Validation and implementation of whole-genome sequencing-based analytical methods for molecular surveillance and relatedness analysis of Mycobacterium tuberculosis complex isolates at a national reference laboratory

Whole genome sequencing-based methodologies have become extremely relevant for the molecular surveillance of human pathogens and are being increasingly introduced into national reference laboratory services. In this study, we describe the validation and implementation of core-genome Multi-Locus Sequence Typing (cgMLST) and whole genome single-nucleotide polymorphism (wgSNP) analysis at the Irish Mycobacteria Reference Laboratory, as a replacement for Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) typing. Concordance of clustering, discriminatory power, and ease-of-use of both WGS analytical methods were evaluated. Although wgSNP analysis (MTBseq) was the most discriminatory method (<i>p</i> < 0,001), we recommend cgMLST (SeqSphere⁺), as the first-line approach for molecular typing of <i>Mycobacterium tuberculosis</i> isolates in the context of routine surveillance work due to its ease of use and decreased turnaround time, while reserving wgSNP-analysis for a more in-depth cluster analysis of new isolates that show a distance of ≤12 alleles to any other isolate(s) in the cgMLST database.