Whole Genome Sequencing of Bacterial Strains

Whole genome sequencing was performed on 74 strains at the University of Toronto in Canada. DNA was extracted and prepared by using the robotic setup described previously [50 (link)]. The genomes were sequenced using an Illumina GAIIx on 250 bp paired-end libraries in 8-fold multiplexes. The remaining 26 strains were sequenced at SSI in Denmark. DNA was extracted and prepared using Promega Wizard Genomic DNA Purification kit (Promega, Madison, USA) and Nextera XT v2 DNA Library Preparation kit (Illumina, San Diego, USA) according to the manufacturer protocol. Whole genome sequencing was performed using an Illumina MiSeq with 250 bp paired-end technology. All genomes were de novo assembled using CLC Genomic Workbench (Qiagen, USA).