8% (Table 2). The probability that a pair of isolates selleck compound with the same ribotype also shared identical TRST sequence types was 89.6% (Wallace index 0.896). Accordingly, ribotypes usually corresponded to specific TRST sequence types (Figure 2). For example, 18 isolates with ribotype 027, originating from

six different European countries, displayed identical sequences at TR6 and TR10 that discriminated them from all other isolates, and jointly were assigned TRST sequence type tr-027 (Additional file 1, Figure 2). Similarly, four isolates with ribotype 017 from three different countries, including the reference strain for toxinotype VIII, were assigned sequence type tr-017 (Additional file 1, Figure 2). Future work on larger numbers of isolates may reveal that sequencing a single locus (TR6 or TR10) will suffice to identify epidemiologically relevant strains. For the sake of concordance with PCR ribotyping, however, we presently suggest to sequence both loci. As outlined above, this strategy will also detect the impact of recombination. Tandem repeat sequences are phylogenetically

informative Discrepancies between TRST and ribotyping were apparent where either method split a particular group of isolates into two or three classes, whereas the other lumped them into one (Figure 2). In virtually all of these cases, however, the respective isolates were affiliated to identical MLST sequence types or to single locus variants with respect to MLST (i. e., identical sequences Sotrastaurin nmr at six out of seven MLST loci), indicating their close phylogenetic relatedness. Phylogenetic coherence of these additional (sub-)classes will remain unclear as long as there are no phylogenetic markers available to PF-01367338 price investigate the detailed evolutionary history of C. difficile within MLST sequence types. MLVA typically resolves dozens

of distinct genotypes within individual ribotypes [20, 21]. However, MLVA provided little insight to the genetic relatedness within our collection, since almost all isolates differed from each other CYTH4 at four or more loci [20], even when they were affiliated to identical TRST sequence types or ribotypes (Figure 3). The sole useful exception was represented by isolates JW611148 and CL39, which shared identical alleles at five MLVA loci (Figure 3). The summed tandem-repeat difference between these two isolates was four repeats, which is below the threshold (= 10) previously suggested to indicate close genetic relationship based on MLVA [21]. MLST identity confirmed the relatedness of these isolates (Figure 3), and their close phylogenetic relationship also was correctly reflected by identical sequences at TR6 and TR10 (tr-070, Figure 3). However, these isolates displayed a distinct one-band difference between their ribotyping patterns, corresponding to ribotypes 078 and RKI35, respectively (Figure 4).