Emerging and well‐characterized chlamydial infections detected in a wide range of wild Australian birds

Abstract

Birds can act as successful long‐distance vectors and reservoirs for numerous zoonotic bacterial, parasitic and viral pathogens, which can be a concern given the interconnectedness of animal, human and environmental health. Examples of such avian pathogens are members of the genus Chlamydia. Presently, there is a lack of research investigating chlamydial infections in Australian wild and captive birds and the subsequent risks to humans and other animals. In our current study, we investigated the prevalence and genetic diversity of chlamydial organisms infecting wild birds from Queensland and the rate of co‐infections with beak and feather disease virus (BFDV). We screened 1114 samples collected from 564 different birds from 16 orders admitted to the Australia Zoo Wildlife Hospital from May 2019 to February 2021 for Chlamydia and BFDV. Utilizing species‐specific quantitative polymerase chain reaction (qPCR) assays, we revealed an overall Chlamydiaceae prevalence of 29.26% (165/564; 95% confidence interval (CI) 25.65–33.14), including 3.19% (18/564; 95% CI 2.03–4.99%) prevalence of the zoonotic Chlamydia psittaci. Chlamydiaceae co‐infection with BFDV was detected in 9.75% (55/564; 95% CI 7.57–12.48%) of the birds. Molecular characterization of the chlamydial 16S rRNA and ompA genes identified C. psittaci, in addition to novel and other genetically diverse Chlamydia species: avian Chlamydia abortus, Ca. Chlamydia ibidis and Chlamydia pneumoniae, all detected for the first time in Australia within a novel avian host range (crows, figbirds, herons, kookaburras, lapwings and shearwaters). This study shows that C. psittaci and other emerging Chlamydia species are prevalent in a wider range of avian hosts than previously anticipated, potentially increasing the risk of spill‐over to Australian wildlife, livestock and humans. Going forward, we need to further characterize C. psittaci and other emerging Chlamydia species to determine their exact genetic identity, potential reservoirs, and factors influencing infection spill‐over.

One clone to rule them all: Culture-independent genomics of Chlamydia psittaci from equine and avian hosts in Australia

“…Our phylogenetic analyses: (i) reiterate the clonality and generalist host nature of the ST24 lineage; (ii) support lower genetic diversity and host association within the 'pigeon-type' PG4, where our pigeon strain RacingPigeon_24 clustered; and (iii) demonstrate that overall, the C. psittaci population is genetically diverse in agreement with previous studies [7,11,13,14,17]. Whilst we have now expanded Australian psittacine C. psittaci ST24 genomes from one (CR009) to six, provided the first pigeon C. psittaci from Australia and confirmed that the ST24 clonality of the equine reproductive loss strains, another limitation of our study was that we were not able to obtain additional samples containing previously genotyped contemporary diverse strains from other Australian non-psittacine, human, livestock and/or marsupials hosts [15,44,45].…”

“…psittaci ST24 genomes from one (CR009) to six, provided the first pigeon C. psittaci from Australia and confirmed that the ST24 clonality of the equine reproductive loss strains, another limitation of our study was that we were not able to obtain additional samples containing previously genotyped contemporary diverse strains from other Australian non-psittacine, human, livestock and/or marsupials hosts [15, 44, 45].…”

“…psittaci strains causing equine reproductive loss and the factors that increase the risk of infection spillover [5] but also to assess the genetic diversity of C. psittaci in the broader range of avian and non-avian hosts, including humans [14, 15, 44, 45, 58]. The opportunities for ongoing spillover due to habitat degradation/encroachment (or increase) of the wildlife/livestock interface and reduced food/water resources for birds driving them into paddocks to feed on horse food are plausible [59].…”

“…Molecular and/or cell biology/infection studies to dissect the significant pathogenicity of C. psittaci and to understand the risk posed by C. psittaci to livestock and humans are being increasingly conducted in Australia and worldwide [7,11,14,15,[55][56][57]. In Australia, further studies must focus on understanding the pathogenicity of C. psittaci strains causing equine reproductive loss and the factors that increase the risk of infection spillover [5] but also to assess the genetic diversity of C. psittaci in the broader range of avian and non-avian hosts, including humans [14,15,44,45,58]. The opportunities for ongoing spillover due to habitat degradation/encroachment (or increase) of the wildlife/livestock interface and reduced food/water resources for birds driving them into paddocks to feed on horse food are plausible [59].…”

Unexpected Pathogen Diversity Detected in Australian Avifauna Highlights Potential Biosecurity Challenges

“…Some wildlife pathogens, such as Beak and feather disease virus (BFDV), are well-studied in Australia [ 10 ]. However, the prevalence of other pathogens that may contribute to the decline in avian wildlife populations, including herpesviruses ( Columbid alphaherpesvirus 1 (CoAHV1) and Psittacid alphaherpesvirus 1 (PsAHV1)) and members of the avipoxviruses and Chlamydia genus remain understudied [ 5 , 6 , 11 , 12 , 13 ]. Australia and its offshore islands host over 890 avian species, with approximately 45% of them being endemic [ 14 ].…”