Whole-genome sequencing of Chlamydia psittaci from Australasian avian hosts: A genomics approach to a pathogen that still ruffles feathers

Abstract

<i>Chlamydia psittaci</i> is a globally distributed veterinary pathogen with zoonotic potential. Although <i>C. psittaci</i> infections have been reported in various hosts, isolation and culture of <i>Chlamydia</i> is challenging, hampering efforts to produce contemporary global <i>C. psittaci</i> genomes. This is particularly evident in the lack of avian <i>C. psittaci</i> genomes from Australia and New Zealand. In this study, we used culture-independent probe-based whole-genome sequencing to expand the global <i>C. psittaci</i> genome catalogue. Here, we provide new <i>C. psittaci</i> genomes from two pigeons, six psittacines, and novel hosts such as the Australian bustard (<i>Ardeotis australis</i>) and sooty shearwater (<i>Ardenna grisea</i>) from Australia and New Zealand. We also evaluated <i>C. psittaci</i> genetic diversity using multilocus sequence typing (MLST) and major outer membrane protein (<i>omp</i>A) genotyping on additional <i>C. psittaci</i>-positive samples from various captive avian hosts and field isolates from Australasia. We showed that the first <i>C. psittaci</i> genomes sequenced from New Zealand parrots and pigeons belong to the clonal sequence type (ST)24 and diverse 'pigeon-type' ST27 clade, respectively. Australian parrot-derived strains also clustered in the ST24 group, whereas the novel ST332 strain from the Australian bustard clustered in a genetically diverse clade of strains from a fulmar, parrot, and livestock. MLST and <i>omp</i>A genotyping revealed ST24/<i>omp</i>A genotype A in wild and captive parrots and a sooty shearwater, whilst 'pigeon-types' (ST27/35 and <i>omp</i>A genotypes B/E) were found in pigeons and other atypical hosts, such as captive parrots, a little blue penguin/Kororā (<i>Eudyptula minor</i>) and a zebra finch (<i>Taeniopygia guttata castanotis</i>) from Australia and New Zealand. This study provides new insights into the global phylogenomic diversity of <i>C. psittaci</i> and further demonstrates the multi-host generalist capacity of this pathogen.