Clostridium difficile infections (CDI) are a growing concern in North America, because of their increasing incidence and severity. Using integrated approaches, we correlated pathogen genotypes and host clinical characteristics for 46 C. difficile infections in a tertiary care medical center, during a six-month interval from January to June 2010. Multi-locus sequence typing (MLST) demonstrated 21 known and two novel sequence types (STs), suggesting that the institution's C. difficile strains are genetically diverse. ST1 (which corresponds to pulsed-field gel electrophoresis strain type NAP1/ribotype 027), was the most prevalent (32.6%), 43.5% of the isolates were binary toxin gene positive, of which 75% were ST1. All strains were ciprofloxacin resistant and metronidazole susceptible, and 8.3% and 13.0% of the isolates were resistant to clindamycin and tetracycline, respectively. The corresponding resistance loci, including potential novel mutations, were identified from the whole genome sequencing (WGS) of the resistant strains. Core genome SNPs determining the phylogenetic relatedness of the 46 strains recapitulated MLST types, and provided greater inter-strain differentiation. Disease severity was greatest in patients infected with ST-1 and/or binary gene positive strains, but genome-wide SNP analysis failed to provide additional associations with CDI severity within the same STs. We conclude MLST and core genome SNP typing result in the same phylogenetic grouping of the 46 C. difficile strains collected in a single hospital. WGS also has the capacity to differentiate those strains within STs, and allows the strains comparison at individual gene level and at whole genome level.