title: Clostridioides difficile Genomic Evolution in a Tertiary German Hospital
design: Genomic DNA was extracted with the InnuPrep Bacteria DNA kit. A total of 500ng of DNA was used as input for barcoded-library preparations with the Ion Xpress Library Plus kit . Pooled samples were sequenced using the HiQ 200-bp sequencing chemistry. Quality control and raw data processing was carried out with the PrinSeq software. Sequencing reads were filtered by a minimum length (100 bp) and quality (>Q20, 5 bp sliding window).