Computational protocol: Vancomycin-resistant Enterococcus faecium sequence type 796 - rapid international dissemination of a new epidemic clone

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Protocol publication

[…] Short read sequencing libraries were generated from genomic DNA using the Illumina Nextera XT DNA sample preparation kit. Libraries were sequenced on the Illumina platform using either the MiSeq with 250-cycle paired end chemistry or the NextSeq 500 with 150-cycle paired end chemistry according to the manufacturer’s instructions.Snippy v3.2 (https://github.com/tseemann/snippy) was used to map sequence reads against the fully assembled Ef_aus0233 genome (GenBank accession no. PRJEB14733), a representative of the ST796 lineage []. Single nucleotide polymorphisms (SNPs) in core genome positions were used to construct a Maximum Likelihood tree with FastTree v2.1.8 []. The tree was used as a guide for ClonalFrame v1.7 to infer regions of recombination []. As previously described, a robust and recombination-free tree was generated []. Tree branches with less than 70% bootstrap support (500 replicates) were collapsed. Pairwise core non-recombinogenic SNP differences between isolates were tabulated and visualized using a custom R-script (https://github.com/MDU-PHL/pairwise_snp_differences). […]

Pipeline specifications

Software tools Snippy, FastTree, ClonalFrame
Application WGS analysis
Organisms Enterococcus faecium, Homo sapiens
Diseases Infection
Chemicals Vancomycin