Evaluation of drug susceptibility profile of mycobacterium tuberculosis lineage 1 from brazil based on whole genome sequencing and phenotypic methods
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Digital do Instituto Evandro Chagas (Patuá) |
Texto Completo: | https://patua.iec.gov.br/handle/iec/4220 |
Resumo: | 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 resistanceassociated mutations, therefore facilitating rapid access to effective treatment. |
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Guimarães, Arthur Emil dos SantosSharma, AbhinavFurlaneto, Ismari PeriniRutaihwa, LilianaCardoso, Jedson FerreiraConceição, Marília Lima daSpinassé, Lizânia BorgesMachado, EdsonLopes, Maria LuizaDuarte, Rafael SilvaGagneux, SebastienSuffys, Philip NoelLima, Karla Valéria BatistaConceição, Emilyn Costa2021-01-26T11:08:16Z2021-01-26T11:08:16Z2020GUIMARÃES, 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, v. 115, e200250, p. 1-6, Nov. 2020.1678-8060https://patua.iec.gov.br/handle/iec/422010.1590/0074-02760200520BACKGROUND 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 resistanceassociated mutations, therefore facilitating rapid access to effective treatment.CNPq (207,071/2014-4), CAPES (Finance Code 001), Swiss National Science Foundation (grants 310030_166687 and IZRJZ3_164171)Universidade do Estado do Pará. Instituto de Ciências Biológicas e da Saúde. Pós-Graduação em Biologia Parasitária na Amazônia. Belém, PA, Brasil / Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. 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.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Centro de Inovações Tecnológicas. 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 / Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. 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 / Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. 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.engInstituto Oswaldo CruzEvaluation 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/articleTuberculose / tratamento farmacológicoMycobacterium tuberculosis / patogenicidadeGenoma / efeitos dos fármacosSequenciamento Completo do GenomaResistência a Medicamentosinfo:eu-repo/semantics/openAccessreponame:Repositório Digital do Instituto Evandro Chagas (Patuá)instname:Instituto Evandro Chagas (IEC)instacron:IECORIGINALEvaluation of drug susceptibility profile of mycobacterium tuberculosis lineage 1 from brazil based on whole genome sequencing and phenotypic methods.pdfEvaluation of drug susceptibility profile of mycobacterium tuberculosis lineage 1 from brazil based on whole genome sequencing and phenotypic methods.pdfapplication/pdf1231361https://patua.iec.gov.br/bitstreams/d79bbede-61fd-4b6c-959f-5e7b45be1de1/download64be488447b06b0a5463873766027a1eMD51LICENSElicense.txtlicense.txttext/plain; charset=utf-82182https://patua.iec.gov.br/bitstreams/c802db86-a547-4a2e-a164-7132a7d4a402/download11832eea31b16df8613079d742d61793MD52TEXTEvaluation of drug susceptibility profile of mycobacterium tuberculosis lineage 1 from brazil based on whole genome sequencing and phenotypic methods.pdf.txtEvaluation of drug susceptibility profile of mycobacterium tuberculosis lineage 1 from brazil based on whole genome sequencing and phenotypic methods.pdf.txtExtracted texttext/plain28862https://patua.iec.gov.br/bitstreams/a763b344-94e5-4c08-a9ed-549fc47203bc/downloade2eae6b2020a6709208f0dd70d550f06MD55THUMBNAILEvaluation of drug susceptibility profile of mycobacterium tuberculosis lineage 1 from brazil based on whole genome sequencing and phenotypic methods.pdf.jpgEvaluation of drug susceptibility profile of mycobacterium tuberculosis lineage 1 from brazil based on whole genome sequencing and phenotypic methods.pdf.jpgGenerated Thumbnailimage/jpeg5752https://patua.iec.gov.br/bitstreams/9ae32cc1-8df0-453b-bf4b-9b77844728ae/download071a0f65bb1d19c435cdcd8cd7001b5cMD56iec/42202022-10-20 23:55:53.394oai:patua.iec.gov.br:iec/4220https://patua.iec.gov.brRepositório InstitucionalPUBhttps://patua.iec.gov.br/oai/requestclariceneta@iec.gov.br || Biblioteca@iec.gov.bropendoar:2022-10-20T23:55:53Repositório Digital do Instituto Evandro Chagas (Patuá) - Instituto Evandro Chagas (IEC)falsePGI+TGljZW7Dp2EgZGUgRGlzdHJpYnVpw6fDo28gTsOjbyBFeGNsdXNpdmE8L2I+DQoNClRvZG8gZGVwb3NpdGFudGUgZGUgbWF0ZXJpYWwgbm8gUGF0dcOhIGRldmUgY29uY2VkZXIgYW8gSW5zdGl0dXRvIEV2YW5kcm8gQ2hhZ2FzIHVtYSBMaWNlbsOnYSBkZSBEaXN0cmlidWnDp8OjbyBOw6NvIEV4Y2x1c2l2YSBwYXJhIHRvcm5hciBlIG1hbnRlciBhY2Vzc8OtdmVpcyBvcyBzZXVzIGRvY3VtZW50b3MgZW0gZm9ybWF0byBkaWdpdGFsLiANCg0KQ29tIGEgY29uY2Vzc8OjbyBkZXNzYSBsaWNlbsOnYSBuw6NvIGV4Y2x1c2l2YSwgbyBkZXBvc2l0YW50ZSBjb250aW51YSBhIHJldGVyIHRvZG9zIG9zIGRpcmVpdG9zIGRlIGF1dG9yLg0KDQpBbyBhc3NpbmFyIGUgZW50cmVnYXIgZXN0YSBsaWNlbsOnYSB2b2PDqiAoYXV0b3Igb3UgZGV0ZW50b3IgZG9zIGRpcmVpdG9zIGF1dG9yYWlzKQ0KDQphKSBEZWNsYXJhIHF1ZSBjb25oZWNlIGEgcG9sw610aWNhIGRlIGNvcHlyaWdodCBkYSBlZGl0b3JhIGRlIHNldSBkb2N1bWVudG8uDQoNCmIpIENvbmNlZGUgYW8gSW5zdGl0dXRvIEV2YW5kcm8gQ2hhZ2FzIG8gZGlyZWl0byBuw6NvIGV4Y2x1c2l2byBkZSBhcnF1aXZhciwgcmVwcm9kdXppciwgY29udmVydGVyIChjb21vIGRlZmluaWRvIGEgc2VndWlyKSwgY29tdW5pY2FyIGUvb3UgZGlzdHJpYnVpciBubyA8Yj5QYXR1w6E8L2I+LCBvIGRvY3VtZW50byBlbnRyZWd1ZSAoaW5jbHVpbmRvIG8gcmVzdW1vL2Fic3RyYWN0KSBlbSBmb3JtYXRvIGRpZ2l0YWwgb3UgcG9yIHF1YWxxdWVyIG91dHJvIG1laW8uDQoNCmMpIERlY2xhcmEgcXVlIGF1dG9yaXphIG8gSW5zdGl0dXRvIEV2YW5kcm8gQ2hhZ2FzIGEgYXJxdWl2YXIgbWFpcyBkZSB1bWEgY8OzcGlhIGRlc3NlIGRvY3VtZW50byBlIGNvbnZlcnTDqi1sbywgc2VtIGFsdGVyYXIgbyBzZXUgY29udGXDumRvLCBwYXJhIHF1YWxxdWVyIGZvcm1hdG8gZGUgZmljaGVpcm8sIG1laW8gb3Ugc3Vwb3J0ZSwgcGFyYSBlZmVpdG9zIGRlIHNlZ3VyYW7Dp2EsIHByZXNlcnZhw6fDo28gKGJhY2t1cCkgZSBhY2Vzc28uDQoNCmQpIERlY2xhcmEgcXVlIG8gZG9jdW1lbnRvIHN1Ym1ldGlkbyDDqSBvIHNldSB0cmFiYWxobyBvcmlnaW5hbCBlIHF1ZSBkZXTDqW0gbyBkaXJlaXRvIGRlIGNvbmNlZGVyIGEgdGVyY2Vpcm9zIG9zIGRpcmVpdG9zIGNvbnRpZG9zIG5lc3RhIGxpY2Vuw6dhLiBEZWNsYXJhIHRhbWLDqW0gcXVlIGEgZW50cmVnYSBkbyBkb2N1bWVudG8gbsOjbyBpbmZyaW5nZSBvcyBkaXJlaXRvcyBkZSBxdWFscXVlciBvdXRyYSBwZXNzb2Egb3UgZW50aWRhZGUuDQoNCmUpIERlY2xhcmEgcXVlLCBubyBjYXNvIGRvIGRvY3VtZW50byBzdWJtZXRpZG8gY29udGVyIG1hdGVyaWFsIGRvIHF1YWwgbsOjbyBkZXTDqW0gb3MgZGlyZWl0b3MgZGUgYXV0b3IsIG9idGV2ZSBhIGF1dG9yaXphw6fDo28gaXJyZXN0cml0YSBkbyByZXNwZWN0aXZvIGRldGVudG9yIGRlc3NlcyBkaXJlaXRvcywgcGFyYSBjZWRlciBhbyBJbnN0aXR1dG8gRXZhbmRybyBDaGFnYXMgb3MgZGlyZWl0b3MgcmVxdWVyaWRvcyBwb3IgZXN0YSBMaWNlbsOnYSBlIGF1dG9yaXphciBhIHV0aWxpesOhLWxvcyBsZWdhbG1lbnRlLiBEZWNsYXJhIHRhbWLDqW0gcXVlIGVzc2UgbWF0ZXJpYWwgY3Vqb3MgZGlyZWl0b3Mgc8OjbyBkZSB0ZXJjZWlyb3MgZXN0w6EgY2xhcmFtZW50ZSBpZGVudGlmaWNhZG8gZSByZWNvbmhlY2lkbyBubyB0ZXh0byBvdSBjb250ZcO6ZG8gZG8gZG9jdW1lbnRvIGVudHJlZ3VlLg0KDQpmKSBTRSBPIERPQ1VNRU5UTyBFTlRSRUdVRSBGT1IgQkFTRUFETyBFTSBUUkFCQUxITyBGSU5BTkNJQURPIE9VIEFQT0lBRE8gUE9SIE9VVFJBIElOU1RJVFVJw4fDg08gUVVFIE7Dg08gTyBJTlNUSVRVVE8gRVZBTkRSTyBDSEFHQVMsIERFQ0xBUkEgUVVFIENVTVBSSVUgUVVBSVNRVUVSIE9CUklHQcOHw5VFUyBFWElHSURBUyBQRUxPIFJFU1BFQ1RJVk8gQ09OVFJBVE8gT1UgQUNPUkRPLg0KDQpPIEluc3RpdHV0byBFdmFuZHJvIENoYWdhcyBpZGVudGlmaWNhcsOhIGNsYXJhbWVudGUgbyhzKSBub21lKHMpIGRvKHMpIGF1dG9yKGVzKSBkb3MgZGlyZWl0b3MgZG8gZG9jdW1lbnRvIGVudHJlZ3VlIGUgbsOjbyBmYXLDoSBxdWFscXVlciBhbHRlcmHDp8OjbyBhbMOpbSBkbyBwcmV2aXN0byBuYSBhbMOtbmVhIGIpLg== |
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 Tuberculose / tratamento farmacológico Mycobacterium tuberculosis / patogenicidade Genoma / efeitos dos fármacos Sequenciamento Completo do Genoma Resistência a Medicamentos |
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 Spinassé, 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 Spinassé, 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 Spinassé, Lizânia Borges Machado, Edson Lopes, Maria Luiza Duarte, Rafael Silva Gagneux, Sebastien Suffys, Philip Noel Lima, Karla Valéria Batista Conceição, Emilyn Costa |
dc.subject.decsPrimary.pt_BR.fl_str_mv |
Tuberculose / tratamento farmacológico Mycobacterium tuberculosis / patogenicidade Genoma / efeitos dos fármacos Sequenciamento Completo do Genoma Resistência a Medicamentos |
topic |
Tuberculose / tratamento farmacológico Mycobacterium tuberculosis / patogenicidade Genoma / efeitos dos fármacos Sequenciamento Completo do Genoma Resistência a Medicamentos |
description |
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 resistanceassociated mutations, therefore facilitating rapid access to effective treatment. |
publishDate |
2020 |
dc.date.issued.fl_str_mv |
2020 |
dc.date.accessioned.fl_str_mv |
2021-01-26T11:08:16Z |
dc.date.available.fl_str_mv |
2021-01-26T11:08:16Z |
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, v. 115, e200250, p. 1-6, Nov. 2020. |
dc.identifier.uri.fl_str_mv |
https://patua.iec.gov.br/handle/iec/4220 |
dc.identifier.issn.-.fl_str_mv |
1678-8060 |
dc.identifier.doi.-.fl_str_mv |
10.1590/0074-02760200520 |
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, v. 115, e200250, p. 1-6, Nov. 2020. 1678-8060 10.1590/0074-02760200520 |
url |
https://patua.iec.gov.br/handle/iec/4220 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.publisher.none.fl_str_mv |
Instituto Oswaldo Cruz |
publisher.none.fl_str_mv |
Instituto Oswaldo Cruz |
dc.source.none.fl_str_mv |
reponame:Repositório Digital do Instituto Evandro Chagas (Patuá) instname:Instituto Evandro Chagas (IEC) instacron:IEC |
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Instituto Evandro Chagas (IEC) |
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IEC |
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IEC |
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Repositório Digital do Instituto Evandro Chagas (Patuá) |
collection |
Repositório Digital do Instituto Evandro Chagas (Patuá) |
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