W Crook; A Sarah Walker; Tim E A Peto
Journal:  PLoS One       Date:  2013-11-12       Impact factor: 3.240

8.  Whole-genome sequencing demonstrates that fidaxomicin is superior to vancomycin for preventing reinfection and relapse of infection with Clostridium difficile.

Authors:  David W Eyre; Farah Babakhani; David Griffiths; Jaime Seddon; Carlos Del Ojo Elias; Sherwood L Gorbach; Tim E A Peto; Derrick W Crook; A Sarah Walker
Journal:  J Infect Dis       Date:  2013-11-11       Impact factor: 5.226

9.  Microevolutionary analysis of Clostridium difficile genomes to investigate transmission.

Authors:  Xavier Didelot; David W Eyre; Madeleine Cule; Camilla L C Ip; M Azim Ansari; David Griffiths; Alison Vaughan; Lily O'Connor; Tanya Golubchik; Elizabeth M Batty; Paolo Piazza; Daniel J Wilson; Rory Bowden; Peter J Donnelly; Kate E Dingle; Mark Wilcox; A Sarah Walker; Derrick W Crook; Tim E A Peto; Rosalind M Harding
Journal:  Genome Biol       Date:  2012-12-21       Impact factor: 13.583
  9 in total
  2 in total

1.  Evaluation of a Combined Multilocus Sequence Typing and Whole-Genome Sequencing Two-Step Algorithm for Routine Typing of Clostridioides difficile.

Authors:  Mini Kamboj; Tracy McMillen; Mustafa Syed; Hoi Yan Chow; Krupa Jani; Anoshe Aslam; Jennifer Brite; Brian Fanelli; Nur A Hasan; Manoj Dadlani; Lars Westblade; Ahmet Zehir; Matthew Simon; N Esther Babady
Journal:  J Clin Microbiol       Date:  2021-01-21       Impact factor: 5.948

2.  Genotypic correlation between post discharge Clostridiodes difficle infection (CDI) and previous unit-based contacts.

Authors:  N E Babady; A Aslam; T McMillen; M Syed; A Zehir; M Kamboj
Journal:  J Hosp Infect       Date:  2020-11-07       Impact factor: 3.926
  2 in total

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