Computational protocol: Identification and diversity of multiresistant Corynebacterium striatum clinical isolates by MALDI TOF mass spectrometry and by a multigene sequencing approach

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Protocol publication

[…] Allele and nucleotide diversities were calculated from the gene sequences with the DnaSP package, version 3.51 []. For identification purposes, distinct allele sequences were assigned arbitrary allele numbers for each locus. For each isolate, the combination of alleles obtained at each locus defined its allelic profile. Each allelic profile constitutes a sequence type (ST), and isolates with identical profiles belonged to the same ST. Clustering of STs was performed with the Sequence Type Analysis and Recombinational Tests (START) program []. The matrix of pair-wise distances between the allelic profiles was converted to NEXUS files, and the split decomposition was analysed with the SplitsTree software program, vs. 4 []. Splits tree allowed researchers to visualise clustering within the population and to detect recombination between STs. The nucleotide sequences determined in this study for the different alleles of each locus have been deposited in the EMBL database under the accession numbers HE586270 to HE586309. […]

Pipeline specifications

Software tools DnaSP, SplitsTree
Application Phylogenetics
Organisms Corynebacterium striatum, Homo sapiens
Diseases Pulmonary Disease, Chronic Obstructive