Computational protocol: Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC

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Protocol publication

[…] Fastq files for the isolates were mapped against the mecC-MRSA reference genome LGA251 (EMBL accession no: FR821779) using SMALT (http://www.sanger.ac.uk/smalt) in order to identify SNPs, as previously described (Koser et al, ). SNPs located in mobile genetic elements (Supporting Information Table 1) or low quality regions (insertions and deletions (Indels)/low coverage/repeat regions) (Supporting Information Table 2) were identified by manual inspection and removed from the alignment. The maximum likelihood tree was generated from the resulting SNPs present in the core genome (the core genome being defined as the regions of the chromosome not excluded when all Indel and mobile genetic elements were removed) usingRAxML (Stamatakis et al, ). Insertions and deletions (indels) were identified as previously described (Croucher et al, ). Indels of potential biological interest were manually accessed using BAM files mapped on the reference. Comparison of the mobile genetic content of the isolates was assessed by BLAST analysis against Velvet de novo assemblies using known S. aureus mobile elements and phage integrases downloaded from EMBL and NCBI databases (Zerbino & Birney, ). Comparative genomics were carried out using Velvet de novo assemblies with contigs realigned using Mauve (Darling et al, ) and manually using Artemis comparison tool (Carver et al, ). S. aureus virulence factors from the literature were identified using BLAST against Velvet assemblies. […]

Pipeline specifications

Software tools SMALT, Velvet, Mauve, ACT
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Staphylococcus aureus, Homo sapiens
Diseases Bacterial Infections, Infection
Chemicals Methicillin, Nucleotides