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

Vasilli Kasimov; Rhys T White; Jonathan Foxwell; Cheryl Jenkins; Kristene Gedye; Yvonne Pannekoek; Martina Jelocnik

doi:10.1099/mgen.0.001072

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

Microb Genom. 2023 Jul;9(7):mgen001072. doi: 10.1099/mgen.0.001072.

Authors

Vasilli Kasimov¹, Rhys T White^{1

2

3

4}, Jonathan Foxwell⁵, Cheryl Jenkins⁶, Kristene Gedye⁷, Yvonne Pannekoek⁸, Martina Jelocnik¹

Affiliations

¹ University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, QLD 4557, Australia.
² The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, Brisbane, Queensland 4072, Australia.
³ The University of Queensland, Australian Centre for Ecogenomics, Brisbane, Queensland 4072, Australia.
⁴ Institute of Environmental Science and Research, Wellington, New Zealand.
⁵ Animal Health Laboratory, Ministry for Primary Industries, 66 Ward Street, Upper Hutt 5018, New Zealand.
⁶ NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales 2568, Australia.
⁷ Massey University, School of Veterinary Science, Palmerston North 4442, New Zealand.
⁸ University of Amsterdam, Amsterdam UMC, Department of Medical Microbiology and Infection Prevention, Amsterdam 1105, Netherlands.

Abstract

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

Keywords: Australia; Chlamydia psittaci; New Zealand; birds; culture-independent sequencing; multi-locus sequence typing (MLST); novel sequence type (ST); phylogenomics.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Australia
Chlamydophila psittaci* / genetics
Columbidae
Feathers
Genomics
Multilocus Sequence Typing
Psittacosis* / veterinary