Evaluation of drug susceptibility profile of Mycobacterium tuberculosis Lineage 1 from Brazil based on whole genome sequencing and phenotypic methods

Detalhes bibliográficos
Autor(a) principal: Guimarães, Arthur Emil dos Santos
Data de Publicação: 2020
Outros Autores: Sharma, Abhinav, Furlaneto, Ismari Perini, Rutaihwa, Liliana, Cardoso, Jedson Ferreira, Conceição, Marília Lima da, Spinasse, Lizânia Borges, Machado, Edson, Lopes, Maria Luiza, Duarte, Rafael Silva, Gagneux, Sebastien, Suffys, Philip Noel, Lima, Karla Valéria Batista, Conceição, Emilyn Costa
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/46373
Resumo: Universidade do Estado do Pará. Instituto de Ciências Biológicas e da Saúde. Pós-Graduação em Biologia Parasitária na Amazônia. Belém, PA, Brasil / Instituto Evandro Chagas. Seção de Bacteriologia e Micologia. Ananindeua, PA, Brasil.
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spelling Guimarães, Arthur Emil dos SantosSharma, AbhinavFurlaneto, Ismari PeriniRutaihwa, LilianaCardoso, Jedson FerreiraConceição, Marília Lima daSpinasse, Lizânia BorgesMachado, EdsonLopes, Maria LuizaDuarte, Rafael SilvaGagneux, SebastienSuffys, Philip NoelLima, Karla Valéria BatistaConceição, Emilyn Costa2021-03-17T14:05:56Z2021-03-17T14:05:56Z2020GUIMARÃES, Arthur Emil dos Santos et al. Evaluation of drug susceptibility profile of Mycobacterium tuberculosis Lineage 1 from Brazil based on whole genome sequencing and phenotypic methods. Memórias do Instituto Oswaldo Cruz, Rio de Janeiro, v. 115, p. 1-6, 2020.0074-0276https://www.arca.fiocruz.br/handle/icict/4637310.1590/0074-027602005201678-8060engFiocruz/IOCMycobacterium tuberculosisTuberculoseGenômicaResistência às drogasLinhagem 1BrasilTuberculosisGenomicDrug resistanceMycobacterium tuberculosisLineage 1BrazilEvaluation of drug susceptibility profile of Mycobacterium tuberculosis Lineage 1 from Brazil based on whole genome sequencing and phenotypic methodsinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleUniversidade do Estado do Pará. Instituto de Ciências Biológicas e da Saúde. Pós-Graduação em Biologia Parasitária na Amazônia. Belém, PA, Brasil / Instituto Evandro Chagas. Seção de Bacteriologia e Micologia. Ananindeua, PA, Brasil.International Institute of Information Technology. Department of Data Science. Bangalore, India.Universidade do Estado do Pará. Instituto de Ciências Biológicas e da Saúde. Pós-Graduação em Biologia Parasitária na Amazônia. Belém, PA, Brasil.University of Basel. Basel, Switzerland / Swiss Tropical & Public Health Institute. Basel, Switzerland.Centro de Inovações Tecnológicas, Instituto Evandro Chagas. Ananindeua, PA, Brasil.Universidade do Estado do Pará. Instituto de Ciências Biológicas e da Saúde. Pós-Graduação em Biologia Parasitária na Amazônia. Belém, PA, Brasil / Instituto Evandro Chagas. Seção de Bacteriologia e Micologia. Ananindeua, PA, Brasil.Universidade Federal do Espírito Santo. Núcleo de Doenças Infecciosas. Vitória, ES, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular de Microrganismos. Rio de Janeiro, RJ, Brasil.Universidade do Estado do Pará. Instituto de Ciências Biológicas e da Saúde. Pós-Graduação em Biologia Parasitária na Amazônia. Belém, PA, Brasil.Universidade Federal do Rio de Janeiro. Instituto de Microbiologia Professor Paulo de Góes. Laboratório de Micobactérias. Rio de Janeiro, RJ, Brasil.University of Basel. Basel, Switzerland / Swiss Tropical & Public Health Institute. Basel, Switzerland.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactérias. Rio de Janeiro, RJ, Brasil,Universidade do Estado do Pará. Instituto de Ciências Biológicas e da Saúde. Pós-Graduação em Biologia Parasitária na Amazônia. Belém, PA, Brasil / Instituto Evandro Chagas. Seção de Bacteriologia e Micologia. Ananindeua, PA, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactérias. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Programa de Pós-Graduação em Pesquisa Clínica e Doenças Infecciosas. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Bacteriologia e Bioensaios em Micobactérias. Rio de Janeiro, RJ, Brasil.Background: The evaluation of procedures for drug susceptibility prediction of Mycobacterium tuberculosis based on genomic data against the conventional reference method test based on culture is realistic considering the scenario of growing number of tools proposals based on whole-genome sequences (WGS). Objectives: This study aimed to evaluate drug susceptibility testing (DST) outcome based on WGS tools and the phenotypic methods performed on isolates of M. tuberculosis Lineage 1 from the state of Pará, Brazil, generally associated with low levels of drug resistance. Methodology: Culture based DST was performed using the Proportion Method in Löwenstein-Jensen medium on 71 isolates that had been submitted to WGS. We analysed the seven main genome sequence-based tools for resistance and lineage prediction applied to M. tuberculosis and for comparison evaluation we have used the Kappa concordance test. Findings: When comparing the WGS-based tools against the DST, we observed the highest level of agreement using TBprofiler. Among the tools, TB-profiler, KvarQ and Mykrobe were those which identified the largest number of TB-MDR cases. Comparing the four most sensitive tools regarding resistance prediction, agreement was observed for 43 genomes. Main Conclusions: Drug resistance profiling using next-generation sequencing offers rapid assessment of resistance associated mutations, therefore facilitating rapid access to effective treatment.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/46373/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALEdsonMachado_PhilipSuffys_etal_IOC_2020.pdfEdsonMachado_PhilipSuffys_etal_IOC_2020.pdfapplication/pdf1231371https://www.arca.fiocruz.br/bitstream/icict/46373/2/EdsonMachado_PhilipSuffys_etal_IOC_2020.pdf0fab22844307d196c04f1b0035e01df0MD52TEXTEdsonMachado_PhilipSuffys_etal_IOC_2020.pdf.txtEdsonMachado_PhilipSuffys_etal_IOC_2020.pdf.txtExtracted 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dc.title.pt_BR.fl_str_mv Evaluation of drug susceptibility profile of Mycobacterium tuberculosis Lineage 1 from Brazil based on whole genome sequencing and phenotypic methods
title Evaluation of drug susceptibility profile of Mycobacterium tuberculosis Lineage 1 from Brazil based on whole genome sequencing and phenotypic methods
spellingShingle Evaluation of drug susceptibility profile of Mycobacterium tuberculosis Lineage 1 from Brazil based on whole genome sequencing and phenotypic methods
Guimarães, Arthur Emil dos Santos
Mycobacterium tuberculosis
Tuberculose
Genômica
Resistência às drogas
Linhagem 1
Brasil
Tuberculosis
Genomic
Drug resistance
Mycobacterium tuberculosis
Lineage 1
Brazil
title_short Evaluation of drug susceptibility profile of Mycobacterium tuberculosis Lineage 1 from Brazil based on whole genome sequencing and phenotypic methods
title_full Evaluation of drug susceptibility profile of Mycobacterium tuberculosis Lineage 1 from Brazil based on whole genome sequencing and phenotypic methods
title_fullStr Evaluation of drug susceptibility profile of Mycobacterium tuberculosis Lineage 1 from Brazil based on whole genome sequencing and phenotypic methods
title_full_unstemmed Evaluation of drug susceptibility profile of Mycobacterium tuberculosis Lineage 1 from Brazil based on whole genome sequencing and phenotypic methods
title_sort Evaluation of drug susceptibility profile of Mycobacterium tuberculosis Lineage 1 from Brazil based on whole genome sequencing and phenotypic methods
author Guimarães, Arthur Emil dos Santos
author_facet Guimarães, Arthur Emil dos Santos
Sharma, Abhinav
Furlaneto, Ismari Perini
Rutaihwa, Liliana
Cardoso, Jedson Ferreira
Conceição, Marília Lima da
Spinasse, Lizânia Borges
Machado, Edson
Lopes, Maria Luiza
Duarte, Rafael Silva
Gagneux, Sebastien
Suffys, Philip Noel
Lima, Karla Valéria Batista
Conceição, Emilyn Costa
author_role author
author2 Sharma, Abhinav
Furlaneto, Ismari Perini
Rutaihwa, Liliana
Cardoso, Jedson Ferreira
Conceição, Marília Lima da
Spinasse, Lizânia Borges
Machado, Edson
Lopes, Maria Luiza
Duarte, Rafael Silva
Gagneux, Sebastien
Suffys, Philip Noel
Lima, Karla Valéria Batista
Conceição, Emilyn Costa
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Guimarães, Arthur Emil dos Santos
Sharma, Abhinav
Furlaneto, Ismari Perini
Rutaihwa, Liliana
Cardoso, Jedson Ferreira
Conceição, Marília Lima da
Spinasse, Lizânia Borges
Machado, Edson
Lopes, Maria Luiza
Duarte, Rafael Silva
Gagneux, Sebastien
Suffys, Philip Noel
Lima, Karla Valéria Batista
Conceição, Emilyn Costa
dc.subject.other.pt_BR.fl_str_mv Mycobacterium tuberculosis
Tuberculose
Genômica
Resistência às drogas
Linhagem 1
Brasil
topic Mycobacterium tuberculosis
Tuberculose
Genômica
Resistência às drogas
Linhagem 1
Brasil
Tuberculosis
Genomic
Drug resistance
Mycobacterium tuberculosis
Lineage 1
Brazil
dc.subject.en.pt_BR.fl_str_mv Tuberculosis
Genomic
Drug resistance
Mycobacterium tuberculosis
Lineage 1
Brazil
description Universidade do Estado do Pará. Instituto de Ciências Biológicas e da Saúde. Pós-Graduação em Biologia Parasitária na Amazônia. Belém, PA, Brasil / Instituto Evandro Chagas. Seção de Bacteriologia e Micologia. Ananindeua, PA, Brasil.
publishDate 2020
dc.date.issued.fl_str_mv 2020
dc.date.accessioned.fl_str_mv 2021-03-17T14:05:56Z
dc.date.available.fl_str_mv 2021-03-17T14:05:56Z
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.citation.fl_str_mv GUIMARÃES, Arthur Emil dos Santos et al. Evaluation of drug susceptibility profile of Mycobacterium tuberculosis Lineage 1 from Brazil based on whole genome sequencing and phenotypic methods. Memórias do Instituto Oswaldo Cruz, Rio de Janeiro, v. 115, p. 1-6, 2020.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/46373
dc.identifier.issn.pt_BR.fl_str_mv 0074-0276
dc.identifier.doi.none.fl_str_mv 10.1590/0074-02760200520
dc.identifier.eissn.none.fl_str_mv 1678-8060
identifier_str_mv GUIMARÃES, Arthur Emil dos Santos et al. Evaluation of drug susceptibility profile of Mycobacterium tuberculosis Lineage 1 from Brazil based on whole genome sequencing and phenotypic methods. Memórias do Instituto Oswaldo Cruz, Rio de Janeiro, v. 115, p. 1-6, 2020.
0074-0276
10.1590/0074-02760200520
1678-8060
url https://www.arca.fiocruz.br/handle/icict/46373
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
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dc.publisher.none.fl_str_mv Fiocruz/IOC
publisher.none.fl_str_mv Fiocruz/IOC
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