Figure 1.
Clustering of C. difficile PCR-ribotypes.
(A) Clustering of PRC-ribotypes based on fingerprinting profiles generated by capillary gel electrophoresis-based PCR-ribotyping. Dendrogram is color coded according to MLST type. The exact lengths of the bands, representing the 16S-23S rRNA intergenic spacer regions are given in Table S1. (B) Minimum spanning tree of MLST results showing relatedness of PCR-ribotypes. Each circle represents one sequence type (ST) and is subdivided into sectors corresponding to the number of PCR-ribotypes represented with this ST. The numbers between circles represent number of differing loci between the STs.
Table 1.
Overview of C. difficile strains/genomes included in the analysis.
Figure 2.
Schematic representation of the modular structure of C. difficile 16S-23S rRNA intergenic spacer region.
Start (29 bp) – 5' end of the ISR sequence; Ntrna (26 bp) – part of the ISR without a gene for tRNAAla; Trna (186 bp) – part of the ISR with a gene for tRNAAla; DR – 9 bp long direct repeat; 53 bp, 33 bp, 20 bp – spacers of 53 bp, 33 bp and 20 bp, respectively and End (103–114 bp) is the 3' end of the ISR. The size of each structural group is given on the right. The inverse spacer arrangements can be seen in groups 6 and 7, 10 and 11, 12 and 13 and in groups 15 and 16.
Table 2.
Consensus sequence and number of sequence variants found in ISR building blocks.
Figure 3.
Indication of homologous recombination in C. difficile 16S-23S rRNA intergenic spacer region.
(A) Phylogenetic network constructed for 95 representative ISR sequences from 43 different C. difficile strains. (B) Phylogenetic network of 29 ISR sequences (279–282 bp) from 29 different strains of C. difficile. Only one ISR per strain was included in the analysis. Box-like branches seen on both figures indicate relative support for alternative relationships among ISRs, probably resulting from homologous recombination that was subsequently confirmed by statistical analysis. In groups I, II and III the ISRs without a gene for tRNAAla are clustered and in group IV the ISRs with a tRNA gene.