Corresponding ribotypes, TRST types, and MLST sequence types are indicated. Clonal evolution of tandem repeat regions Genomic regions with short tandem repeat regions may evolve fast due to intra-molecular recombination and frequent polymerase slippage during DNA replication [43–45]. Accordingly, loci TR6 and TR10 displayed both, sequence polymorphisms, generated through exchange of individual nucleobases (Additional files 3, 4), and length polymorphisms, as a consequence of repeat copy number variation (Additional file 2). Sequences of individual repeats were highly

variable, with a nucleotide diversity π of 0.28 ± 0.01 for TR6 and 0.23 ± 0.01 for TR10. The majority of nucleotide substitutions at locus TR6 were synonymous, i. e., they left the encoded amino acid sequence unaffected, and hence may be considered selectively neutral. This was reflected by a Ka/Ks value of 0.39, suggesting TR6 MK-2206 price sequences evolve under purifying selection.

Locus TR10 does not encode any protein and, hence, sequence variation Dabrafenib chemical structure likely is neutral, too. Furthermore, there is evidence of rare recombination between chromosomes from different strains, affecting tandem repeat sequences. One homologous recombination event apparently generated TRST type tr-021. While tr-021 shares an identical TR6 sequence with tr-011 (Additional file 2), its TR10 allele differs profoundly from that of tr-011 in both, length and sequence (Additional files 4 and 2), even though isolates displaying tr-011 (isolate N551) and tr-021 (SMI037) are affiliated to the same MLST type (ST-39) and ribotype (011; Figure 3).

Interestingly, the TR10 allele of tr-021 is identical to the one of tr-005 (Additional file 2). Hence, the drastic Cyclin-dependent kinase 3 difference between central parts of TR10 in tr-011 and tr-021 may be explained through a single event of horizontal gene transfer from an unrelated strain. Very similarly, tr-066 and tr-045 share identical alleles with closely related TRST types at either TR6 or TR10, respectively, yet differ drastically along a contiguous stretch of central repeats at the other tandem repeat locus. Again, identical alleles may be found elsewhere in the database (Additional file 2), suggesting they were horizontally transferred. In our dataset, these three TRST types displayed the only such discrepancies. We conclude that genetic recombination between unrelated chromosomes was involved in the evolution of maximally three TRST types out of 72 that were included in our set of isolates. Hence, the evolution of tandem repeats TR6 and TR10 is driven largely through clonal diversification, whereas the impact of recombination is extremely small. These results fully corroborate a previous estimate of a very low recombination rate in C. difficile, which had been based on MLST data [31]. Figure 3 Comparison of MLST, PCR ribotyping, TRST and MLVA for 43 C. difficile isolates.