Literature DB >> 26019203

Direct DNA Extraction from Mycobacterium tuberculosis Frozen Stocks as a Reculture-Independent Approach to Whole-Genome Sequencing.

K Bjorn-Mortensen1, J Zallet2, T Lillebaek3, A B Andersen4, S Niemann2, E M Rasmussen3, T A Kohl5.   

Abstract

Culturing before DNA extraction represents a major time-consuming step in whole-genome sequencing of slow-growing bacteria, such as Mycobacterium tuberculosis. We report a workflow to extract DNA from frozen isolates without reculturing. Prepared libraries and sequence data were comparable with results from recultured aliquots of the same stocks.
Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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Year:  2015        PMID： 26019203      PMCID： PMC4508433          DOI： 10.1128/JCM.00662-15

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


  23 in total

1.  Genotypic identification of mycobacteria by nucleic acid sequence determination: report of a 2-year experience in a clinical laboratory.

Authors:  P Kirschner; B Springer; U Vogel; A Meier; A Wrede; M Kiekenbeck; F C Bange; E C Böttger
Journal:  J Clin Microbiol       Date:  1993-11       Impact factor: 5.948

2.  The competitive cost of antibiotic resistance in Mycobacterium tuberculosis.

Authors:  Sebastien Gagneux; Clara Davis Long; Peter M Small; Tran Van; Gary K Schoolnik; Brendan J M Bohannan
Journal:  Science       Date:  2006-06-30       Impact factor: 47.728

Review 3.  Genomic insights into tuberculosis.

Authors:  James E Galagan
Journal:  Nat Rev Genet       Date:  2014-03-25       Impact factor: 53.242

4.  Tracking a tuberculosis outbreak over 21 years: strain-specific single-nucleotide polymorphism typing combined with targeted whole-genome sequencing.

Authors:  David Stucki; Marie Ballif; Thomas Bodmer; Mireia Coscolla; Anne-Marie Maurer; Sara Droz; Christa Butz; Sonia Borrell; Christel Längle; Julia Feldmann; Hansjakob Furrer; Carlo Mordasini; Peter Helbling; Hans L Rieder; Matthias Egger; Sébastien Gagneux; Lukas Fenner
Journal:  J Infect Dis       Date:  2014-10-30       Impact factor: 5.226

5.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.

Authors:  Helga Thorvaldsdóttir; James T Robinson; Jill P Mesirov
Journal:  Brief Bioinform       Date:  2012-04-19       Impact factor: 11.622

6.  Mycobacterial DNA extraction for whole-genome sequencing from early positive liquid (MGIT) cultures.

Authors:  Antonina A Votintseva; Louise J Pankhurst; Luke W Anson; Marcus R Morgan; Deborah Gascoyne-Binzi; Timothy M Walker; T Phuong Quan; David H Wyllie; Carlos Del Ojo Elias; Mark Wilcox; A Sarah Walker; Tim E A Peto; Derrick W Crook
Journal:  J Clin Microbiol       Date:  2015-01-28       Impact factor: 5.948

7.  Evolution of extensively drug-resistant Mycobacterium tuberculosis from a susceptible ancestor in a single patient.

Authors:  Vegard Eldholm; Gunnstein Norheim; Bent von der Lippe; Wibeke Kinander; Ulf R Dahle; Dominique A Caugant; Turid Mannsåker; Anne Torunn Mengshoel; Anne Ma Dyrhol-Riise; Francois Balloux
Journal:  Genome Biol       Date:  2014-11-07       Impact factor: 13.583

8.  Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.

Authors:  Andreas Roetzer; Roland Diel; Thomas A Kohl; Christian Rückert; Ulrich Nübel; Jochen Blom; Thierry Wirth; Sebastian Jaenicke; Sieglinde Schuback; Sabine Rüsch-Gerdes; Philip Supply; Jörn Kalinowski; Stefan Niemann
Journal:  PLoS Med       Date:  2013-02-12       Impact factor: 11.069

9.  Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study.

Authors:  Timothy M Walker; Camilla L C Ip; Ruth H Harrell; Jason T Evans; Georgia Kapatai; Martin J Dedicoat; David W Eyre; Daniel J Wilson; Peter M Hawkey; Derrick W Crook; Julian Parkhill; David Harris; A Sarah Walker; Rory Bowden; Philip Monk; E Grace Smith; Tim E A Peto
Journal:  Lancet Infect Dis       Date:  2012-11-15       Impact factor: 25.071

10.  Whole genome sequencing reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in patients.

Authors:  Matthias Merker; Thomas A Kohl; Andreas Roetzer; Leona Truebe; Elvira Richter; Sabine Rüsch-Gerdes; Lanfranco Fattorini; Marco R Oggioni; Helen Cox; Francis Varaine; Stefan Niemann
Journal:  PLoS One       Date:  2013-12-06       Impact factor: 3.240
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  8 in total

1.  Successful Direct Whole Genome Sequencing and Revivification of Freeze-Dried Nontuberculous Mycobacteria after More than Half a Century of Storage.

Authors:  Xenia Emilie Sinding Iversen; Anders Norman; Dorte Bek Folkvardsen; Erik Svensson; Erik Michael Rasmussen; Troels Lillebaek
Journal:  Microbiol Spectr       Date:  2022-05-19

2.  A Predominant Variable-Number Tandem-Repeat Cluster of Mycobacterium tuberculosis Isolates among Asylum Seekers in the Netherlands and Denmark, Deciphered by Whole-Genome Sequencing.

Authors:  Rana Jajou; Albert de Neeling; Erik Michael Rasmussen; Anders Norman; Arnout Mulder; Rianne van Hunen; Gerard de Vries; Walid Haddad; Richard Anthony; Troels Lillebaek; Wim van der Hoek; Dick van Soolingen
Journal:  J Clin Microbiol       Date:  2018-01-24       Impact factor: 5.948

3.  A SIMPLE METHOD OF DNA EXTRACTION OF MYCOBACTERIUM TUBERCULOSIS FROM SPUTUM CULTURES FOR SEQUENCING ANALYSIS.

Authors:  Maharani Pertiwi Koentjoro; Adyan Donastin; Endry Nugroho Prasetyo
Journal:  Afr J Infect Dis       Date:  2021-09-01

4.  Tracing Mycobacterium tuberculosis transmission by whole genome sequencing in a high incidence setting: a retrospective population-based study in East Greenland.

Authors:  K Bjorn-Mortensen; B Soborg; A Koch; K Ladefoged; M Merker; T Lillebaek; A B Andersen; S Niemann; T A Kohl
Journal:  Sci Rep       Date:  2016-09-12       Impact factor: 4.379

Review 5.  Molecular Diagnosis of Tuberculosis.

Authors:  Fariz Nurwidya; Diah Handayani; Erlina Burhan; Faisal Yunus
Journal:  Chonnam Med J       Date:  2018-01-25

6.  An attenuated Mycobacterium tuberculosis clinical strain with a defect in ESX-1 secretion induces minimal host immune responses and pathology.

Authors:  Helena Strand Clemmensen; Niels Peter Hell Knudsen; Erik Michael Rasmussen; Jessica Winkler; Ida Rosenkrands; Ahmad Ahmad; Troels Lillebaek; David R Sherman; Peter Lawætz Andersen; Claus Aagaard
Journal:  Sci Rep       Date:  2017-04-24       Impact factor: 4.379

7.  Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture.

Authors:  Camus Nimmo; Liam P Shaw; Ronan Doyle; Rachel Williams; Kayleen Brien; Carrie Burgess; Judith Breuer; Francois Balloux; Alexander S Pym
Journal:  BMC Genomics       Date:  2019-05-20       Impact factor: 3.969

8.  A scalable, efficient, and safe method to prepare high quality DNA from mycobacteria and other challenging cells.

Authors:  L Elaine Epperson; Michael Strong
Journal:  J Clin Tuberc Other Mycobact Dis       Date:  2020-02-04
  8 in total

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