Macedo, RitaPinto, MiguelBorges, VítorNunes, AlexandraOliveira, OlenaPortugal, IsabelDuarte, RaquelGomes, João Paulo2020-04-232020-04-232019-03Tuberculosis (Edinb). 2019 Mar;115:81-88. doi: 10.1016/j.tube.2019.02.006. Epub 2019 Feb 251472-9792http://hdl.handle.net/10400.18/6500Supplementary 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.engGenes, BacterialGenome, BacterialGenotypeHumansMycobacterium tuberculosisPhylogenyPolymorphism, Single NucleotidePortugalProspective StudiesTuberculosis, Multidrug-ResistantWhole Genome SequencingInfecções Respiratóriasjournal article10.1016/j.tube.2019.02.006