The first DNA sequence from Orientia appeared in a report about the Sta58 (scrub typhus antigen-58 kDa) gene of the Karp strain of Orientia tsutsugamuchi (Stover CK, Marana DP, Dasch GA, Oaks EV. 1990 : Molecular cloning and sequence analysis of the Sta58 major antigen gene of Rickettsia tsutsugamushi: sequence homology and antigenic comparison of Sta58 to the 60-Kilodalton family of stress proteins. Infect Immunol 58:1360-1368.) The Sta58 gene turned out to be a composite of two heat shock proteins ubiquitous in bacteria now commonly referred to as GroES and GroEL.
Since 1990, more than 6700 DNA sequences from various isolates of O. tsutsugamushi have been published or deposited in the international DNA databases (such as GenBank or DDBJ). A large proportion of the sequences in the DNA databases involves partial segments of the genome sequences of less than 20 isolates. However, these databases also contain information about sequences of some specific genes from multiple isolates. The most common sequence in the DNA databases from isolates of O. tsutsugamushi are those from the genetic region coding for the hypervariable 56-kDa TSA (Type-Specific Antigen) of the organism.
Attempts to relate isolates of O.tsutsugamushi using genetic methods first 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.
Unlike most other species of rickettsiae, or many other obligate intracellular bacteria, O. tsutsugamushi displays extreme genetic heterogeneity between isolates for some genes, as well as showing what appears to be unusual variability in the structure of its genome.
Genetic heterogeneity is particularly true of the gene coding for the 56-kDa Type Specific Antigen. As of July 2017, over 1000 complete or partial sequences of the 56-kDa TSA gene from various isolates of O.tsutsugamushi have been deposited in the international DNA databases. Sequences have been obtained from disease cases throughout much of the ever-growing endemic regions for scrub typhus. Interestingly, efforts to correlate the earlier serological typing methods with the newer genotyping have proven problematic. Since geographic and temporal origins of strains are becoming increasingly well documented, it is becoming possible to better examine the geographic distribution of strain types.
A significant characteristic of the Orientia genome is its dramatic strain structural variation. This may be related to a greatly increased level of genetic recombination within Orientia compared to other rickettsiales, potentially due to the hyper-duplication of genetic elements related to recombination. This hyper-duplication of some sequences also contributes to difficulties in completely reconstructing the genome sequences of an isolate, since it makes the question of gene order more difficult to answer unambiguously.
[UNDER CONSTRUCTION: The material below is being added to actively, and the structure of the page and its links are likely to change as the page matures].
INDIVIDUAL GENES USED IN THE STUDY OF SCRUB TYPHUS VARIATION
The genes that have been studied in scrub typhus fall into several categories:
Group 1) Antigen genes (Details)
Genes that represent proteins appearing as prominent antigens in early studies of scrub typhus. These genes may have increased importance in considerations related to vaccine development. These tend to be principally membrane bound genes exposed on the cells outer surface. They may or may not be useful in defining the evolutionary relationships among isolates of Orientia, depending on how natural selection has acted on their products. For instance, does selection act to produce differences between alleles in order for the bacterial cell to better evade immune responses by mammalian hosts. Alternatively, does selection act to homogenize the protein in order to facilitate its function, for instance in attachment to a host cell.
Genes in this group would include those coding for the sta22 (22-kDa scrub typhus) antigen, the sta47 (47-kDa STA) antigen, the sta56 protein (the 56-kDa antigen that is now recognized to represent the groEL/groES heat shock proteins) and the sta57-kDa type specific antigen (TSA).
Group 2) rRNA genes (Details)
genes primarily involved in determining the position of Orientia with respect to other alphaproteobacteria, especially the members of the rickettsiaceae. These tend to genes that are universally found among bacteria. Central among these genes are the genes whose products form the scaffold for the subunits of the ribosome, i.e., the 16S and 23S ribosomal rRNA genes.
Group 3) Metabolic / MLST genes (Details)
genes that may be useful for defining evolutionary relationships between isolates, because their products are part of the normal metabolic machinery of the cell and can tolerate small random changes in nucleotide sequence that can provide phylogenetic information. These genes have become parts of several gene arrays that have been used for multi-locus sequence typing (MLST) analysis of isolates.
Finally, Group 4) Genes with antibiotic resistance potential (Details)
A number of genes exist in the genomes of isolates of Orientia that may have the potential to be involved in antibiotic resistance. These genes are identified by homology with genes known to confer resistance in other bacteria.
For each of these groups, in the future we will endeavor to provide information about the relative levels of genetic variation, and phylogenetic information in a standard array of isolates. This array of isolates is being defined by the isolates that have been chose by various groups for whole genome analysis (see page on genomes). As additional whole genome sequences are added to the list of scrub typhus isolate genomes, we hope to continue to update the information on this site.