WGS of C difficile isolate
C. difficile sequencing libraries were prepared by using either the TruSeq DNA Sample Prep Kits (TruSeq) or the Nextera DNA Flex Library Prep Kit (Flex), both from Illumina (San Diego, CA, USA). When using the TruSeq kit, genomic DNAs are first mechanically sheared by a Covaris ME220 (Woburn, MA, USA) sonication instrument using the settings recommended by the manufacturer. After sonication, the TruSeq universal adapters are added to the ends of the genomic DNA fragments by ligation, followed by bead cleanup, size selection and quantification according to the manufacturers protocol. When using the Flex kit, genomic DNAs are first tagmented (transposon-mediated fragmentation) and universal adapters are added to the ends of the DNA fragments by PCR, according to the manufacturers protocol. DNA libraries (paired end, 2 x 300) were loaded on the Illumina Miseq for whole genome sequencing of the respective C. difficile genomes.