Computational protocol: Diversity of Group I and II Clostridium botulinum Strains from France Including Recently Identified Subtypes

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Protocol publication

[…] Whole genome sequencing using the NEBNext Ultra DNA Library Prep kit for Illumina (New England Biolabs) were performed using MiSeq machine (Illumina) in paired-end reads of 250 bases or on HiSeq2000 machine (Illumina) in single reads of 96 bases or 101 bases. Sequence files were generated using Illumina Analysis Pipeline version 1.8 (CASAVA). After quality filtering, reads were assembled using CLC software version 4 (CLC Bio). [...] Multilocus sequence typing of group II strains was based on 12 housekeeping gene sequences (oppB, pta, recA, rpoB, pyc, gyrB, lepA, ilvD, guaA, atpD, trpB, 23S) as described in (; ). Allele sequences were concatenated and were aligned with Muscle (default parameters). Maximum Likelihood phylogenetic tree was built based on the Kimura 2-parameter model (). About 1,000 boostrap experiments were performed to assess the robustness of the topology and percent are indicated on nodes. Evolutionary analyses were conducted in MEGA (). […]

Pipeline specifications

Software tools BaseSpace, MEGA
Applications Phylogenetics, WGS analysis
Organisms Clostridium botulinum, Homo sapiens
Diseases Botulism