Chlamydia trachomatis causes sexually transmitted infections and the blinding disease trachoma. Current data on C. trachomatis phylogeny show that there is only a single trachoma-causing clade, which is distinct from the lineages causing urogenital tract (UGT) and lymphogranuloma venerum diseases. Here we report the whole-genome sequences of ocular C. trachomatis isolates obtained from young children with clinical signs of trachoma in a trachoma endemic region of northern Australia. The isolates form two lineages that fall outside the classical trachoma lineage, instead being placed within UGT clades of the C. trachomatis phylogenetic tree. The Australian trachoma isolates appear to be recombinants with UGT C. trachomatis genome backbones, in which loci that encode immunodominant surface proteins (ompA and pmpEFGH) have been replaced by those characteristic of classical ocular isolates. This suggests that ocular tropism and association with trachoma are functionally associated with some sequence variants of ompA and pmpEFGH.

Chlamydia pneumoniae is a common human and animal pathogen associated with a wide range of diseases. Since the first isolation of C. pneumoniae TWAR in 1965, all human isolates have been essentially clonal, providing little evolutionary insight. To address this gap, we investigated the genetic diversity of 30 isolates from diverse geographical locations, from both human and animal origin (amphibian, reptilian, equine and marsupial). Based on the level of variation that we observed at 23 discreet gene loci, it was clearly evident that the animal isolates were more diverse than the isolates of human origin. Furthermore, we show that C. pneumoniae isolates could be grouped into five major genotypes, A-E, with A, B, D and E genotypes linked by geographical location, whereas genotype C was found across multiple continents. Our evidence strongly supports two separate animal-to-human cross species transfer events in the evolutionary history of this pathogen. The C. pneumoniae human genotype identified in the USA, Canada, Taiwan, Iran, Japan, Korea and Australia (non-Indigenous) most likely originated from a single amphibian or reptilian lineage, which appears to have been previously geographically widespread. We identified a separate human lineage present in two Australian Indigenous isolates (independent geographical locations). This lineage is distinct and is present in Australian amphibians as well as a range of Australian marsupials.

We report successful culture of Calymmatobacterium granulomatis by standard cell culture methods. Swabs were obtained from lesions in three patients with a clinical diagnosis of donovanosis. For two patients, there was histological confirmation of the disease (i.e., the presence of Donovan bodies in Giemsa-stained smears). Specimens were inoculated onto cycloheximide-treated HEp-2 cell monolayers in RPMI 1640 medium (supplemented with fetal calf serum, NaHCO 3 , vancomycin hydrochloride, and benzylpenicillin). At 48 h, organisms resembling Donovan bodies were identified in monolayer cultures from all three specimens. The organisms appeared as pleomorphic bacilli with characteristic bipolar staining and "safety pin" appearance. Using a PCR designed to differentiate C. granulomatis from the Klebsiella species (which have a high degree of molecular homology), we were able to demonstrate that the cultured organisms produced a PCR product identical to that obtained from the original swab specimens. It is now possible to test in vitro susceptibility of C. granulomatis to antibiotics and to provide a ready source of DNA and antigenic material to enable the development of serological tests and, possibly in the future, a vaccine.