Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosis
Autor(a) principal: | |
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Data de Publicação: | 2019 |
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/10400.18/6500 |
Resumo: | Supplementary data to this article can be found online at https:// doi.org/10.1016/j.tube.2019.02.006. |
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Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosisGenes, BacterialGenome, BacterialGenotypeHumansMycobacterium tuberculosisPhylogenyPolymorphism, Single NucleotidePortugalProspective StudiesTuberculosis, Multidrug-ResistantWhole Genome SequencingInfecções RespiratóriasSupplementary data to this article can be found online at https:// doi.org/10.1016/j.tube.2019.02.006.Whole-genome sequencing (WGS) offers unprecedented resolution for tracking Mycobacterium tuberculosis transmission and antibiotic-resistance spread. Still, the establishment of standardized WGS-based pipelines and the definition of epidemiological clusters based on genetic relatedness are under discussion. We aimed to implement a dynamic gene-by-gene approach, fully relying on freely available software, for prospective WGS-based tuberculosis surveillance, demonstrating its application for detecting transmission chains by retrospectively analysing all M/XDR strains isolated in 2013-2017 in Portugal. We observed a good correlation between genetic relatedness and epidemiological links, with strongly epilinked clusters displaying mean pairwise allele differences (AD) always below 0.3% (ratio of mean AD over the total number of shared loci between same-cluster strains). This data parallels the genetic distances acquired by the core-SNV analysis, while providing higher resolution and epidemiological concordance than MIRU-VNTR genotyping. The dynamic analysis of strain sub-sets (i.e., increasing the number of shared loci within each sub-set) also strengthens the confidence in detecting epilinked clusters. This gene-by-gene strategy also offers several practical benefits (e.g., reliance on freely-available software, scalability and low computational requirements) that further consolidated its suitability for a timely and robust prospective WGS-based laboratory surveillance of M/XDR-TB cases.O. Oliveira is supported by the Project NORTE-08-5369-FSE000041, financed by the Operational Program NORTE 2020 and cofinanced by the European Social Fund through a doctoral grant (grant number UMINHO/BD/47/2016).Elsevier/ Churchill LivingstoneRepositório Científico do Instituto Nacional de SaúdeMacedo, RitaPinto, MiguelBorges, VítorNunes, AlexandraOliveira, OlenaPortugal, IsabelDuarte, RaquelGomes, João Paulo2020-04-23T17:11:11Z2019-032019-03-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.18/6500engTuberculosis (Edinb). 2019 Mar;115:81-88. doi: 10.1016/j.tube.2019.02.006. Epub 2019 Feb 251472-979210.1016/j.tube.2019.02.006info:eu-repo/semantics/embargoedAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-20T15:41:43Zoai:repositorio.insa.pt:10400.18/6500Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T18:41:34.809308Repositório 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 |
Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosis |
title |
Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosis |
spellingShingle |
Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosis Macedo, Rita Genes, Bacterial Genome, Bacterial Genotype Humans Mycobacterium tuberculosis Phylogeny Polymorphism, Single Nucleotide Portugal Prospective Studies Tuberculosis, Multidrug-Resistant Whole Genome Sequencing Infecções Respiratórias |
title_short |
Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosis |
title_full |
Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosis |
title_fullStr |
Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosis |
title_full_unstemmed |
Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosis |
title_sort |
Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosis |
author |
Macedo, Rita |
author_facet |
Macedo, Rita Pinto, Miguel Borges, Vítor Nunes, Alexandra Oliveira, Olena Portugal, Isabel Duarte, Raquel Gomes, João Paulo |
author_role |
author |
author2 |
Pinto, Miguel Borges, Vítor Nunes, Alexandra Oliveira, Olena Portugal, Isabel Duarte, Raquel Gomes, João Paulo |
author2_role |
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 |
Macedo, Rita Pinto, Miguel Borges, Vítor Nunes, Alexandra Oliveira, Olena Portugal, Isabel Duarte, Raquel Gomes, João Paulo |
dc.subject.por.fl_str_mv |
Genes, Bacterial Genome, Bacterial Genotype Humans Mycobacterium tuberculosis Phylogeny Polymorphism, Single Nucleotide Portugal Prospective Studies Tuberculosis, Multidrug-Resistant Whole Genome Sequencing Infecções Respiratórias |
topic |
Genes, Bacterial Genome, Bacterial Genotype Humans Mycobacterium tuberculosis Phylogeny Polymorphism, Single Nucleotide Portugal Prospective Studies Tuberculosis, Multidrug-Resistant Whole Genome Sequencing Infecções Respiratórias |
description |
Supplementary data to this article can be found online at https:// doi.org/10.1016/j.tube.2019.02.006. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-03 2019-03-01T00:00:00Z 2020-04-23T17:11:11Z |
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/10400.18/6500 |
url |
http://hdl.handle.net/10400.18/6500 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Tuberculosis (Edinb). 2019 Mar;115:81-88. doi: 10.1016/j.tube.2019.02.006. Epub 2019 Feb 25 1472-9792 10.1016/j.tube.2019.02.006 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/embargoedAccess |
eu_rights_str_mv |
embargoedAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Elsevier/ Churchill Livingstone |
publisher.none.fl_str_mv |
Elsevier/ Churchill Livingstone |
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 |
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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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1799132160755499008 |