The array was designed to cover the previously sequenced strain C. difficile 630, the preliminary 454 sequence **data** of the 027 strain R20291 and the unannotated sequence of the Canadian 027 isolate QCD32g58 in a strategy similar to that used by Witney et al [49]. The R20291 genome sequence was generated by 454/Roche GS20 as discussed in Stabler et al [32]. Genome annotation of strain R20291 and QCD32g58 was based on previously published annotations of C. difficile strain 630 [17]. The genomic sequences were compared against the database of strain 630 proteins by blastx, and a CDS feature in the query genome was created when a hit of over 90% identity was found. Glimmer3 was used to predict CDSs in genomic regions where no significant hits were found [50]. Any unique genomic regions left were examined and annotated manually in Artemis [51]. The genome comparisons were visualized in Artemis and ACT (Artemis Comparison Tool; [52]. In silico comparison against the Canadian strain QCD32g58 was also performed.