Molecular typing of bacteria from the Mycobacterium tuberculosis complex (MTBC)
is essential for epidemiological purposes such as investigating the spreading of
specific genotypes. Recently, mycobacterial interspersed repetitive units (MIRU)
typing has become an important method, as it allows high-throughput, discriminatory
and reproducible analysis of clinical isolates.
MIRU is a MTBC specific name of a multiple locus VNTR [variable number of tandem repeats] analysis (MLVA) bacterial typing scheme.
Because of its portable data format, MIRU typing
has the potential to be a versatile tool for individual strain identification based on large
However, specialized bioinformatic web tools to analyze MIRU data and public reference databases are not available.
To meet this need, a collection of 186 strains representing the major MTBC lineages
was used for implementing a
web server, MIRU-VNTRplus (http://www.miru-vntrplus.org/). For each strain species, lineage, and epidemiologic
information was stored together with copy numbers of 24 MIRU loci, spoligotyping patterns, regions of difference (RD)
profiles, single nucleotide polymorphisms (SNPs), susceptibility data, and IS6110 RFLP fingerprint images.
Via the freely accessible MIRU-VNTRplus service users can compare their strain(s) with the reference strains for the assignment
of MTBC species, lineages, and genotypes. For easier scientific communication a universal expanding nomenclature (MLVA MtbC15-9) to name
different MIRU genotypes is maintained at the server. Comparisons can be based on MIRU-, spoligo-, RD-, SNP-, susceptibility-typing
data, or by a combination of different data types. Several distance coefficients are available, including Jaccard's and
categorical. Based upon the respective distance matrix, a dendrogram can be calculated using UPGMA or neighbor-joining clustering
algorithms. The resulting trees may be exported in various data formats. MIRU-VNTRplus provides also functions for the user to
analyze own strains without interrogating the reference database. Extensive documentation (manual and tutorials) of the service
is available to make best use of all features.
Users are asked to cite
Weniger T, Krawczyk J, Supply P, Niemann S, Harmsen, D.
MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis
Nucleic Acids Res 2010, 38 Suppl:W326-331
Allix-Béguec C, Harmsen D, Weniger T, Supply P, Niemann S.
Evaluation and user-strategy of MIRU-VNTRplus, a multifunctional database for online analysis of
genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates.
J Clin Microbiol 2008, 46(8):2692-2699 [Pubmed]
in publications that benefit from this database.