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

Handle URI:
http://hdl.handle.net/10754/556149
Title:
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences
Authors:
Coll, Francesc; McNerney, Ruth; Preston, Mark D; Guerra-Assunção, José Afonso; Warry, Andrew; Hill-Cawthorne, Grant A. ( 0000-0002-3828-5473 ) ; Mallard, Kim; Nair, Mridul; Miranda, Anabela; Alves, Adriana; Perdigão, João; Viveiros, Miguel; Portugal, Isabel; Hasan, Zahra; Hasan, Rumina; Glynn, Judith R; Martin, Nigel; Pain, Arnab ( 0000-0002-1755-2819 ) ; Clark, Taane G
Abstract:
Mycobacterium 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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences 2015, 7 (1) Genome Medicine
Journal:
Genome Medicine
Issue Date:
27-May-2015
DOI:
10.1186/s13073-015-0164-0
PubMed ID:
26019726
PubMed Central ID:
PMC4446134
Type:
Article
ISSN:
1756-994X
Additional Links:
http://genomemedicine.com/content/7/1/51
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorColl, Francescen
dc.contributor.authorMcNerney, Ruthen
dc.contributor.authorPreston, Mark Den
dc.contributor.authorGuerra-Assunção, José Afonsoen
dc.contributor.authorWarry, Andrewen
dc.contributor.authorHill-Cawthorne, Grant A.en
dc.contributor.authorMallard, Kimen
dc.contributor.authorNair, Mridulen
dc.contributor.authorMiranda, Anabelaen
dc.contributor.authorAlves, Adrianaen
dc.contributor.authorPerdigão, Joãoen
dc.contributor.authorViveiros, Miguelen
dc.contributor.authorPortugal, Isabelen
dc.contributor.authorHasan, Zahraen
dc.contributor.authorHasan, Ruminaen
dc.contributor.authorGlynn, Judith Ren
dc.contributor.authorMartin, Nigelen
dc.contributor.authorPain, Arnaben
dc.contributor.authorClark, Taane Gen
dc.date.accessioned2015-06-02T14:28:08Zen
dc.date.available2015-06-02T14:28:08Zen
dc.date.issued2015-05-27en
dc.identifier.citationRapid determination of anti-tuberculosis drug resistance from whole-genome sequences 2015, 7 (1) Genome Medicineen
dc.identifier.issn1756-994Xen
dc.identifier.pmid26019726en
dc.identifier.doi10.1186/s13073-015-0164-0en
dc.identifier.urihttp://hdl.handle.net/10754/556149en
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.en
dc.relation.urlhttp://genomemedicine.com/content/7/1/51en
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.en
dc.titleRapid determination of anti-tuberculosis drug resistance from whole-genome sequencesen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalGenome Medicineen
dc.identifier.pmcidPMC4446134en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionFaculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UKen
dc.contributor.institutionAdvanced Data Analysis Centre, University of Nottingham, Wollaton Road, Nottingham NG8 1BB, UKen
dc.contributor.institutionSydney Emerging Infections and Biosecurity Institute and School of Public Health, University of Sydney, Sydney, Australiaen
dc.contributor.institutionTuberculosis Laboratory, Instituto Nacional de Saude Dr. Ricardo Jorge, Porto, Portugalen
dc.contributor.institutionCentro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, Lisbon, Portugalen
dc.contributor.institutionGrupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugalen
dc.contributor.institutionDepartment of Pathology & Microbiology, Aga Khan University Hospital, Karachi, Pakistanen
dc.contributor.institutionKaronga Prevention Study, Chilumba, Malawien
dc.contributor.institutionDepartment of Computer Science, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UKen
kaust.authorHill-Cawthorne, Grant A.en
kaust.authorNair, Mridulen
kaust.authorPain, Arnaben

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