C. difficile whole genome sequencing (WGS) analysis

WGS typing is the most discriminatory typing method available for C. difficile studies.  After growth, we can extract C. difficile DNA, sequenced it, and generate fastq files. We then conduct phylogenetic analyses in the overall population and per intervention analysis, as appropriate.  Presence of other known antimicrobial resistance genes in the C. difficile genome is also analyzed based on treatment.