Several phylogenetic trees have previously been constructed based on the ompA gene [14–17]. These trees separate the serovars into three groups: B complex (serovars B, Ba, D, E, L1

and Epigenetics Compound Library L2), C complex (serovars A, C, H, I, Ia, J, K and L3) and the intermediate complex (serovars F and G). This classification does not represent biological differences in that both ocular strains and LGV strains are classified into the B and C complex. A phylogenetic analysis based on a concatenated nucleotide sequence from nine housekeeping genes, six intergenic non-coding segments and the porB gene gives a different classification in which the ocular and LGV strains are in separate clades [17]. That tree resembles the phylogenetic tree based on hctB, where the ocular strains are found in clade I and the LGV strains in clade V (Figure 3), thus it reflects the biological separation in distinct disease causing groups. Interestingly, both trees separate the reference strains for serotype D strains in the same way: D/UW-3 (10_DGHIIa) Selleck FK506 among serovar B (genital), G, H, I, Ia, J and K and

D/IC-Cal8 (13_D) among serovar E and F. The hctB gene with its high variability has proven to be a valuable target for discrimination between different C. trachomatis specimens in MLST analysis. For example, specimens with ompA genotype identical to the reference strain E/Bour constitute 37-45% in two major Swedish genotyping studies [18, 19] and are abundant in the MLST database (allele number 1, 3-5, 7, 14, 21-25, 35 in Figure 3A). However, the hctB gene can discriminate these samples because of ten configurations of 4 and 5 elements in the repetitive region. Hc2 in Chlamydiales spp Comparisons of hctB nucleotide sequences for other species in the Chlamydiales-order show that they have a similar structure with a region of repetitive elements built up by pentamers (Figure 4) and conserved flanking regions. The Hc2 sequence from the most closely-related species, Chlamydia muridarum, has the highest similarity to C. trachomatis, with three repetitive elements similar to the 1, 2 and 6 elements. The repetitive elements are shorter in Chlamydophila

abortus, Chlamydophila caviae and Chlamydophila pneumoniae but longer in Chlamydophila felis and Chlamydophila psittaci. No repetitive oxyclozanide elements were found in the more distantly related protochlamydial amoeba symbionts Protochlamydia amoebophila and Protochlamydia naegleriophila, and the pentameric structure was vaguer. Figure 4 Schematic overview of repetitive elements in Hc2 in the Chlamydiales order and in an Hc2-like protein in Herminiimonas arsenicoxydans. Repetitive elements of 20 amino acids or longer are shown in black. The hctB gene varies within Chlamydophila abortus and is one of the targets in a recently developed MLVA (multiple loci variable number of tandem repeat analysis) genotyping system [20].