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 tRNA^Ala are clustered and in group IV the ISRs with a tRNA gene.