Attempts to use genetic methods to relate isolates of O. tsutsugamushi to each other and to isolates of other taxa (such as Rickettsia) initially relied on the use of the gene coding for the ribosomal small subunit rRNA (the 16S rRNA gene). The first 16S rRNA sequences for O. tsutsugamushi deposited in the international databases were determined in 1994, from our own work on the phylogeny of rickettsias (Stothard and Fuerst, 1995; Stothard, Ph.D. thesis 1995) . These included the sequences of the gene from the Gilliam, Karp, and Kato isolates. These sequences showed an average of ~10% difference from 15 species of Rickettsia. In addition, In Stothard’s Ph.D. thesis, the 23S rRNA sequence of the Gilliam strain of O. tsutsugamushi was compared to homologous sequences from 12 species of Rickettsia. The Gilliam 23S rRNA sequence showed and average of ~12.5% difference from members of Rickettsia.
For both the 16S and 23S rRNA loci, sequences of the complete genes are now available from genome sequences of 39 isolates (see Genome Page). Information is given on subpages showing the phylogenies of the 16S rRNA gene and of the 23S rRNA gene comparing the phylogenies for each gene and indicating the level of phylogenetic information from the two genes, compared to each other and to protein loci will be posted in the future as we complete various analyses.