Undiagnosed Cases of Human Pneumonia Following Exposure to Chlamydia psittaci from an Infected Rosella Parrot

Chlamydia psittaci detected at a live poultry wholesale market in central China

BACKGROUND

We investigated the presence of Chlamydia psittaci in poultry and the environment in live poultry wholesale markets in Changsha during 2021-2022 and conducted a phylogenetic analysis to understand its distribution in this market.

METHODS

In total, 483 samples were analyzed using real-time polymerase chain reaction and 17 C. psittaci-positive samples using high-throughput sequencing, BLAST similarity, and phylogenetic analysis.

RESULTS

Twenty-two out of 483 poultry and environmental samples were positive for C. psittaci (overall positivity rate: 4.55%) with no difference in positivity rates over 12 months. Chlamydia psittaci was detected at 11 sampling points (overall positivity rate: 27.5%), including chicken, duck, and pigeon/chicken/duck/goose shops, with pigeon shops having the highest positivity rate (46.67%). The highest positivity rates were found in sewage (12.5%), poultry fecal (7.43%), cage swab (6.59%), avian pharyngeal/cloacal swab (3.33%), and air (2.29%) samples. The ompA sequences were identified in two strains of C. psittaci, which were determined to bear genotype B using phylogenetic analysis. Thus, during monitoring, C. psittaci genotype B was detected in the poultry and environmental samples from the poultry wholesale market in Changsha.

CONCLUSIONS

To address the potential zoonotic threat, C. psittaci monitoring programs in live poultry markets should be enhanced.

Case Report: Metagenomic next-generation sequencing applied in diagnosing psittacosis caused by Chlamydia psittaci infection

Background

Chlamydia psittaci is the causative agent of psittacosis in humans, while its rapid identification is hampered due to the lack of specificity of laboratory testing methods.

Case presentation

This study reports four cases of C. psittaci infection after contact with a domestic parrot, all belonging to the same family. Common manifestations like fever, cough, headache, nausea, and hypodynamia appeared in the patients. Metagenomic next-generation sequencing (mNGS) aided the etiological diagnosis of psittacosis, revealing 58318 and 7 sequence reads corresponding to C. psittaci in two cases. The detected C. psittaci was typed as ST100001 in the Multilocus-sequence typing (MLST) system, a novel strain initially reported. Based on the results of pathogenic identification by mNGS, the four patients were individually, treated with different antibiotics, and discharged with favorable outcomes.

Conclusion

In diagnosing psittacosis caused by a rare C. psittaci agent, mNGS provides rapid etiological identification, contributing to targeted antibiotic therapy and favorable outcomes. This study also reminds clinicians to raise awareness of psittacosis when encountering family members with a fever of unknown origin.

Psittacosis: An Underappreciated and Often Undiagnosed Disease

The bacterial agent Chlamydia psittaci, and the resulting disease of psittacosis, is a little-known and underappreciated infectious disease by healthcare practitioners and in public health in general. C. psittaci infections can cause significant psittacosis outbreaks, with person-to-person transmission documented in the last decade. In this publication, we review the pathogen and its disease, as well as examine the potential for genetic manipulation in this organism to create a more deadly pathogen. Recent disease surveys indicate that currently, the highest incidences of human disease exist in Australia, Germany and the UK. We recommend the universal public health reporting of C. psittaci and psittacosis disease and increasing the promotion of public health awareness.

The first genomic insight into Chlamydia psittaci sequence type (ST)24 from a healthy captive psittacine host in Australia demonstrates evolutionary proximity with strains from psittacine, human, and equine hosts

Chlamydia psittaci is a zoonotic pathogen that infects birds, humans, and other mammals. Notably, recent studies suggested the human-to-human transmission of C. psittaci, and this pathogen also causes equine reproductive loss in Australia. Molecular studies in Australia to date have focused on and described clonal sequence type (ST)24 strains infecting horses, wild psittacine, and humans. In contrast, the genetic identity of C. psittaci strains from captive psittacine hosts is scarce. In 2022, C. psittaci was detected in the faeces of a healthy captive blue-fronted parrot (Amazona aestiva). Genomic DNA was extracted and underwent whole-genome sequencing. Here we report the 1,160,701 bp circular chromosome of C. psittaci strain BF_amazon_parrot13 and the 7,553 bp circular plasmid pCpsBF_amazon_parrot13. Initial in silico multi-locus sequence typing and ompA genotyping revealed that BF_amazon_parrot13 belongs to the clonal ST24 lineage and has an ompA genotype A. Further context involved the genomes of 31 published ST24 strains, utilising a single-nucleotide variant (SNV) based clustering approach. Despite temporal, host, and biogeographical separation, a core-genome SNV-based phylogeny revealed that BF_amazon_parrot13 clustered in a distinct subcluster with seven C. psittaci strains from equines in Australia (maximum pairwise distance of 13 SNVs). BF_amazon_parrot13 represents the first complete C. psittaci ST24 genome from a captive psittacine in Australia. Furthermore, by using whole-genome sequencing to coordinate surveillance, we can also learn more about the possible health risks and routes of chlamydia transmission among people, livestock, wild animals, and domesticated animals.

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

Chlamydia psittaci is an avian pathogen with zoonotic potential. In Australia, C. psittaci has been well reported as a cause of reproductive loss in mares which subsequently have been the source of infection and illness in some in-contact humans. To date, molecular typing studies describe the predominant and clonal C. psittaci sequence type (ST)24 strains in horse, psittacine, and human infections. We sought to assess the clonality between ST24 strains and the emergence of equine ST24 with a comprehensive genomics approach. We used culture-independent probe-based and metagenomic whole-genome sequencing to investigate 13 C. psittaci genomes from horses, psittacines, and a pigeon from Australia. Published genomes of 36 C. psittaci strains were also used to contextualise our Australian dataset and investigate lineage diversity. We utilised a single-nucleotide polymorphism (SNP) based clustering and multi-locus sequence typing (MLST) approach. C. psittaci has four major phylogenetic groups (PG1-4) based on core-genome SNP-based phylogeny. PG1 contained clonal global and Australian equine, psittacine, and human ST24 genomes, with a median pairwise SNP distance of 68 SNPs. PG2, PG3, and PG4 had greater genomic diversity, including diverse STs collected from birds, livestock, human, and horse hosts from Europe and North America and a racing pigeon from Australia. We show that the clustering of C. psittaci by MLST was congruent with SNP-based phylogeny. The monophyletic ST24 clade has four major sub-lineages. The genomes of 17 Australian human, equine, and psittacine strains collected between 2008 and 2021 formed the predominant ST24 sub-lineage 1 (emerged circa 1979). Despite a temporal distribution of 13 years, the genomes within sub-lineage 1 had a median pairwise SNP distance of 32 SNPs, suggesting a recent population expansion or potential cross-host transmission. However, two C. psittaci genomes collected in 2015 from Victorian parrots clustered into distinct ST24 sub-lineage 4 (emerged circa 1965) with ovine strain C19/98 from Germany. This work describes a comprehensive phylogenomic characterisation of ST24 and identifies a timeline of potential bird-to-equine spillover events.

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.