Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosis

Detalhes bibliográficos
Autor(a) principal: Macedo, Rita
Data de Publicação: 2019
Outros Autores: Pinto, Miguel, Borges, Vítor, Nunes, Alexandra, Oliveira, Olena, Portugal, Isabel, Duarte, Raquel, Gomes, João Paulo
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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spelling 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
instname_str 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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