Dissemination and genetic diversity of chlamydial agents in Polish wildfowl: Isolation and molecular characterisation of avian Chlamydia abortus strains

Molecular detection of Chlamydia psittaci in birds: a systematic review

Molecular methods are currently the most sensitive for detecting Chlamydia psittaci in birds. Most laboratories have developed their own molecular assays or adapted published protocols, often making slight modifications to fit their specific study purposes. The sensitivity and specificity of a molecular test depend on the target gene, primer sequences, types of molecular test, DNA extraction method, and sampling methods. We reviewed 120 articles published between 2000 and 2020 to compile information on the molecular detection of C. psittaci in birds. Of the ten genomic targets currently available to detect C. psittaci in birds, the ompA gene was the most widely used. In published surveillance studies, of the fourteen molecular test types, conventional PCR and quantitative PCR were applied the most. A testing strategy using a hierarchical approach that includes molecular tests of genus- and species-specific targets is recommended to detect other avian chlamydial species besides the well-recognized C. psittaci. Samples should be sourced from both the respiratory and gastrointestinal tracts whenever possible for better accuracy. High-quality DNA can be obtained when the sample is preserved in optimal medium and temperature, and an optimized DNA extraction protocol is applied. Standardization and validation of molecular Chlamydia tests are needed to enhance the comparability and reliability of assays to detect C. psittaci and other chlamydiae species in birds.RESEARCH HIGHLIGHTSHierarchical molecular testing is recommended for the detection of avian C. psittaci.Key molecular tests for surveillance were conventional PCR and quantitative PCR.The most used genomic target to detect C. psittaci in birds was the ompA gene.

Cross-European laboratory evaluation of commercial and in-house real-time PCR assays for the detection of Chlamydia abortus in small ruminants

Chlamydia abortus is a bacterial pathogen that causes enzootic abortion of ewes (EAE), a disease of sheep and goats with potential risks to human health. Accurate detection is essential for disease management and prevention. While serological tests have been widely used for herd screening, they are lacking in terms of sensitivity and specificity. PCR methods, particularly real-time PCR, are now preferred due to their improved sensitivity and accuracy for confirmation of clinical cases and for use in routine surveillance. This study aimed to compare and evaluate the analytical parameters and diagnostic performance of two commercial PCR tests and four in-house PCR methods for their suitability for diagnosing EAE. Two of the in-house methods are based on the ompA gene, which is specifically used to detect C. abortus in ruminants. The other two tests target different genetic markers, that also allow the detection of avian C. abortus strains. The study found that all PCR tests had a similar analytical sensitivity and were effective in identifying C. abortus in clinical samples, such as placentas, vaginal swabs and fetal organs especially in animals showing symptoms. However, detection in asymptomatic carriers was more difficult. One of the ompA-based assays showed superior diagnostic accuracy, particularly compared to the commercial kits, with a diagnostic sensitivity of 98.0 % and a diagnostic specificity of 96.6 % and is thus the one recommended for routine testing. The study also concluded that the interpretation criteria of the commercial kits should be reviewed to improve their reliability.

Seroprevalence of Chlamydia abortus infection in Tibetan sheep in Qinghai Province, China

Chlamydia abortus (C. abortus) is an obligate intracellular, Gram-negative bacterium, causing ovine enzootic abortion (OEA). No data about C. abortus infection are available in Tibetan sheep in Qinghai, China. A total of 1043 Tibetan sheep serum samples were collected from 8 regions in Qinghai, China, and for specific antibodies against C. abortus using a commercial ELISA Kit. The results showed that the overall seroprevalence of C. abortus in Tibetan sheep was 153/1043 (14.7 %, 95 % confidence interval [CI] 12.5-16.8). The prevalence in female and male Tibetan sheep was 58/421 (13.8 %, 95 % CI 10.5-17.1) and 95/622 (15.3 %, 95 % CI 18.6-26.6), respectively with no significant difference (P > 0.05). The seroprevalence of antibodies to C. abortus in Tibetan sheep ranged from 10.0 to 21.7 % among the eight different areas, and the difference was also without statistical significance. The prevalence among different age groups ranged from 14.0 to 16.5 %, with a higher prevalence among 1 to 1.5 years age category. The results demonstrate the presence of C. abortus infection in Tibetan sheep in Qinghai and its potential impact on public health and the local Tibetan economy. To our knowledge, this is the first seroprevalence survey of C. abortus in Tibetan sheep in Qinghai, China.

Community-Acquired Pneumonia Caused by Avian Chlamydia abortus, the Netherlands

We report avian Chlamydia abortus pneumonia in an immunocompetent elderly patient in the Netherlands after environmental exposure to wild aquatic birds, including seabirds. New molecular surveillance studies are needed in wild and captive birds, as well as increased awareness to establish occurrence, clinical manifestations, and geographic distribution of this rare zoonotic disease.

Limited transmission of avian influenza viruses, avulaviruses, coronaviruses and Chlamydia sp. at the interface between wild birds and a free-range duck farm

Recent outbreaks of highly pathogenic avian influenza in Europe have raised questions regarding the epidemiological role of commensal wild birds on free-range poultry farms. This study aimed to assess the prevalence of avian influenza viruses (AIV), avulaviruses, coronaviruses and Chlamydia sp. in commensal wild birds on a free-range duck farm in southwestern France and to evaluate possible transmission events at the wild‒domestic interface. From 2019 through 2021, a longitudinal study was conducted on wild birds, domestic ducks and their shared environment on farms. Commensal wild birds were captured and sampled for blood and swabs, and fresh feces from cattle egrets visiting the farm were collected. In parallel, domestic ducks were sampled, and environmental samples were collected. The presence of the four pathogens was tested by q(RT-)PCR, and the immunity of wild birds to AIV and Newcastle disease virus (NDV) was tested by ELISA. Wild birds were found to shed AIV and Chlamydia only, with a low prevalence (< 3%). The seroprevalence rates were less than 10% for AIV and less than 4.5% for NDV. No significant temporal trend was identified. Ducks and their environment frequently test simultaneously positive for the same pathogens (19 to 44% of flocks), mostly during fall‒winter. In addition to unrelated temporal patterns, the identification of pathogens in wild birds seemed unrelated to that in domestic ducks. These results suggest a low transmissibility of the avian pathogens tested in our study at the wild‒domestic interface and highlight the limited contribution of commensal wild birds in comparison with free-range poultry to the global microbiological pressure on the environment.

Circulation of avian Chlamydia abortus in the Netherlands and community-acquired pneumonia: an outbreak investigation and retrospective cohort study

BACKGROUND

In 2021, a novel group of Chlamydia strains in wild birds was classified as avian Chlamydia abortus, with unknown zoonotic potential. We report relevant features of avian C abortus infections from a Dutch family cluster and unrelated historical cases using clinical, epidemiological, and microbiological data.

METHODS

An outbreak of avian C abortus started in the Netherlands in December, 2022. Source investigation was done using questionnaires to interview patients and environmental sampling. The outbreak strain of avian C abortus was cultured from three patients from whom sufficient material was available for culture and underwent whole-genome analysis. The outbreak strains and retrospective cohort study strains previously submitted to the National Human Psittacosis surveillance programme in the Netherlands between 2010 and 2022 were typed by partial ompA sequencing. Strains with the same aberrant ompA genotype were further analysed with XerC gene plasmid analysis and compared with closely related Chlamydia sequences available in GenBank.

FINDINGS

An avian C abortus strain caused a cluster of respiratory illness in four family members. Three patients were hospitalised with community-acquired pneumonia, one of whom was admitted to the intensive care unit. The faeces of wild birds were considered a probable source for the index infection. For two family members, human-to-human transmission was a plausible route. Ten historical cases could be identified with avian C abortus with the same ompA genotype. All patients had been admitted to hospital, at least five developed pneumonia, and one died.

INTERPRETATION

This cluster supports that avian C abortus strains can cause human infections and underlines that human-to-human transmission should be considered when tracing the source of such infections.

FUNDING

National Institute for Public Health and the Environment and Dutch Ministry of Agriculture, Fisheries, Food Security and Nature.

TRANSLATION

For the Dutch translation of the abstract see Supplementary Materials section.

Chlamydia psittaci: A zoonotic pathogen causing avian chlamydiosis and psittacosis

Chlamydia psittaci is an obligate intracellular gram-negative bacterium with a unique biphasic developmental cycle. It is a zoonotic pathogen with a wide range of hosts and can cause avian chlamydiosis in birds and psittacosis in humans. The pathogen is transmitted mainly through horizontal transmission between birds. Cross-species transmission sometimes occurs and human-to-human transmission has recently been confirmed. This review provides an updated overview of C. psittaci from the perspective of both avian chlamydiosis and psittacosis. We include the aspects of genotype, host-pathogen interaction, transmission, epidemiology, detection and diagnosis, clinical manifestation, management, and prevention, aiming to provide a basic understanding of C. psittaci and offer fresh insights focused on zoonosis and cross-species transmission.

Chlamydiosis in Animals

The Chlamydiaceae family consists of Gram-negative, obligate intracellular bacteria that replicate within the cells of a diverse range of hosts. These hosts include domesticated animals such as cats, dogs, and livestock, as well as wildlife like koalas and birds, exotic species such as reptiles and amphibians, and humans. Chlamydial infection can result in various clinical signs, including respiratory diseases, reproductive failures, ocular pathologies, and enteritis, though the infected organism may remain asymptomatic. In recent years, chlamydial nomenclature has undergone several revisions due to the wide range of hosts, the frequent discovery of novel strains, and the reclassification of existing ones. Given this and the clinical significance of these infections, ranging from asymptomatic to fatal, an updated review is essential. This article outlines key characteristics of Chlamydia species and provides an updated overview of their nomenclature, offering a concise reference for future research on chlamydial diseases.

Outbreak of Chlamydia psittaci Infection in a Commercial Psittacine Breeding Aviary in Argentina

Chlamydiosis, caused by Chlamydia psittaci is a bacterial infection found in at least 465 species of birds worldwide. It is highly contagious among birds and can spread to humans. In birds, the disease can manifest itself in acute, subacute, and chronic forms with signs including anorexia, diarrhea, lethargy, weight loss, or, occasionally, mucopurulent or serous oculonasal discharge. This article describes an outbreak of chlamydiosis that occurred in a commercial psittacine breeding aviary in 2021 in Buenos Aires province, Argentina. In total, 16 juvenile blue-fronted parrots, more than 60 blue-fronted parrot chicks, and 2 adult macaws died during the outbreak. In all cases, clinical signs were weight loss, diarrhea, yellowish green excrement, and respiratory distress. The necropsy of four juvenile blue-fronted parrots, two blue-fronted parrot chicks, and two adult macaws revealed cachexia, hepatomegaly, splenomegaly, splenic petechial hemorrhages, ascites, pulmonary edema, and hydropericardium. Histologically, multifocal lymphoplasmacytic and heterophilic airsaculitis, multifocal lymphoplasmacytic and necrotizing hepatitis with intracytoplasmic elementary bodies, multifocal necro-heterophilic hepatitis, multifocal lymphoplasmacytic nephritis, and diffuse heterophilic pneumonia were found. A presumptive diagnosis was established based on gross and microscopic lesions, and it was confirmed using immunohistochemistry and polymerase chain reactions. The sequencing and phylogenetic analysis of the ompA gene revealed genotype A and B of Chlamydia psittaci.

Zoonotic and other veterinary chlamydiae - an update, the role of the plasmid and plasmid-mediated transformation

The obligate intracellular bacterial genus Chlamydia harbours species with zoonotic potential, particularly C. psittaci, causative agent of psittacosis, and C. abortus, which may lead to miscarriage in pregnant women. The impact of other bird chlamydiae such as C. avium, C. gallinaceae, and C. buteonis, or reptilian species such as C. crocodili, amongst others, on human health is unclear. The chlamydial native plasmid, a suspected virulence factor, is present in all currently described 14 Chlamydia species except for some plasmid-free strains. The plasmid is also the primary tool to study chlamydial genetics, a still developing field that has mostly focused on C. trachomatis. Only recently, genetic transformation of C. felis, C. pecorum, C. pneumoniae, C. psittaci, and C. suis has succeeded, but existing methods have yet to be refined. In this review article, we will provide an update on the recent developments concerning the zoonotic potential of chlamydiae. Furthermore, we present an overview about the current state of knowledge regarding the chlamydial plasmid in terms of prevalence and significance as a virulence factor. Finally, we give insights into the progress of developing genetic tools for chlamydial species other than C. trachomatis with a special focus on zoonotic and veterinary chlamydiae.

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.

Draft genomes of novel avian Chlamydia abortus strains from Australian Torresian crows (Corvus orru) shed light on possible reservoir hosts and evolutionary pathways

Chlamydia abortus, an obligate intracellular bacterium, is a major causative agent of reproductive loss in ruminants, with zoonotic potential. Though this pathogen is primarily known to infect livestock, recent studies have detected and isolated genetically distinct avian strains of C. abortus from wild birds globally. Before this study, only five avian C. abortus genomes were publicly available. Therefore, we performed culture-independent probe-based whole-genome sequencing on clinical swabs positive for avian C. abortus obtained from Australian Torresian crows (Corvus orru) in 2019 and 2020. We successfully obtained draft genomes for three avian C. abortus strains (C1, C2 and C3), each comprising draft chromosomes with lengths of 1 115 667, 1 120 231 and 1 082 115 bp, and associated 7 553 bp plasmids, with a genome completeness exceeding 92 %. Molecular characterization revealed that these three strains comprise a novel sequence type (ST333), whilst phylogenetic analyses placed all three strains in a cluster with other avian C. abortus genomes. Interestingly, these three strains share a distant genomic relation (2693 single nucleotide variants) with the reference strain 15-58d/44 (ST152), isolated from a Eurasian magpie (Pica pica) in Poland, highlighting the need for more publicly available genomes. Broad comparative analyses with other avian C. abortus genomes revealed that the three draft genomes contain conserved Chlamydia genomic features, including genes coding for type III secretion system and polymorphic membrane proteins, and potential virulence factors such as the large chlamydial cytotoxin, warranting further studies. This research provides the first avian C. abortus draft genomes from Australian birds, highlighting Torresian crows as novel reservoir hosts for these potential pathogens, and demonstrates a practical methodology for sequencing novel Chlamydia genomes without relying on traditional cell culture.

First detection of Chlamydia avium in healthy Amazon parrots (Amazona aestiva) in Argentina

In recent years, new Chlamydia species, other than Chlamydia psittaci, have been confirmed in birds. One of these new species, Chlamydia avium, was reported mainly in pigeons and parrots in Europe. Analyzing multimucosal swabs obtained from 7 Amazon parrots (Amazona aestiva) from illegal trade and admitted to the Reserva Experimental Horco Molle (Tucuman, Argentina) for their rehabilitation, we describe the finding of the genetic material of C. avium in 2 of these birds. There were no signs compatible with the chlamydiosis-like disease in the studied birds or in the rehabilitation center staff. The use of sensitive and wide-ranging molecular tools is necessary for the detection of all Chlamydiaceae present in birds and would aid in the selection of control measures in wildlife rehabilitation centers to prevent outbreaks in the facilities and the introduction of pathogens in nature. We provide the first molecular evidence of the presence of C. avium in Argentina and a new species of psittacine host.

Three Cases of Atypical Pneumonia with Chlamydia psittaci: The Role of Laboratory Vigilance in the Diagnosis of Psittacosis

Chlamydia psittaci is an established zoonotic agent causing respiratory disease in humans. An infection often remains asymptomatic but can also result in flu-like illness, pneumonia or even multi-organ failure. This paper describes three patients, hospitalised at AZ Sint-Lucas Hospital, with atypical pneumonia who were diagnosed with C. psittaci after an in-depth anamnesis and laboratory investigation in the midst of the COVID pandemic. All three infections were confirmed with PCR and serology, whereas viable bacteria were only present for one patient. Genotyping revealed the presence of genotype B for patient 1 and 2 whereas ompA genotyping was unsuccessful for patient 3. This case report demonstrates the importance of a thorough patient history as close contact with birds is one of the main risk factors to contract the pathogen. Once exposure to birds has been confirmed, a diagnosis by a combination of PCR and serology is essential in order to initiate a treatment with the proper antibiotics. As psittacosis is still an underestimated and underdiagnosed disease, communication between laboratory, clinicians and bird fanciers is encouraged.

Chlamydia psittaci in Faecal Samples of Feral Pigeons (Columba livia forma urbana) in Urban Areas of Lublin city, Poland

Pigeons are a typical host and natural reservoir of Chlamydia psittaci, the etiological agent of avian chlamydiosis, considered as a neglected zoonotic diseases. The aim of the study was to determine the prevalence of C. psittaci in faecal samples of feral pigeons (Columba livia forma urbana) as a potential source of infection related to the presence of synanthropic birds in urban areas. A total of 143 samples of dry and fresh faeces of feral pigeons, were collected in the city of Lublin (Poland), from April to September 2021. Molecular detection of C. psittaci was performed by nested-PCR and real-time PCR, confirmed by sequencing. Among the collected samples, 5 positive results were obtained in nested-PCR (3.5%), while in real-time PCR, the number of positive samples increased to 11 (7.7%). The positive samples showed 100% identity to the C. psittaci strain AMK (CP047319.1). C. psittaci was found in 7 out of 111 (6.3%) faecal samples collected in public places, and in 4 out of 32 (12.5%) samples from the nesting site (4.9% and 2.8% among a total of 143 samples, respectively). The infection was detected in both dry and fresh faeces (9.1% and 4.5%, respectively). The highest number of positive results was obtained in June—5 (3.5%). Feral pigeons occurring in urban areas are a natural reservoir of C. psittaci posing a potential risk of zoonotic infections. However, further studies on exposure to contaminated pigeon faeces in terms of occupational and non-occupational risk of chlamydiosis are needed.

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.

Prevalence of New and Established Avian Chlamydial Species in Humans and Their Psittacine Pet Birds in Belgium

The presence and zoonotic transfer of four different avian Chlamydia spp. was assessed in an epidemiological study in a psittacine bird population and its owners. Fecal swabs from 84 pet birds and pharyngeal swabs from 22 bird owners were collected from 21 locations in Flanders. Samples were examined using established and novel PCR platforms combined with culture on PCR-positive samples. Chlamydiaceae DNA was detected in 33 of 84 (39.3%) birds. The predominant part of the avian infections could be attributed to C. psittaci (22 of 84; 26.2%), followed by C. avium (11 of 84; 13.1%). C. gallinacea and C. abortus were not detected in birds or humans. C. psittaci was the only species detected in pet bird owners (4 of 22; 18.2%), stressing its zoonotic importance. This study showed that C. psittaci and the more recently discovered novel avian species C. avium are undoubtedly present in the Flemish psittacine bird population. Our results justify additional research in a larger psittacine bird population and its owners, focusing on C. psittaci and C. avium. In the meantime, increased awareness among pet bird owners and the implementation of preventive measures in the pet bird industry is advised to limit the circulation of established and novel emerging avian chlamydial species.

Recent advances and public health implications for environmental exposure to Chlamydia abortus: from enzootic to zoonotic disease

Environmental transmission of Chlamydia abortus as a result of enzootic disease or disease outbreaks and the threats posed by this pathogen has been previously reported, however a state-of-the-science review of these reports and the identification of future research priorities in this area is still lacking. This study provides an overview of the current knowledge of host–pathogen–environment interactions, addressing public health risks and identifying critical questions and research gaps. We performed a systematic PubMed and Web of Science search for publications related to Chlamydia abortus in the past four decades, and we reviewed and combined the evidence critically discussing and commenting the results. A total of 182 studies, 5 chapters of specific books and the “OIE terrestrial manual” were included in this review. There were substantial variations between the studies in topic addressed and experimental design. Overall, the literature largely supports the crucial role played by environmental exposure on the acquisition of zoonotic disease caused by Chlamydia abortus. We also identify the paucity of information related to interspecies transmission and pathogen adaptation in relation to environmental dissemination and zoonotic risk. This analysis further highlights the need for additional research given that environmental transmission represents a serious risk not only to susceptible patients (pregnant women and immunocompromised individuals), but also for other species including wildlife.

Occurrence of Chlamydiae in Corvids in Northeast Italy

Simple Summary

The continuous improvement of next-generation sequencing techniques has led to an expansion of the number of Chlamydia species, as well as their host range. Recent studies performed on wild birds have detected Chlamydia strains with characteristics intermediate between Chlamydia psittaci and Chlamydia abortus. In this study, 12/108 corvids tested positive for Chlamydia by real-time PCR. Molecular characterisation at the species level was possible for eight samples, with one positive for C. psittaci and seven for C. abortus. Considering the well-known zoonotic role of C. psittaci and that a potential zoonotic role of avian C. abortus strains cannot be excluded, people who may have professional or other contact with wild birds should take appropriate preventive measures.

Abstract

Chlamydiaceae occurrence has been largely evaluated in wildlife, showing that wild birds are efficient reservoirs for avian chlamydiosis. In this study, DNA extracted from cloacal swabs of 108 corvids from Northeast Italy was screened for Chlamydiaceae by 23S real-time (rt)PCR. The positive samples were characterised by specific rtPCRs for Chlamydia psittaci, Chlamydia abortus, Chlamydia gallinacea, Chlamydia avium, Chlamydia pecorum and Chlamydia suis. Cloacal shedding of Chlamydiaceae was detected in 12 out of 108 (11.1%, 5.9%–18.6% 95% CI) corvids sampled. Molecular characterisation at the species level was possible in 8/12 samples, showing C. psittaci positivity in only one sample from a hooded crow and C. abortus positivity in seven samples, two from Eurasian magpies and five from hooded crows. Genotyping of the C. psittaci-positive sample was undertaken via PCR/high-resolution melting, clustering it in group III_pigeon, corresponding to the B genotype based on former ompA analysis. For C. abortus genotyping, multilocus sequence typing was successfully performed on the two samples with high DNA load from Eurasian magpies, highlighting 100% identity with the recently reported Polish avian C. abortus genotype 1V strain 15-58d44. To confirm the intermediate characteristics between C. psittaci and C. abortus, both samples, as well as two samples from hooded crows, showed the chlamydial plasmid inherent in most C. psittaci and avian C. abortus, but not in ruminant C. abortus strains. The plasmid sequences were highly similar (≥99%) to those of the Polish avian C. abortus genotype 1V strain 15-58d44. To our knowledge, this is the first report of avian C. abortus strains in Italy, specifically genotype 1V, confirming that they are actively circulating in corvids in the Italian region tested.

Chlamydial species among wild birds and livestock in the foothills of Mt. Afadjato, Ghana

The members of family Chlamydiaceae have a broad host range and cause many kinds of diseases in humans and animals. Several cases of Chlamydiaceae being detected in atypical hosts have been reported recently. Consequently, cross-species monitoring of Chlamydia in wildlife and livestock is pertinent for public health, animal hygiene and wildlife conservation. In this study, we conducted molecular surveillance of Chlamydia in wild birds and livestock around a small village in the foothills of Mt. Afadjato, Ghana where direct contact between wildlife and livestock occurs. Among 29 captured wild birds and 63 livestock, 5 sheep, 30 goats and 28 chickens, the positive ratios of Chlamydia were 24.1%, 40.0%, 43.3% and 26.9%, respectively. Chlamydia pecorum was detected in wild birds, goats, sheep and chickens. On the basis of the variable domain 2 region of ompA, several samples from different hosts showed identical sequences and were phylogenetically located to the same clusters. In addition, using ompA, C. psittaci, C. abortus and C. gallinacea were also detected in this small habitat. Further genetic and pathogenic analyses of the chlamydial distribution in this area, which represents the interface of wild and domestic animal interactions, may improve our knowledge of their transmission among different hosts.

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.

Whole Genome Sequencing and Comparative Genome Analyses of Chlamydia abortus Strains of Avian Origin Suggests That Chlamydia abortus Species Should Be Expanded to Include Avian and Mammalian Subgroups

A variety of Chlamydia species belonging to the Chlamydiaceae family have been reported in birds. Until recently, C. psittaci was considered to be the most common avian species, although found in both birds and mammals, while C. abortus has only been found in mammals. Recently, a new group of avian C. abortus strains with worldwide distribution in various wild bird families has been described. In this study, whole genome sequencing (WGS) of three of these strains (15-70d24, 15-49d3 and 15-58d44, representing genotypes G1, G2 and 1V, respectively) that were isolated from wild birds were analysed. Genome assemblies based on both short-read Illumina and long-read Nanopore data indicate that these avian C. abortus strains show features characteristic of both C. abortus and C. psittaci species, although phylogenetic analyses demonstrate a closer relationship with classical C. abortus strains. Currently, species classification established by the ICSP Subcommittee on the taxonomy of Chlamydiae, determines that these avian C. abortus strains 15-70d24, 15-49d3 and 15-58d44 should be classified as C. abortus. However, the authors of this study conclude that the current taxonomic definition of C. abortus is outdated and should be amended to include two subgroups, mammalian and avian, the latter of which would include all isolates so far referred to as atypical C. psittaci or C. psittaci/C. abortus intermediates.

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.

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.

A comprehensive review on avian chlamydiosis: a neglected zoonotic disease

Avian chlamydiosis is one of the important neglected diseases with critical zoonotic potential. Chlamydia psittaci, the causative agent, affects most categories of birds, livestock, companion animals, and humans. It has many obscured characters and epidemiological dimensions, which makes it unique among other bacterial agents. Recent reports on transmission from equine to humans alarmed the public health authorities, and it necessitates the importance of routine screening of this infectious disease. High prevalence of spill-over infection in equines was associated with reproductive losses. Newer avian chlamydial species are being reported in the recent years. It is a potential biological warfare agent and the disease is an occupational hazard mainly to custom officers handling exotic birds. Prevalence of the disease in wild birds, pet birds, and poultry causes economic losses to the poultry industry and the pet bird trade. Interestingly, there are speculations on the ‘legal’ and ‘illegal’ bird trade that may be the global source of some of the most virulent strains of this pathogen. The mortality rate generally ranges from 5 to 40% in untreated cases, but it can sometimes be higher in co-infection. The intracellular lifestyle of this pathogen makes the diagnosis more complicated and there is also lack of accurate diagnostics. Resistance to antibiotics is reported only in some pathogens of the Chlamydiaceae family, but routine screening may assess the actual situation in all pathogens. Due to the diverse nature of the pathogen, the organism necessitates the One Health partnerships to have complete understanding. The present review focuses on the zoonotic aspects of avian chlamydiosis with its new insights into the pathogenesis, transmission, treatment, prevention, and control strategies. The review also briefs on the basic understandings and complex epidemiology of avian chlamydiosis, highlighting the need for research on emerging one health perspectives.

Presence and shedding of Chlamydia psittaci in waterfowl in a rehabilitation facility and in the wild in New Zealand

AIMS

To determine the frequency of Chlamydia psittaci infection, shedding dynamics of C. psittaci, and C. psittaci genotype diversity in waterfowl temporarily resident in a rehabilitation facility and in mallards in the wild.

METHODS

Conjunctival-choanal-cloacal swabs were collected from apparently healthy captive wild mallards (Anas platyrhynchos; n = 114) and paradise shelducks (Tadorna variegata; n = 10) temporarily housed at a waterfowl breeding and rehabilitation facility (Wellington, NZ) and from wild mallards in Palmerston North (n = 50), and Southland (n = 50). DNA extracted from the swabs was analysed using quantitative PCR (qPCR) high-resolution melt curve (HRM) analysis, targeting the ompA gene of C. psittaci.

RESULTS

Of the captive waterfowl, 39/114 (34%) mallards and 6/10 (60%) paradise shelducks were positive for C. psittaci as were 24/100 (24%) wild mallards. All wild mallards and paradise shelducks carried only C. psittaci genotype C. In captive wild mallards, genotypes A and C, and a mixed infection of both genotypes were found. Captive wild mallards and paradise shelducks were found to be shedding 4 to 5 × 10⁴ and 1 × 10⁵ to 4 × 10⁵ copies of C. psittaci DNA per swab, respectively, with wild mallards shedding 4-677 DNA copies/swab.

CONCLUSIONS

Based on qPCR-HRM analysis, a high proportion of wild mallards were infected with C. psittaci but these birds were shedding only a small amount of bacterial DNA. The proportion of sampled ducks that were infected and the extent of bacterial shedding were higher in the birds in a wildlife rehabilitation facility. The major C. psittaci genotype found in the mallards and paradise shelducks was genotype C. This is the first detection of C. psittaci genotype A and co-infection of genotype A and C in ducks.

CLINICAL RELEVANCE

These results indicate that mallards are a reservoir of C. psittaci and therefore may pose a zoonotic risk to people involved in duck hunting, wildlife care and recreational duck feeding. Mallards may also pose a transmission risk to native birds, especially in captive facilities and this has conservation implications for the management of endangered native birds.

Global prevalence of chlamydial infections in birds: A systematic review and meta-analysis

Chamydia species are bacterial pathogens that can infect a wide range of animal hosts including humans. In birds, Chlamydia psittaci is a leading cause of chlamydial infections (avian chlamydiosis) and is a zoonotic pathogen causing human psittacosis. The objectives of this study were to estimate the global prevalence of chlamydial infections in birds, to assess heterogeneity of the prevalence for some particular characteristics (continents, bird orders, specimen types, and diagnostic techniques), and to determine the trend of the prevalence over time. The relevant citations on the prevalence of chlamydial infections in birds were retrieved from PubMed, Scopus, and Web of Science. Titles and abstracts of the retrieved citations were screened for possible eligibility. Then, full-texts of eligible articles were assessed for data extraction. A random effects model was used for estimating the global prevalence of chlamydial infections in birds and for all other meta-analyses. Subgroup meta-analysis was used to assess heterogeneity of the prevalence for the characteristics mentioned above. Meta-regression analysis and cumulative meta-analysis were used to determine the trend of the prevalence over time. The quality of each included study was also evaluated. Of 579 citations, 74 studies (a total of 39,225 bird samples from 26 countries, five continents) were included in meta-analysis. Almost all included studies reported birds with C. psittaci infections. The global prevalence of chlamydial infections in birds was 19.5 % (95 % CI, 16.3 %-23.1 %). No significant differences of the prevalence were observed among continents, the prevalence ranged from 16.5 % (95 % CI, 9.8 %-26.5 %) in South America to 21.7 % (95 % CI, 12.1 %-35.9 %) in North America. No significant differences of the prevalence were observed among bird orders, the prevalence ranged from 13.4 % (95 % CI, 7.0 %-23.9 %) in Passeriformes to 32.0 % (95 % CI, 20.6 %-46.1 %) in Galliformes. No significant differences of the prevalence were observed between specimen types; the prevalence was 18.4 % (95 % CI, 15.2 %-22.2 %) for live specimens and 26.3 % (95 % CI, 17.1 %-38.1 %) for carcass specimens. The prevalence was significantly higher in non-PCR techniques (29.5 %, [95 % CI, 22.4 %-37.8 %]) than in PCR techniques (15.3 %, [95 % CI, 12.1 %-19.1 %]). The cumulative evidence showed that the prevalence of chlamydial infections in birds has been relatively stable around 20 % since 2012. This study indicates that the global prevalence of chlamydial infections in birds is quite high and all bird orders are potential sources for human psittacosis.

Draft Genome Sequences of Avian Chlamydia abortus Genotype G2 Strain 15-49d3, Isolated from Mallard, and Genotype 1V Strain 15-58d44, Isolated from Magpie in Poland

Here, we report the draft genome sequences of avian Chlamydia abortus genotype G2 strain 15-49d3, isolated from mallard, and genotype 1V strain 15-58d44, isolated from magpie in Poland. The total genome assembly lengths are 1,140,139 bp and 1,158,207 bp, respectively.

Here, we report the draft genome sequences of avian Chlamydia abortus genotype G2 strain 15-49d3, isolated from mallard, and genotype 1V strain 15-58d44, isolated from magpie in Poland. The total genome assembly lengths are 1,140,139 bp and 1,158,207 bp, respectively.

Evidence for the existence of a new genus Chlamydiifrater gen. nov. inside the family Chlamydiaceae with two new species isolated from flamingo (Phoenicopterus roseus): Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov

The family Chlamydiaceae currently comprises a single genus Chlamydia, with 11 validly published species and seven more taxa. It includes the human pathogens Chlamydia (C.) trachomatis, C. pneumoniae and C. psittaci, a zoonotic agent causing avian chlamydiosis and human psittacosis, as well as other proven or potential pathogens in ruminants, birds, snakes, reptiles and turtles. During routine testing of 15 apparently healthy captive flamingos in a zoo in 2011, an atypical strain of Chlamydiaceae was detected by real-time PCR of cloacal swab samples. Sequence analysis of the 16S rRNA gene revealed high similarity to the uncultured Chlamydiales bacterium clone 122, which previously had been found in gulls. As more samples were collected during annual campaigns of the flamingo ringing program in southern France from 2012 to 2015, Chlamydiaceae-specific DNA was detected by PCR in 30.9% of wild birds. From these samples, three strains were successfully grown in cell culture. Ultrastructural analysis, comparison of 16S and 23S rRNA gene sequences, whole-genome analysis based on de novo hybrid-assembled sequences of the new strains as well as subsequent calculation of taxonomic parameters revealed that the relatedness of the flamingo isolates to established members of the family Chlamydiaceae was sufficiently distant to indicate that the three strains belong to two distinct species within a new genus. Based on these data, we propose the introduction of Chlamydiifrater gen. nov., as a new genus, and Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov., as two new species of the genus.

A New SNP-Based Genotyping Method for C. psittaci: Application to Field Samples for Quick Identification

Chlamydia (C.) psittaci is the causative agent of avian chlamydiosis and human psittacosis. In this study, we extracted single-nucleotide polymorphisms (SNPs) from the whole genome sequences of 55 C. psittaci strains and identified eight major lineages, most of which are host-related. A combined PCR/high-resolution melting (HRM) assay was developed to screen for eight phylogenetically informative SNPs related to the identified C. psittaci lineages. The PCR-HRM method was validated on 11 available reference strains and with a set of 118 field isolates. Overall, PCR-HRM clustering was consistent with previous genotyping data obtained by ompA and/or MLST analysis. The method was then applied to 28 C. psittaci-positive samples from animal or human cases. As expected, PCR-HRM typing results from human samples identified genotypes linked to ducks and pigeons, a common source of human exposure, but also to the poorly described Mat116-like genotype. The new genotyping method does not require time-consuming sequencing and allows a quick identification of the source of infection.

Whole genome de novo sequencing and comparative genomic analyses suggests that Chlamydia psittaci strain 84/2334 should be reclassified as Chlamydia abortus species

BACKGROUND

Chlamydia abortus and Chlamydia psittaci are important pathogens of livestock and avian species, respectively. While C. abortus is recognized as descended from C. psittaci species, there is emerging evidence of strains that are intermediary between the two species, suggesting they are recent evolutionary ancestors of C. abortus. Such strains include C. psittaci strain 84/2334 that was isolated from a parrot. Our aim was to classify this strain by sequencing its genome and explore its evolutionary relationship to both C. abortus and C. psittaci.

RESULTS

In this study, methods based on multi-locus sequence typing (MLST) of seven housekeeping genes and on typing of five species discriminant proteins showed that strain 84/2334 clustered with C. abortus species. Furthermore, whole genome de novo sequencing of the strain revealed greater similarity to C. abortus in terms of GC content, while 16S rRNA and whole genome phylogenetic analysis, as well as network and recombination analysis showed that the strain clusters more closely with C. abortus strains. The analysis also suggested a closer evolutionary relationship between this strain and the major C. abortus clade, than to two other intermediary avian C. abortus strains or C. psittaci strains. Molecular analyses of genes (polymorphic membrane protein and transmembrane head protein genes) and loci (plasticity zone), found in key virulence-associated regions that exhibit greatest diversity within and between chlamydial species, reveal greater diversity than present in sequenced C. abortus genomes as well as similar features to both C. abortus and C. psittaci species. The strain also possesses an extrachromosomal plasmid, as found in most C. psittaci species but absent from all sequenced classical C. abortus strains.

CONCLUSION

Overall, the results show that C. psittaci strain 84/2334 clusters very closely with C. abortus strains, and are consistent with the strain being a recent C. abortus ancestral species. This suggests that the strain should be reclassified as C. abortus. Furthermore, the identification of a C. abortus strain bearing an extra-chromosomal plasmid has implications for plasmid-based transformation studies to investigate gene function as well as providing a potential route for the development of a next generation vaccine to protect livestock from C. abortus infection.

Development of a species-specific real-time PCR test for Chlamydia psittaci and its employment in the investigation of zoonotic transmission from racing pigeons in Denmark

Species-specific detection of Chlamydia psittaci is challenging and all published PCR tests have so far shown deficiencies in specificity or sensitivity. The present investigation reports on the development of a species-specific real-time PCR assay for C. psittaci. The test is based on an 84 bp indel in a gene of unknown function that is unique to C. psittaci. The Cps-indel84-PCR assay was validated on a wide range of chlamydial and other bacterial strains as well as on clinical samples from animals and humans in two different diagnostic laboratories in Germany and Denmark. Furthermore, the test was employed for investigating samples from racing pigeon flocks in Denmark. The evaluation showed that the Cps-indel84-PCR assay has excellent test characteristics and is a highly reliable method for identifying C. psittaci in clinical samples both from humans and animals.

Chlamydiae - What's New?

This paper provides an overview of the current knowledge of chlamydiae. These intracellular microorganisms belonging to the Chlamydiaceae family are widely distributed throughout the world. Constant development of culture-independent approaches for characterisation of microbial genomes enables new discoveries in the field of Chlamydia. The number of new taxa is continuously increasing as well as the range of hosts. New species and genotypes are constantly being discovered, particularly new avian and reptilian agents, which are discussed in this article. Interestingly, wild animals are the main hosts for new Chlamydia species including different species of bird, turtle and snake. The availability of next-generation sequencing opens up a new prospect for research and leads to deeper knowledge of these interesting microorganisms about which much is still to discover.

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.

Comparative Genome Analysis of 33 Chlamydia Strains Reveals Characteristic Features of Chlamydia Psittaci and Closely Related Species

To identify genome-based features characteristic of the avian and human pathogen Chlamydia(C.) psittaci and related chlamydiae, we analyzed whole-genome sequences of 33 strains belonging to 12 species. Using a novel genome analysis tool termed Roary ILP Bacterial Annotation Pipeline (RIBAP), this panel of strains was shown to share a large core genome comprising 784 genes and representing approximately 80% of individual genomes. Analyzing the most variable genomic sites, we identified a set of features of C. psittaci that in its entirety is characteristic of this species: (i) a relatively short plasticity zone of less than 30,000 nt without a tryptophan operon (also in C. abortus, C. avium, C. gallinacea, C. pneumoniae), (ii) a characteristic set of of Inc proteins comprising IncA, B, C, V, X, Y (with homologs in C. abortus, C. caviae and C. felis as closest relatives), (iii) a 502-aa SinC protein, the largest among Chlamydia spp., and (iv) an elevated number of Pmp proteins of subtype G (14 in C. psittaci, 14 in Cand. C. ibidis). In combination with future functional studies, the common and distinctive criteria revealed in this study provide important clues for understanding the complexity of host-specific behavior of individual Chlamydia spp.

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.

Detection of Chlamydia psittaci and Chlamydia ibidis in the Endangered Crested Ibis (Nipponia nippon)

Chlamydia spp. are a group of obligate intracellular pathogens causing a number of diseases in animals and humans. Avian chlamydiosis (AC), caused by Chlamydia psittaci (C. psittaci) as well as new emerging C. avium, C. gallinacea and C. ibidis, have been described in nearly 500 avian species worldwidely. The Crested Ibis (Nipponia nippon) is a world endangered avian species with limited population and vulnerable for various infections. To get a better understanding of the prevalence of Chlamydia spp. in the endangered Crested Ibis, faecal samples were collected and analysed. The results confirmed that 20.20% (20/99) of the faecal samples were positive for Chlamydiaceae and were identified as C. ibidis with co-existence of C. psittaci in one of the 20 positive samples. In addition, ompA sequence of C. psittaci obtained in this study was classified into the provisional genotype Matt116, while that of C. ibidis showed high genetic diversity, sharing only 77% identity with C. ibidis reference strain 10-1398/6. We report for the first time the presence of C. ibidis and C. psittaci in the Crested Ibis, which may indicate a potential threat to the endangered birds and should be aware of the future protection practice.

Chlamydiaceae in wild, feral and domestic pigeons in Switzerland and insight into population dynamics by Chlamydia psittaci multilocus sequence typing

Feral pigeons, common wood pigeons and Eurasian collared doves are the most common representatives of the Columbidae family in Switzerland and are mostly present in highly populated, urban areas. Pigeons may carry various members of the obligate intracellular Chlamydiaceae family, particularly Chlamydia (C.) psittaci, a known zoonotic agent, and C. avium. The objective of the study was to identify the infection rates of common free-roaming pigeons for different Chlamydia species with the overall aim to assess the risk pigeons pose to public health. In this study, 431 pigeons (323 feral pigeons, 34 domestic pigeons, 39 Eurasian collared doves, 35 common wood pigeons) from several geographic locations in Switzerland were investigated for the presence of Chlamydiaceae. Samples consisted of pooled choanal-cloacal swabs (n = 174), liver samples (n = 52), and paired swab and liver samples from 205 pigeons (n = 410). All 636 samples were screened using a Chlamydiaceae family-specific 23S rRNA real-time PCR (qPCR). Subsequent species identification was performed by DNA-microarray assay, sequencing of a 16S rRNA gene fragment and a C. psittaci specific qPCR. In total, 73 of the 431 pigeons tested positive for Chlamydiaceae, of which 68 were positive for C. psittaci, four were C. avium-positive and one pigeon was co-infected with C. avium and C. psittaci. The highest infection rates were detected in feral (64/323) and domestic pigeons (5/34). Common wood pigeons (2/35) and Eurasian collared doves (2/39) revealed lower infection rates. Additionally, multilocus sequence typing of twelve selected C. psittaci-positive samples revealed closely related sequence types (ST) between and within different Swiss cities. Furthermore, liver and corresponding swab samples from the same bird were colonized by the same ST. Considering the high infection rates of C. psittaci in domestic and feral pigeons, close or frequent contact to these birds poses a human health risk.

Survey on Chlamydiaceae in cloacal swabs from Swiss turkeys demonstrates absence of Chlamydia psittaci and low occurrence of Chlamydia gallinacean

In Switzerland, domestic turkey meat is a niche product. Turkeys are fattened on mixed family-based farms scattered across the country, with most providing access to an uncovered outdoor pasture for the birds. Swiss fattening turkeys may therefore get infected with Chlamydiaceae via wild birds or their faeces, potentially shedding these bacteria at a later stage. The aim of the present study was to acquire baseline data about the shedding of Chlamydiaceae in clinically unremarkable Swiss fattening turkeys at slaughter, potentially exposing slaughterhouse workers to infection. In this large-scale study, 1008 cloacal swabs of Swiss turkeys out of 53 flocks from 28 different grow-out farms with uncovered outdoor pasture were collected over the course of 14 months and examined for the occurrence of Chlamydiaceae by a family-specific 23S-rRNA real-time PCR. Positive samples were further analyzed by Chlamydia psittaci (C. psittaci)-specific real-time PCR and the Arraymate DNA Microarray for species identification. All samples were negative for C. psittaci, but seven swabs out of one flock were tested positive for Chlamydia gallinacea (0.7%). Although turkeys with access to pasture may have contact with Chlamydiaceae-harbouring wild birds or their faeces, the infection rate in Swiss turkeys was shown to be low.

Draft Genome Sequence of Avian Chlamydia abortus Genotype G1 Strain 15-70d24, Isolated from Eurasian Teal in Poland

Here, we report the draft genome sequence of avian Chlamydia abortus genotype G1 strain 15-70d24, isolated from Eurasian teal in Poland. The total genome assembly length is 1,149,382 bp.

Here, we report the draft genome sequence of avian Chlamydia abortus genotype G1 strain 15-70d24, isolated from Eurasian teal in Poland. The total genome assembly length is 1,149,382 bp.

Chlamydia buteonis, a new Chlamydia species isolated from a red-shouldered hawk

Chlamydiaceae are obligate intracellular bacterial pathogens for humans and animals. A recent study highlighted that a Chlamydiaceae intermediary between C. psittaci and C. abortus can infect hawks. Here, an isolate was obtained upon passage of cloacal and conjunctival sac material collected from a female hatch-year red-shouldered hawk (Buteo lineatus) in cultured cells. The diseased bird, one of 12 birds housed in a rehabilitation center, developed conjunctivitis and later died. Swabs from both sites tested positive for Chlamydia using the QuickVue Chlamydia test. The isolate, named RSHA, tested negative in qPCR assays specific for C. psittaci and C. abortus, respectively. Analysis of the 16S rRNA, 23S rRNA and whole genome sequences as well as MLST, ANIb and TETRA values reveal that C. psittaci and C. abortus are the closest relatives of RSHA. However, the overall results strongly suggest a phylogenetic intermediate position between these two species. Therefore, we propose the introduction of a new species designated Chlamydia buteonis with RSHA^T as the type strain.

Prevalence and Genotyping of Chlamydia psittaci from Domestic Waterfowl, Companion Birds, and Wild Birds in Taiwan

Chlamydia psittaci, the causative agent of avian chlamydiosis, an important zoonotic disease, infects a wide range of birds. Infected birds, whether symptomatic or asymptomatic, intermittently shed the agent through respiratory and intestinal routes. Therefore, it is essential to investigate the epizootiology of C. psittaci in poultry, pet birds, and wild birds. In this study, cloacal or fecal swabs collected from domestic waterfowl, psittacine birds, Columbidae, and wild birds were used to determine the prevalence of C. psittaci in Taiwan between 2014 and 2017. The C. psittaci infection rate was as high as 34.2% among domestic waterfowl farms. The waterfowl isolates clustered into two groups based on ompA phylogeny: one group (G1-like) clustered with the Polish G1 strains; the other group (waterfowl-TW) clustered near, but independently from, the classical ABE genotype cluster. Separately, 3.1% of parrot samples tested positive for C. psittaci belonging to genotype A. C. psittaci isolates of genotype B were detected in 10.1% of racing pigeons and other Columbidae. Wild bird samples from a wildlife refuge had a 2.2% prevalence rate; among these, two atypical C. psittaci genotypes were detected in samples from a Malayan night heron (Gorsachius melanolophus) and a Taiwan barbet (Megalaima nuchalis). Taken together, our results revealed that the risk of C. psittaci transmission from domestic waterfowl and Columbidae birds to humans could be underestimated, given the high prevalence rates in these birds. Furthermore, the free-range rearing system of waterfowl in Taiwan may promote C. psittaci transmission between poultry and wild birds. Pet birds and racing pigeons, which are in close contact with people, are also possible sources for cross-species transmission. Further studies are necessary to elucidate the virulence, biological and genetic characteristics, and modes of transmission of Taiwanese C. psittaci isolates to facilitate the prevention and control of C. psittaci infection.

First Report of Chlamydia abortus in Farmed Fur Animals

Chlamydia (C.) abortus, a globally distributed obligate intracellular bacterium, has attracted increasing interest according to its veterinary importance and zoonotic nature. C. abortus can infect a variety of animals and cause foetal loss in livestock resulting in economic loss. In this study, the samples collected from two farms of foxes (n=20), raccoon dogs (n=15) and minks (n=20), were investigated by Chlamydiaceae- and Chlamydia species-specific real-time PCR. The results showed that all the tested foxes (20/20) and raccoon dogs (15/15) harbored Chlamydia spp., while 5% of minks (1/20) were positive for Chlamydia spp. C. abortus was identified in all positive samples as the dominant Chlamydia species, with C. pecorum DNA coexistence in some of the rectal samples (7/20) taken from foxes. Phylogenetic analysis based on specific gene fragments of 16S rRNA, IGS-23S rRNA, and ompA revealed that all sequences obtained in this study were assigned to the Chlamydiaceae family with high similarity to C. abortus S26/3 and B577 previously identified in ruminants. This is the first report confirming that farmed foxes, raccoon dogs, and minks carry C. abortus. Further studies are needed to fully elucidate the epidemiology and pathogenicity of this pathogen in farmed fur animals as well as the potential risks to public health.

Detection and molecular characterization of Chlamydia psittaci and Chlamydia abortus in psittacine pet birds in Buenos Aires province, Argentina

In order to determine the presence and genetic diversity of Chlamydia spp. in the north-eastern area of Buenos Aires province, Argentina, conjunctival, oropharyngeal, cloacal swab and tissues were collected from a total of 90 psittacine pet birds of different age and clinical manifestations. Through molecular methods, Chlamydiaceae was detected in 30% (27/90) of the samples, out of which 70.3% (19/27) were positive for Chlamydia psittaci and 14.9% (4/27) for Chlamydia abortus. Nine C. psittaci positive samples were genotyped by ompA gene sequences, 8 clustered within genotype A and 1 within genotype B. A significant association was observed between the presence of Chlamydia spp. and the manifestation of clinical signs compatible with chlamydiosis, as well as with the age of the birds (younger than one year old). This report contributes to the improvement of our understanding of chlamydial agents in our country.

Prevalence, Diagnosis, and Vaccination Situation of Animal Chlamydiosis in China

Since the first case of Chlamydia infection in duck had been reported in 1956 and the first case from domestic animal had been reported in 1979 in China, the chlamydia prevalence in China was heavily according to the published data. The Chlamydia in avian prevalence has been reported at least 11 provinces, Chlamydia in sheep and goats at least 11 provinces, in swine at least 15 provinces, in cows at least 13 provinces and in yaks at least 5 provinces with result of IHA detection. Different diagnostic method such as CFT, ELISA and ABC-ELISA (avidin-biotin-complex ELISA) had been established besides IHA. The inactivated vaccines have been developed with isolated strains from sheep, goats, swine and cows. These inactivated vaccines have been used since 1980s and Chlamydia prevalence in China has been successfully controlled in domestic animal. However, the inactivated vaccines of Chlamydia isolated from avian species have not been successful, although a series of experimental vaccine have been done. Due to the unsustainable eradication plan of Chlamydia in China, sporadic outbreak in animal would happen if the vaccinations were suspended and economy lose in some farmers. Although Chlamydia prevalence in China has a long history, however, almost all published studies are in Chinese, which, in some degree, blocked scientists in other countries to understand the prevalence situation and control measures of Chlamydia in China.

Molecular evidence to suggest pigeon-type Chlamydia psittaci in association with an equine foal loss

Chlamydia psittaci is an important avian pathogen with spillover from infected wild and domesticated birds also posing a risk to human health. We recently reported a case of C. psittaci equine placentitis associated with further spillover to humans. Molecular typing of this case revealed it belonged to the 6BC clade of C. psittaci, a globally distributed highly virulent set of strains, typically linked to infection spillover from parrots. Equine chlamydiosis associated with C. psittaci infection has previously been reported elsewhere in countries where parrots are not endemic, however, raising questions over the identity of infecting C. psittaci strains and the potential infection reservoirs. In this study, we describe the detection and molecular characterization of C. psittaci in a case of equine abortion in southern Queensland. Equine placenta and fresh liver and lung tissue from the necropsied foetus were positive by C. psittaci-specific qPCR. Chlamydia psittaci-specific multilocus sequence typing and ompA genotyping were used to further characterize the detected equine strains and an additional strain obtained from a dove from a different geographic region presenting with psittacosis. Molecular typing of this case revealed that the infecting equine strains were closely related to the C0sittaci detected in dove, all belonging to an evolutionary lineage of C. psittaci strains typically associated with infections of pigeons globally. This finding suggests a broader diversity of C. psittaci strains may be detected in horses and in association with reproductive loss, highlighting the need for an expansion of surveillance studies globally to understand the epidemiology of equine chlamydiosis and the associated zoonotic risk.