The ribosomal RNA operon (rrn) of Campylobacter concisus supports molecular typing to genomospecies level

Campylobacter concisus is an emerging pathogen of the human intestinal tract. This heterogeneous species of phenotypically indistinguishable strains has been divided into genomospecies A and genomospecies B by amplification of the 23S rRNA gene. The diversity of the ribosomal RNA (rrn) operon can be a useful tool for differentiation of C. concisus. In this study we investigated the rrn operon (5S rRNA, 16S rRNA, 23S rRNA genes, and the ITS regions) to differentiate and establish a systematic relationship among C. concisus isolates. The rrn operons were identified from two oral and two intestinal C. concisus whole genomes sequenced at RMIT University, Melbourne. The rrn operon sequences of eight C. concisus strains downloaded from public databases were also included in the analysis. We examined the potential of the rrn operon to be used in strain typing and delineation of phylogenetic relationships within C. concisus rrn operons. We have identified 38 indels in the rrn operon of the C. concisus genome. Five indels in the 23S rRNA gene were significantly associated with the genomospecies (p < 0.05). The phylogenetic tree generated from the rrn operons demonstrated sequence differences between strains within the 5S rRNA, the 16S rRNA, the 23S rRNA and other intergenic regions. Hence, C. concisus can be classified into two genomospecies (A & B) based on the presence of the indels in the rrn operon. The 23S rRNA gene was found to be more reliable for C. concisus typing than the 16S rRNA gene.