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

2019-03Journal article Restricted access
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dc.contributor.authorMacedo, Rita
dc.contributor.authorPinto, Miguel
dc.contributor.authorBorges, Vítor
dc.contributor.authorNunes, Alexandra
dc.contributor.authorOliveira, Olena
dc.contributor.authorPortugal, Isabel
dc.contributor.authorDuarte, Raquel
dc.contributor.authorGomes, João Paulo
dc.date.accessioned2020-04-23T17:11:11Z
dc.date.available2020-04-23T17:11:11Z
dc.date.issued2019-03
dc.descriptionSupplementary data to this article can be found online at https:// doi.org/10.1016/j.tube.2019.02.006.pt_PT
dc.description.abstractWhole-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.pt_PT
dc.description.sponsorshipO. 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).pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationTuberculosis (Edinb). 2019 Mar;115:81-88. doi: 10.1016/j.tube.2019.02.006. Epub 2019 Feb 25pt_PT
dc.identifier.doi10.1016/j.tube.2019.02.006pt_PT
dc.identifier.issn1472-9792
dc.identifier.urihttp://hdl.handle.net/10400.18/6500
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherElsevier/ Churchill Livingstonept_PT
dc.relation.publisherversionhttps://www.sciencedirect.com/science/article/abs/pii/S1472979218304748?via%3Dihubpt_PT
dc.subjectGenes, Bacterialpt_PT
dc.subjectGenome, Bacterialpt_PT
dc.subjectGenotypept_PT
dc.subjectHumanspt_PT
dc.subjectMycobacterium tuberculosispt_PT
dc.subjectPhylogenypt_PT
dc.subjectPolymorphism, Single Nucleotidept_PT
dc.subjectPortugalpt_PT
dc.subjectProspective Studiespt_PT
dc.subjectTuberculosis, Multidrug-Resistantpt_PT
dc.subjectWhole Genome Sequencingpt_PT
dc.subjectInfecções Respiratóriaspt_PT
dc.titleEvaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosispt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.endPage88pt_PT
oaire.citation.startPage81pt_PT
oaire.citation.titleTuberculosispt_PT
oaire.citation.volume115pt_PT
rcaap.embargofctDe acordo com política editorial da revista.pt_PT
rcaap.rightsembargoedAccesspt_PT
rcaap.typearticlept_PT

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