Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences
Autor(a) principal: | |
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Data de Publicação: | 2015 |
Outros Autores: | , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10400.18/3554 |
Resumo: | 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. |
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Rapid determination of anti-tuberculosis drug resistance from whole-genome sequencesTuberculosisDrug ResistanceWhole Genome SequencesInfecções RespiratóriasMycobacterium 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.Bloomsbury Research Fund; Fundação para a Ciência e Tecnologia (grant number PTDC/SAU-ESA/71208/2006); King Abdullah University of Science and Technology (KAUST); Medical Research Council UK (grant number MR/K000551/1); Wellcome Trust (grant number 096249/Z/11/B)BioMed CentralRepositório Científico do Instituto Nacional de SaúdeColl, FrancescMcNerney, RuthPreston, Mark D.Guerra-Assunção, José AfonsoWarry, AndrewHill-Cawthorne, GrantMallard, KimNair, MridulMiranda, AnabelaAlves, AdrianaPerdigão, JoãoViveiros, MiguelPortugal, IsabelHasan, ZahraHasan, RuminaGlynn, Judith R.Martin, NigelPain, ArnabClark, Taane G.2016-03-01T16:36:41Z2015-05-272015-05-27T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.18/3554engGenome Med. 2015 May 27;7(1):51. doi: 10.1186/s13073-015-0164-0. eCollection 2015.1756-994X10.1186/s13073-015-0164-0info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-20T15:39:51Zoai:repositorio.insa.pt:10400.18/3554Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T18:38:24.525530Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences |
title |
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences |
spellingShingle |
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences Coll, Francesc Tuberculosis Drug Resistance Whole Genome Sequences Infecções Respiratórias |
title_short |
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences |
title_full |
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences |
title_fullStr |
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences |
title_full_unstemmed |
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences |
title_sort |
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences |
author |
Coll, Francesc |
author_facet |
Coll, Francesc McNerney, Ruth Preston, Mark D. Guerra-Assunção, José Afonso Warry, Andrew Hill-Cawthorne, Grant 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 Clark, Taane G. |
author_role |
author |
author2 |
McNerney, Ruth Preston, Mark D. Guerra-Assunção, José Afonso Warry, Andrew Hill-Cawthorne, Grant 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 Clark, Taane G. |
author2_role |
author author author author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Repositório Científico do Instituto Nacional de Saúde |
dc.contributor.author.fl_str_mv |
Coll, Francesc McNerney, Ruth Preston, Mark D. Guerra-Assunção, José Afonso Warry, Andrew Hill-Cawthorne, Grant 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 Clark, Taane G. |
dc.subject.por.fl_str_mv |
Tuberculosis Drug Resistance Whole Genome Sequences Infecções Respiratórias |
topic |
Tuberculosis Drug Resistance Whole Genome Sequences Infecções Respiratórias |
description |
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. |
publishDate |
2015 |
dc.date.none.fl_str_mv |
2015-05-27 2015-05-27T00:00:00Z 2016-03-01T16:36:41Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10400.18/3554 |
url |
http://hdl.handle.net/10400.18/3554 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Genome Med. 2015 May 27;7(1):51. doi: 10.1186/s13073-015-0164-0. eCollection 2015. 1756-994X 10.1186/s13073-015-0164-0 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
BioMed Central |
publisher.none.fl_str_mv |
BioMed Central |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
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1799132121609011200 |