92), and the resulting ST recognized 80% of the PCR-ribotypes [21]; the TRST resulted in an allelic diversity (0.967) equal to that of PCR ribotyping (0.967), and is the technique most buy MCC950 related to PCR ribotyping among these studies [20]. In Protein Tyrosine Kinase inhibitor the present study, the ten VNTR loci used in MLVA10 were cd5, cd6, cd7, cd12, cd22, cd27, cd31, H9cd, F3cd, and CDR59, which exhibited a slightly lower allelic diversity (0.54-0.83) than the previously used CDR4, CDR9, CDR48, CDR49, CDR60, and C6cd VNTR loci (0.84-0.96) [13, 14, 19, 20] (Table 1), resulting in a combined allelic diversity

of 0.957 (Table 2). This value is similar to TRST (0.967) and PCR-ribotype (0.967). Therefore, both TRST and MLVA10 showed a high level of agreement with the PCR-ribotype (86.0 and 88.2%, respectively) (Table 2). However, the MLVA technique is easier to perform than the sequence-based techniques, such as TRST and MLST, and MLVA panels are more easily combined, such as when adding the MLVA4 panel for outbreak strain detection. To represent this website the currently known PCR-ribotypes for C. difficile, a combination of multiple VNTR loci with different allelic diversity is recommended. In our initial study, no single VNTR locus was discriminatory enough to recognize all PCR-ribotypes or specific enough to belong to each PCR-ribotype (data not shown), as previously observed for MLVA and MLST of N. meningitidis [24]. Therefore,

40 Etofibrate VNTR loci distributed throughout the genome of the C. difficile 630 strain were used for comparison analyses, and we found that the MLVA34 panel yielded groups most related to the PCR-ribotype groups (Table 2; Figure 1). Our screening method was based on two rationales: 1) the PCR-ribotype recognized the major PFGE type [9] and was expected to be congruent with the major genotypic groups of C. difficile; and 2) the locus markers distributed throughout the chromosome were more likely to identify genotypic change [13]. In the current study we also highlighted the fact that group

definition was required for comparisons. The allelic diversity of MLVA10 types varied among the different PCR-ribotypes (Additional file 4), and led to only 60% congruence between the types of MLVA10 and PCR ribotyping (data not shown). In significant contrast, the congruence reached 98% when groups obtained by the two techniques were compared (Table 2). These observations were similar to those found in the comparison between MLVA34 and PCR-ribotyping (Additional file 4). Even though there was a high level of agreement between groups identified by the two techniques, some discordance was found. For example, PCR-ribotype group 11 was represented by two MLVA10 groups (10_48 and 10_11) (Figure 1), and the isolates in group 11 were suspected to have undergone concerted evolution [30, 31]; however, this assumption needs to be further confirmed by MLST.