Author(s):
Macedo, Rita ; Pinto, Miguel ; Borges, Vítor ; Nunes, Alexandra ; Oliveira, Olena ; Portugal, Isabel ; Duarte, Raquel ; Gomes, João Paulo
Date: 2019
Persistent ID: http://hdl.handle.net/10400.18/6500
Origin: Repositório Científico do Instituto Nacional de Saúde
Subject(s): Genes, Bacterial; Genome, Bacterial; Genotype; Humans; Mycobacterium tuberculosis; Phylogeny; Polymorphism, Single Nucleotide; Portugal; Prospective Studies; Tuberculosis, Multidrug-Resistant; Whole Genome Sequencing; Infecções Respiratórias
Description
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.
