Chlamydia psittaci is an avian pathogen and zoonotic agent of atypical pneumonia. The most pathogenic C. psittaci cluster into the 6BC clade, hypothesized to have recently emerged globally. Exposure to infected parrots is a significant risk factor. Evidence is increasing that indirect exposure may also be an epidemiological factor. Psittacosis is endemic to the Blue Mountains, Australia with ongoing cases of psittacosis leading to serious illness over a 9 year period. The majority of human cases did not have explicit psittacine contact. The study’s objectives were to characterise the identity and relationships of these Australian human and bird isolates.
Sequencing was performed on Australian human and a single avian C. psittaci strain isolated over a 9 year period. Only one human had explicit psittacine contact. Phylogenetic analysis was performed on the resulting near-full length genome sequences and against other available C. psittaci sequences using PhyML. Bayesian analysis of substitution rates and divergence time was performed on these samples along with 16 publically available C. psittaci genome sequences using BEAST. Evidence of recombination within the newly sequenced C. psittaci isolates was detected using Gubbins.
All sequenced Australian human C. psittaci isolates, along with the native Australian parrot isolate, were remarkably similar, sharing < 100 SNPs. Phylogenetic analysis revealed that these newly sequenced strains clustered tightly within the highly pathogenic 6BC clade of C. psittaci with C. psittaci strains in the 6BC clade, including the Australia isolates, have an identical recombination profile. Recalculation of the substitution rate for C. psittaci produced a significantly slower rate of substitutions per year per site than that previously calculated, predicting the emergence of the 6BC clade approximately 2,000 years ago.
These findings reveal a potential Australian natural reservoir of C. psittaci strains from the 6BC clade, highlighting their potential role in the dissemination of these strains globally. This work also further reinforces the public health risks of inadvertent contact with C. psittaci-infected wild birds.