Journal ArticleDOI
DNA fingerprinting of Mycobacterium tuberculosis: from phage typing to whole-genome sequencing.
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TLDR
In order to fully explore the possibilities of genotyping in the molecular epidemiology of tuberculosis and to study the phylogeny of the causative bacteria reliably, the application of whole-genome sequencing (WGS) analysis for all M. tuberculosis isolates is the optimal, although currently still a costly solution.About:
This article is published in Infection, Genetics and Evolution.The article was published on 2012-06-01. It has received 83 citations till now. The article focuses on the topics: Mycobacterium tuberculosis complex & Multilocus sequence typing.read more
Citations
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Journal ArticleDOI
Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study
Timothy M Walker,Camilla L. C. Ip,Ruth H. Harrell,Jason T. Evans,Georgia Kapatai,Martin Dedicoat,David W Eyre,Daniel J. Wilson,Peter M. Hawkey,Peter M. Hawkey,Derrick W. Crook,Julian Parkhill,David Harris,A. Sarah Walker,Rory Bowden,Philip Monk,E. Grace Smith,Tim E. A. Peto +17 more
TL;DR: The genetic diversity of related M tuberculosis strains in the UK Midlands is estimated and the technique could identify super-spreaders and predict the existence of undiagnosed cases, potentially leading to early treatment of infectious patients and their contacts.
Journal ArticleDOI
Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology
Claudio U. Köser,Matthew J. Ellington,Edward J. P. Cartwright,Edward J. P. Cartwright,Stephen H. Gillespie,Nicholas M. Brown,Mark Farrington,Matthew T. G. Holden,Gordon Dougan,Stephen D. Bentley,Julian Parkhill,Sharon J. Peacock +11 more
TL;DR: It is proposed that molecular epidemiology performed for surveillance and outbreak investigation and genotypic antimicrobial susceptibility testing for microbes that are difficult to grow represent the most immediate areas for application of WGS.
Journal ArticleDOI
Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study
Andreas Roetzer,Roland Diel,Thomas Kohl,Christian Rückert,Ulrich Nübel,Jochen Blom,Thierry Wirth,Sebastian Jaenicke,Sieglinde Schuback,Sabine Rüsch-Gerdes,Philip Supply,Jörn Kalinowski,Stefan Niemann +12 more
TL;DR: In an outbreak investigation of Mycobacterium tuberculosis comparing whole genome sequencing (WGS) with traditional genotyping, Stefan Niemann and colleagues found that classical genotypes falsely clustered some strains, and WGS better reflected contact tracing.
Journal ArticleDOI
Genomic insights into tuberculosis
TL;DR: New insights are being generated into the origins and ongoing evolution of M. tuberculosis, as well as the molecular basis for its pathogenicity, which have important implications for the perspective of the disease, development of new drugs and vaccines, and treatment of patients using existing therapeutics.
References
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Journal ArticleDOI
DNA sequencing with chain-terminating inhibitors
TL;DR: A new method for determining nucleotide sequences in DNA is described, which makes use of the 2',3'-dideoxy and arabinon nucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase.
Journal ArticleDOI
Detection of specific sequences among DNA fragments separated by gel electrophoresis.
TL;DR: This paper describes a method of transferring fragments of DNA from agarose gels to cellulose nitrate filters that can be hybridized to radioactive RNA and hybrids detected by radioautography or fluorography.
Journal ArticleDOI
Genome sequencing in microfabricated high-density picolitre reactors
Marcel Margulies,Michael Egholm,William E. Altman,Said Attiya,Joel S. Bader,Lisa A. Bemben,Jan Berka,Michael S. Braverman,Yi-Ju Chen,Zhoutao Chen,Scott Dewell,Lei Du,J. M. Fierro,Xavier V. Gomes,Brian C. Godwin,Wen He,Scott Edward Helgesen,Chun Heen Ho,Gerard P. Irzyk,Szilveszter C. Jando,Maria L. I. Alenquer,Thomas P. Jarvie,Kshama B. Jirage,Jong-Bum Kim,James R. Knight,Janna R. Lanza,John H. Leamon,Steven Lefkowitz,Ming Lei,Jing Li,Kenton Lohman,Hong Lu,Vinod Makhijani,Keith Mcdade,Michael P. McKenna,Eugene W. Myers,Elizabeth Nickerson,John Nobile,Ramona Plant,Bernard P. Puc,Michael T. Ronan,George T. Roth,Gary J. Sarkis,Jan Fredrik Simons,John Simpson,Maithreyan Srinivasan,Karrie R. Tartaro,Alexander Tomasz,Kari A. Vogt,Greg A. Volkmer,Shally H. Wang,Yong Wang,Michael P. Weiner,Pengguang Yu,Richard F. Begley,Jonathan M. Rothberg +55 more
TL;DR: A scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments with 96% coverage at 99.96% accuracy in one run of the machine is described.
Journal ArticleDOI
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
Stewart T. Cole,Roland Brosch,Julian Parkhill,Thierry Garnier,Carol Churcher,David Harris,Stephen V. Gordon,Karin Eiglmeier,S. Gas,Clifton E. Barry,Fredj Tekaia,K. Badcock,D. Basham,D. Brown,Tracey Chillingworth,R. Connor,Robert L. Davies,K. Devlin,Theresa Feltwell,S. Gentles,N. Hamlin,S. Holroyd,T. Hornsby,Kay Jagels,Anders Krogh,J. McLean,Sharon Moule,Lee Murphy,K. Oliver,J. Osborne,Michael A. Quail,Marie-Adèle Rajandream,Jane Rogers,S. Rutter,K. Seeger,Jason Skelton,Rob Squares,S. Squares,John Sulston,K. Taylor,Sally Whitehead,Bart Barrell +41 more
TL;DR: The complete genome sequence of the best-characterized strain of Mycobacterium tuberculosis, H37Rv, has been determined and analysed in order to improve the understanding of the biology of this slow-growing pathogen and to help the conception of new prophylactic and therapeutic interventions.
Journal ArticleDOI
Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology.
Judith Kamerbeek,Leo M. Schouls,Arend H. J. Kolk,M van Agterveld,D. van Soolingen,Sjoukje Kuijper,Annelies Bunschoten,H Molhuizen,R J Shaw,M Goyal,J. D. A. Van Embden +10 more
TL;DR: A novel method based on strain-dependent hybridization patterns of in vitro-amplified DNA with multiple spacer oligonucleotides was found to differentiate M. bovis from M. tuberculosis, a distinction which is often difficult to make by traditional methods.
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