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Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

dc.contributor.authorColl, Francesc
dc.contributor.authorMcNerney, Ruth
dc.contributor.authorPreston, Mark D
dc.contributor.authorGuerra-Assunção, José Afonso
dc.contributor.authorWarry, Andrew
dc.contributor.authorHill-Cawthorne, Grant A.
dc.contributor.authorMallard, Kim
dc.contributor.authorNair, Mridul
dc.contributor.authorMiranda, Anabela
dc.contributor.authorAlves, Adriana
dc.contributor.authorPerdigão, João
dc.contributor.authorViveiros, Miguel
dc.contributor.authorPortugal, Isabel
dc.contributor.authorHasan, Zahra
dc.contributor.authorHasan, Rumina
dc.contributor.authorGlynn, Judith R.
dc.contributor.authorMartin, Nigel
dc.contributor.authorPain, Arnab
dc.contributor.authorClark, Taane G.
dc.date.accessioned2015-06-02T14:28:08Z
dc.date.available2015-06-02T14:28:08Z
dc.date.issued2015-05-27
dc.identifier.citationRapid determination of anti-tuberculosis drug resistance from whole-genome sequences 2015, 7 (1) Genome Medicine
dc.identifier.issn1756-994X
dc.identifier.pmid26019726
dc.identifier.doi10.1186/s13073-015-0164-0
dc.identifier.urihttp://hdl.handle.net/10754/556149
dc.description.abstractMycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequencing approaches could fully characterise DR, data complexity has restricted their clinical application. A library (1,325 mutations) predictive of DR for 15 anti-tuberculosis drugs was compiled and validated for 11 of them using genomic-phenotypic data from 792 strains. A rapid online ‘TB-Profiler’ tool was developed to report DR and strain-type profiles directly from raw sequences. Using our DR mutation library, in silico diagnostic accuracy was superior to some commercial diagnostics and alternative databases. The library will facilitate sequence-based drug-susceptibility testing.
dc.publisherSpringer Nature
dc.relation.urlhttp://genomemedicine.com/content/7/1/51
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.titleRapid determination of anti-tuberculosis drug resistance from whole-genome sequences
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentPathogen Genomics Laboratory
dc.identifier.journalGenome Medicine
dc.identifier.pmcidPMC4446134
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionFaculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
dc.contributor.institutionAdvanced Data Analysis Centre, University of Nottingham, Wollaton Road, Nottingham NG8 1BB, UK
dc.contributor.institutionSydney Emerging Infections and Biosecurity Institute and School of Public Health, University of Sydney, Sydney, Australia
dc.contributor.institutionTuberculosis Laboratory, Instituto Nacional de Saude Dr. Ricardo Jorge, Porto, Portugal
dc.contributor.institutionCentro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, Lisbon, Portugal
dc.contributor.institutionGrupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
dc.contributor.institutionDepartment of Pathology & Microbiology, Aga Khan University Hospital, Karachi, Pakistan
dc.contributor.institutionKaronga Prevention Study, Chilumba, Malawi
dc.contributor.institutionDepartment of Computer Science, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
kaust.personHill-Cawthorne, Grant A.
kaust.personNair, Mridul
kaust.personPain, Arnab
refterms.dateFOA2018-06-14T07:58:05Z
dc.date.published-online2015-05-27
dc.date.published-print2015-12


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