Evaluation and user-strategy of MIRU-VNTRplus, a multifunctional database for on-line analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates.

Because of its portable data, discriminatory power, and recently proposed standardization, mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing has become a major method for epidemiological tracking of Mycobacterium tuberculosis complex (MTBC) clones. However, no public MIRU-VNTR database based on well-characterized reference strains was available hitherto for easy strain identification. Therefore, a collection of 186 reference strains representing the primary MTBC lineages was used to build up a database freely accessible at http://www.MIRU-VNTRplus.org. For each strain, geographical origin and drug-susceptibility profile was stored together with comprehensive genetic lineage information including 24-locus MIRU-VNTR profile, spoligotyping pattern, single nucleotide and large sequence polymorphism profile, and IS6110 restriction fragment length polymorphism fingerprint. Thanks to flexible import functions, single or multiple user strain(s) can be analyzed e.g. for lineage identification with or without using reference strains, by best-match or tree-based analyses employing single or combined marker datasets. Results can be easily exported. Here, we evaluated the database consistency and various analysis parameters, both by testing the reference collection against itself and by using an external population-based dataset comprising 629 different strains. In the optimal conditions found, lineage predictions based on 24-locus MIRU-VNTR-typing optionally combined with spoligotyping were verified in > 99% of the cases. Based on this evaluation, a user-strategy was defined, including best match analysis followed, if necessary, by tree-based analysis. The MIRU-VNTRplus database is a powerful tool for high-resolution clonal identification, which has little equivalent in terms of functionalities among the bacterial genotyping databases available so far.