Identification of Chlamydia gallinacea in a parrot and in free-range chickens in Australia

Belgian Cross-Sectional Epidemiological Study on Zoonotic Avian Chlamydia spp. in Chickens

Chlamydia psittaci, Chlamydia gallinacea, and Chlamydia abortus are the most common Chlamydia spp. in chickens and have a confirmed or suggested zoonotic potential. No recent data are available on their prevalence and impact in the Belgian chicken industry or in the recreational chicken branch. Therefore, a cross-sectional epidemiological study was executed where samples were collected from both factory-farmed and backyard chickens. More specifically, pharyngeal chicken swabs were obtained from 20 chicken farms, 5 chicken abattoirs, and 38 different backyard locations and were analyzed using species-specific Polymerase Chain Reactions (PCRs) for the presence of the three avian Chlamydia spp. To investigate their zoonotic potential, samples were simultaneously collected from 54 backyard chicken caretakes and 37 professional chicken caretakers or abattoir employees and analyzed using species-specific PCRs as well. This study confirmed the presence of DNA of all three Chlamydia species in both the chicken industry and backyard settings. Chlamydia psittaci was the most prevalent in the industry chickens (11.0%), whereas Chlamydia gallinacea was the dominant species in the backyard chickens (14.5%). Chlamydia abortus infections were more common in the commercial chickens (9.0%) compared to the backyard chickens (2.6%). The DNA of all three species was also detected in humans (3.9% Chlamydia psittaci, 2.9% Chlamydia gallinacea, and 1.0% Chlamydia abortus).

New insight on chlamydiae

This article provides an overview of the current knowledge on chlamydiae, which are intracellular bacteria belonging to the Chlamydiaceae family. Whole-genome sequencing leads to great increases in the available data about Chlamydia spp. Recently, novel chlamydial taxons in various hosts living in different environments have been recognised. New species and taxons with Candidatus status have been recorded mainly in birds and reptiles. Chlamydia gallinacea is an emerging infectious agent in poultry with indirectly confirmed zoonotic potential. Recently, a new group of avian C. abortus strains with worldwide distribution in various wild bird families has been described. The definition of C. abortus species became outdated with the discovery of these strains and has been amended. It now includes two subgroups, mammalian and avian, the latter including all isolates hitherto referred to as atypical C. psittaci or C. psittaci/C. abortus intermediates.

Whole Genome Sequencing and Comparative Genomic Analysis of Chlamydia gallinacea Field Strains Isolated from Poultry in Poland

Chlamydia gallinacea is an intracellular bacterium belonging to the Chlamydiaceae family. Poultry is considered to be the major reservoir of this agent, which has worldwide distribution and a particularly consistent worldwide occurrence in chicken flocks. The bacterium has been linked to respiratory disease in humans but without definitive confirmation; nevertheless, while it has not been proved to be the cause of human respiratory disease, a recent report from Italy verified its bird-to-human transmission. This aspect being significant for public health, more research is needed to gain insight into the infection biology of C. gallinacea. In this study, the genomes of eleven novel C. gallinacea field strains from different regions of Poland were analyzed comparatively. It was confirmed that C. gallinacea strains are closely related, with at least 99.46% sequence identity. They possess a conservative genome structure involving the plasticity zone with a complete cytotoxin, the type three secretion system, inclusion membrane proteins, polymorphic membrane proteins, hctA and hctB histone-like proteins, and the chlamydial protease-like activating factor exoenzyme, as well as plasmids. Genetic diversity seems to be restricted. However, some genetic loci, such as ompA and multi-locus sequence typing target genes, are diverse enough to enable high-resolution genotyping and epidemiological tracing.

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

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.

Chlamydia Species and Related Risk Factors in Poultry in North-Western Italy: Possible Bird-to-Human Transmission for C. gallinacea

Chlamydiaceae are obligatory intracellular bacteria causing acute and chronic diseases in animals and humans worldwide, with recently discovered species with a still unclear pathogenic potential (i.e., C. gallinacea). In Italy, Chlamydiaceae infections are underestimated both in animals and humans. To estimate the prevalence of Chlamydiaceae species in poultry and occupationally exposed workers on farm, a cross-sectional study was carried out in north-western Italy. A total of 2063 samples from 83 commercial and 31 backyard poultry farms were analysed using real-time PCRs for Chlamydiaceae screening and species typing. Chlamydiaceae were detected in 23 farms, with a herd prevalence of 20.2% (95%CI: 13.2-28.7), higher in backyard farms (38.7%; 95%CI: 21.8-57.8) compared to commercial ones (13.3%; 95%CI: 6.8-22.5). C. gallinacea was found in 18 chicken farms, both commercial and backyard, and C. psittaci only in 3 backyard farms. Exposure to wild birds and factors related to biosecurity resulted the main risk factors associated with Chlamydia positivity. Out of the 113 sputum samples collected from farmers, 16 tested positive to Chlamydiaceae, with a prevalence of 14.2% (95%CI: 8, 3-22). To the best of our knowledge, for the first time at international level, C. gallinacea was detected in humans with farmer positivity associated with farm infectious status, suggesting a bird-to-human transmission.

A multiplex real-time PCR assay for differential identification of avian Chlamydia

Avian chlamydiosis is an acute or chronic disease of birds after infection by Chlamydia. Although Chlamydia psittaci is the primary agent of the disease, two additional species, Chlamydia avium and Chlamydia gallinacea, have also been recognized as potential disease agents. Therefore, the diagnosis of avian chlamydiosis requires differential identification of these avian Chlamydia species. The objective of the present study was to develop a multiplex real-time polymerase chain reaction (PCR) assay to rapidly differentiate between these three species of avian Chlamydia (C. psittaci, C. avium, and C. gallinacea) as well as the genus Chlamydia. Specific genetic regions of the three species were identified by comparative analysis of their genome sequences. Also, the genus-specific region was selected based on 23S rRNA sequences. PCR primers and probes specific to the genus and each species were designed and integrated in the multiplex real-time PCR assay. The assay was highly efficient (94.8-100.7%). It detected less than 10 copies of each target sequence of the genus and each species. Twenty-five Chlamydia control and field DNA samples were differentially identified while 20 other bacterial strains comprising 10 bacterial genera were negative in the assay. This assay allows rapid, sensitive, and specific detection of the genus and the three species of avian Chlamydia in a single protocol that is suitable for routine diagnostic purposes in avian diagnostic laboratories.

Experimental inoculation of chicken broilers with C. gallinacea strain 15-56/1

Chlamydia gallinacea is one of the new Chlamydia species, encountered predominantly in birds and occasionally in cattle, and its dissemination, pathogenicity and zoonotic potential have not yet been fully elucidated. Until now, no case of clinical infection has been described in poultry, but the number of studies is limited. This study was conducted to evaluate the course of infection and the impact on production parameters in chicken broilers inoculated with the strain 15-56/1 isolated from a Polish flock. The presence of C. gallinacea was confirmed in oropharyngeal and cloacal swabs by real-time PCR from the fifth day post inoculation (dpi). Pathogen DNA was also detected in many internal organs of inoculated chickens. All infected animals remained asymptomatic during the entire experimental period, although statistical analyses showed that broilers in the experimental group exhibited significantly lower body weight gains and feed conversion ratios than animals in the control group. These data indicate that subclinical C. gallinacea infection in broilers may lead to financial losses for poultry farmers.

Falcons From the United Arab Emirates Infected With Chlamydia psittaci/C abortus Intermediates Specified as Chlamydia buteonis by Polymerase Chain Reaction

Chlamydiaceae are obligate intracellular bacteria with a broad host range. Several studies have found chlamydial species that are genetically intermediate between Chlamydia psittaci and Chlamydia abortus in various avian species. One of these intermediate Chlamydia species, found in a red-shouldered hawk (Buteo lineatus), was recently classified as a new species Chlamydia buteonis. This newly described Chlamydia species has, so far, only been reported in hawks exhibiting clinical signs of conjunctivitis, dyspnea, and diarrhea. In the present study, fecal samples of 5 gyrfalcons (Falco rusticolus), 3 gyr/peregrine falcon hybrids (Falco rusticolus × Falco peregrinus), and 15 falcons of unknown species presented to falcon clinics on the Arabian Peninsula were shipped to the Vetsuisse Faculty, University of Zurich (Zurich, Switzerland), for examination for the presence of Chlamydiaceae. A step-wise diagnostic approach was performed to identify the chlamydial species involved. Chlamydiaceae were detected in 21/23 falcons by a family-specific real-time quantitative PCR (qPCR). Further identification with a 23S ribosomal RNA-based microarray assay and 16S conventional PCR and sequencing yielded inconclusive results, indicating the presence of an intermediate Chlamydia species. Because none of the falcons tested positive for Chlamydia psittaci by specific qPCR, all 23 samples were subjected to a Chlamydia buteonis-specific qPCR, which was positive in 16/23 samples. Detailed information regarding clinical history was available for 8 falcons admitted to a falcon clinic in Dubai, United Arab Emirates. Six of those birds that were presented to the clinic because of loss of performance and poor general condition, including vomiting and diarrhea, were positive for C buteonis. In 2 birds without clinical disease signs admitted for a routine health examination, 1 was positive for C buteonis, and 1 was negative. It is yet unknown whether Chlamydia buteonis causes disease in birds, but the findings in this study indicate that Chlamydia buteonis may be an infectious pathogen in falcon species.

Genetic and phenotypic analysis of the pathogenic potential of two novel Chlamydia gallinacea strains compared to Chlamydia psittaci

Chlamydia gallinacea is an obligate intracellular bacterium that has recently been added to the family of Chlamydiaceae. C. gallinacea is genetically diverse, widespread in poultry and a suspected cause of pneumonia in slaughterhouse workers. In poultry, C. gallinacea infections appear asymptomatic, but studies about the pathogenic potential are limited. In this study two novel sequence types of C. gallinacea were isolated from apparently healthy chickens. Both isolates (NL_G47 and NL_F725) were closely related to each other and have at least 99.5% DNA sequence identity to C. gallinacea Type strain 08-1274/3. To gain further insight into the pathogenic potential, infection experiments in embryonated chicken eggs and comparative genomics with Chlamydia psittaci were performed. C. psittaci is a ubiquitous zoonotic pathogen of birds and mammals, and infection in poultry can result in severe systemic illness. In experiments with embryonated chicken eggs, C. gallinacea induced mortality was observed, potentially strain dependent, but lower compared to C. psittaci induced mortality. Comparative analyses confirmed all currently available C. gallinacea genomes possess the hallmark genes coding for known and potential virulence factors as found in C. psittaci albeit to a reduced number of orthologues or paralogs. The presence of potential virulence factors and the observed mortality in embryonated eggs indicates C. gallinacea should rather be considered as an opportunistic pathogen than an innocuous commensal.

A Review of Chlamydial Infections in Wild Birds

The Chlamydia are a globally distributed genus of bacteria that can infect and cause disease in a range of hosts. Birds are the primary host for multiple chlamydial species. The most well-known of these is Chlamydia psittaci, a zoonotic bacterium that has been identified in a range of wild and domesticated birds. Wild birds are often proposed as a reservoir of Chlamydia psittaci and potentially other chlamydial species. The aim of this review is to present the current knowledge of chlamydial infections in wild avian populations. We focus on C. psittaci but also consider other Chlamydiaceae and Chlamydia-related bacteria that have been identified in wild birds. We summarise the diversity, host range, and clinical signs of infection in wild birds and consider the potential implications of these infections for zoonotic transmission and avian conservation. Chlamydial bacteria have been found in more than 70 species of wild birds, with the greatest chlamydial diversity identified in Europe. The Corvidae and Accipitridae families are emerging as significant chlamydial hosts, in addition to established wild hosts such as the Columbidae. Clarifying the effects of these bacteria on avian host fitness and the zoonotic potential of emerging Chlamydiales will help us to understand the implications of these infections for avian and human health.

Species, sex and geographic variation in chlamydial prevalence in abundant wild Australian parrots

Chlamydia psittaci (order: Chlamydiales) is a globally distributed zoonotic bacterium that can cause potentially fatal disease in birds and humans. Parrots are a major host, yet prevalence and risk factors for infection in wild parrots are largely unknown. Additionally, recent research suggests there is a diverse range of novel Chlamydiales circulating in wildlife. We therefore sampled seven abundant parrot species in south-eastern Australia, taking cloacal swabs and serum from n = 132 wild adults. We determined C. psittaci and Chlamydiales prevalence and seroprevalence, and tested for host species, sex, geographical and seasonal differences, and temporal changes in individual infection status. Across all species, Chlamydiales prevalence was 39.8% (95% CI 31.6, 48.7), C. psittaci prevalence was 9.8% (95% CI 5.7, 16.3) and C. gallinacea prevalence was 0.8% (95% CI 0.1, 4.5). Other Chlamydiales species were not identified to species level. We identified two C. psittaci strains within the 6BC clade, which is highly virulent in humans. Seroprevalence was 37.0% (95% CI 28.5, 46.4). Host species (including crimson rosellas, galahs, sulphur-crested cockatoos and blue-winged parrots) differed in seroprevalence and Chlamydiales prevalence. Galahs had both highest Chlamydiales prevalence (54.8%) and seroprevalence (74.1%). Seroprevalence differed between sites, with a larger difference in males (range 20–63%) than females (29–44%). We reveal a higher chlamydial prevalence than previously reported in many wild parrots, with implications for potential reservoirs, and transmission risks to humans and other avian hosts.

Detection of Chlamydiaceae in Swiss wild birds sampled at a bird rehabilitation centre

Background

Annually, 800–1500 wild birds are admitted to the rehabilitation centre of the Swiss Ornithological Institute, Sempach, Lucerne, Switzerland. The workers of the centre come in close contact with the avian patients and might therefore be exposed to zoonotic agents shed by these birds, such as Chlamydia psittaci.

Methods

In the present study, 91 choanal, 91 cloacal and 267 faecal swabs from 339 wild birds of 42 species were investigated using a stepwise diagnostic approach.

Results

Chlamydiaceae were detected in 0.9 per cent (0.3–2.6 per cent) of birds (n=3), all of them members of the Columbidae family. The Chlamydiaceae species of two of these birds (one Eurasian collared dove, one fancy pigeon) were identified as C psittaci types B and E by PCR and outer membrane protein A genotyping.

Conclusion

The findings of the current study suggest that zoonotic transmission of Chlamydiaceae is very unlikely for songbird and waterfowl species tested herein, while pigeons might pose a risk to workers at rehabilitation centres.

A Review of Pathogen Transmission at the Backyard Chicken-Wild Bird Interface

Habitat conversion and the expansion of domesticated, invasive species into native habitats are increasingly recognized as drivers of pathogen emergence at the agricultural-wildlife interface. Poultry agriculture is one of the largest subsets of this interface, and pathogen spillover events between backyard chickens and wild birds are becoming more commonly reported. Native wild bird species are under numerous anthropogenic pressures, but the risks of pathogen spillover from domestic chickens have been historically underappreciated as a threat to wild birds. Now that the backyard chicken industry is one of the fastest growing industries in the world, it is imperative that the principles of biosecurity, specifically bioexclusion and biocontainment, are legislated and implemented. We reviewed the literature on spillover events of pathogens historically associated with poultry into wild birds. We also reviewed the reasons for biosecurity failures in backyard flocks that lead to those spillover events and provide recommendations for current and future backyard flock owners.

Occurrence of Chlamydiaceae in Raptors and Crows in Switzerland

Bacteria of the family Chlamydiaceae are globally disseminated and able to infect many bird species. So far, 11 species of Chlamydia have been detected in wild birds, and several studies found chlamydial strains classified as genetically intermediate between Chlamydia (C.) psittaci and C.abortus. Recently, a group of these intermediate strains was shown to form a separate species, i.e., C.buteonis. In the present study, 1128 samples from 341 raptors of 16 bird species and 253 corvids representing six species were examined using a stepwise diagnostic approach. Chlamydiaceae DNA was detected in 23.7% of the corvids and 5.9% of the raptors. In corvids, the most frequently detected Chlamydia species was C.psittaci of outer membrane protein A (ompA) genotype 1V, which is known to have a host preference for corvids. The most frequently detected ompA genotype in raptors was M56. Furthermore, one of the raptors harbored C.psittaci 1V, and two others carried genotype A. C.buteonis was not detected in the bird population investigated, so it remains unknown whether this species occurs in Switzerland. The infection rate of Chlamydiaceae in corvids was high compared to rates reported in other wild bird species, but neither Chlamydiaceae-positive corvids nor raptors showed overt signs of disease. Since the Chlamydiaceae of both, raptors and crows were identified as C.psittaci and all C.psittaci genotypes are considered to be zoonotic, it can be suggested that raptors and crows pose a potential hazard to the health of their handlers.

Chlamydial diversity and predictors of infection in a wild Australian parrot, the Crimson Rosella (Platycercus elegans)

Members of the Chlamydia genus are known to cause disease in both humans and animals. A variety of other species in the order Chlamydiales are increasingly being discovered and emerging as potential pathogens, yet there are scarce data on the diversity, prevalence and impacts of these pathogens in wild birds. To address this gap, we investigated which Chlamydiales species are present in a wild population of a common Australian parrot, the Crimson Rosella (Platycercus elegans). We collected cloacal swabs and serum from 136 individuals in south-eastern Australia, over two years, and tested several predictors of prevalence: age, sex, season and breeding status. We used multiple PCR assays to determine bacterial prevalence in cloacal swabs and a solid-phase ELISA to determine seroprevalence. We found Chlamydiales PCR prevalence of 27.7% (95% CI 20.2, 36.2) and identified at least two families (Chlamydiaceae and Parachlamydiaceae). Regarding known chlamydial avian pathogens, we found C. psittaci at 6.2% (95% CI 2.7, 11.8) and C. gallinacea at 4.6% (95% CI 1.7, 9.8) prevalence. We also identified at least two potentially novel Chlamydiales species, of unknown pathogenicity. Sex and breeding status predicted Chlamydiales PCR prevalence, with females more likely to be infected than males, and non-breeding birds more likely to be infected than breeding birds. Seroprevalence was 16% (95% CI 8.8, 25.9). Season and breeding status were strong predictors of seroprevalence, with highest seroprevalence in autumn and in non-breeding birds. Our results reveal a diversity of Chlamydiales species in this abundant wild host, and indicate that host-specific and temporal factors are associated with infection risk. Our findings suggest that wild parrots are a reservoir of both known and novel Chlamydiales lineages, of zoonotic and pathogenic potential.

Chlamydiae from Down Under: The Curious Cases of Chlamydial Infections in Australia

In Australia, the most researched and perhaps the most successful chlamydial species are the human pathogen Chlamydia trachomatis, animal pathogens Chlamydia pecorum and Chlamydia psittaci. C. trachomatis remains the leading cause of sexually transmitted infections in Australians and trachoma in Australian Indigenous populations. C. pecorum is globally recognised as the infamous koala and widespread livestock pathogen, whilst the avian C. psittaci is emerging as a horse pathogen posing zoonotic risks to humans. Certainly not innocuous, the human infections with Chlamydia pneumoniae seem to be less prevalent that other human chlamydial pathogens (namely C. trachomatis). Interestingly, the complete host range for C. pecorum and C. psittaci remains unknown, and infections by other chlamydial organisms in Australian domesticated and wildlife animals are understudied. Considering that chlamydial organisms can be encountered by either host at the human/animal interface, I review the most recent findings of chlamydial organisms infecting Australians, domesticated animals and native wildlife. Furthermore, I also provide commentary from leading Australian Chlamydia experts on challenges and future directions in the Chlamydia research field.