Molecular Typing and Phylogenetic Analysis of Mycobacterium tuberculosis

Molecular typing data were analyzed with the BioNumerics software (version 6.5; Applied Maths, Sint-Martens-Latem, Belgium) as instructed by the manufacturer. Similarities of spoligotyping and MIRU-VNTR patterns were calculated by using the categorical coefficient. Classification of the Hamburg strain collection in MTBC genotypes was carried out by using the MIRU-VNTRplus database [14] (link), [19] (link). Analysis of sequence data and SNP detection was performed by using SeqScape v2.6 software (Applied Biosystems). Genome sequences of M. tuberculosis H37Rv (http://tuberculist.epfl.ch/) were used as a reference sequence. Calculation of a maximum parsimony phylogenetic tree based on SNP data of the Hamburg strain collection was performed with BioNumerics. A maximum likelihood phylogenetic tree was constructed based on an alignment of SNPs discovered in 26 genes from the reference collection isolates by applying Treefinder software (available at http://www.treefinder.de/) and using the HKY model of DNA substitution. Bootstrap support was calculated based on 1,000 replicates.
More details about procedures for analysis of typing data are described elsewhere [19] (link)–[21] .

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Homolka S., Projahn M., Feuerriegel S., Ubben T., Diel R., Nübel U, & Niemann S. (2012). High Resolution Discrimination of Clinical Mycobacterium tuberculosis Complex Strains Based on Single Nucleotide Polymorphisms. PLoS ONE, 7(7), e39855.

Publication 2012

Genes Genome Genotypes M tuberculosis h37rv Martens Sequence analysis Snps Strain

Corresponding Organization :

Other organizations : Research Center Borstel - Leibniz Lung Center, Medizinische Hochschule Hannover, Robert Koch Institute

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Variable analysis

independent variables

Molecular typing data analysis with BioNumerics software
Classification of Hamburg strain collection in MTBC genotypes using MIRU-VNTR plus database
Analysis of sequence data and SNP detection using SeqScape v2.6 software
Calculation of maximum parsimony phylogenetic tree based on SNP data using BioNumerics
Construction of maximum likelihood phylogenetic tree based on SNP alignment using Treefinder software

dependent variables

Similarities of spoligotyping and MIRU-VNTR patterns
SNP data of the Hamburg strain collection
SNPs discovered in 26 genes from the reference collection isolates

control variables

Genome sequences of M. tuberculosis H37Rv as a reference sequence

positive controls

None specified

negative controls

None specified

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