Utilize este identificador para referenciar este registo:
https://hdl.handle.net/1822/67295
Título: | Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosis |
Autor(es): | Macedo, Rita Pinto, Miguel Borges, Vítor Nunes, Alexandra Oliveira, Olena Radomska Portugal, Isabel Duarte, Raquel Gomes, João Paulo |
Palavras-chave: | Genes, Bacterial Genome, Bacterial Genotype Humans Mycobacterium tuberculosis Phylogeny Polymorphism, Single Nucleotide Portugal Prospective Studies Tuberculosis, Multidrug-Resistant Whole Genome Sequencing Surveillance Gene-by-gene approach Multidrug-resistance |
Data: | 2019 |
Editora: | Elsevier |
Revista: | Tuberculosis |
Resumo(s): | 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. |
Tipo: | Artigo |
URI: | https://hdl.handle.net/1822/67295 |
DOI: | 10.1016/j.tube.2019.02.006 |
ISSN: | 1472-9792 |
Versão da editora: | https://www.sciencedirect.com/science/article/pii/S1472979218304748#! |
Arbitragem científica: | yes |
Acesso: | Acesso restrito UMinho |
Aparece nas coleções: | ICVS - Artigos em revistas internacionais / Papers in international journals |
Ficheiros deste registo:
Ficheiro | Descrição | Tamanho | Formato | |
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Macedo-2019-Evaluation-of-a-gene-by-gene-approa.pdf Acesso restrito! | 3,63 MB | Adobe PDF | Ver/Abrir |