Chlamydia psittaci: an emerging cause of equine abortion and fatal neonatal illness in south-eastern Australia.

While well known as a zoonotic pathogen of birds, Chlamydia psittaci is less well recognised as a cause of abortion in mares and severe infection in foals. However, in the past decade it has been causing epizootics of both in south-eastern Australia, as Charles El-Hage and James Gilkerson explain.

Chlamydia psittaci seropositivity in workers exposed to birds and review of the literature: Evidence of circulation in Antioquia / Seropositividad de Chlamydia psittaci en trabajadores expuestos a aves y revisión de la literatura: evidencia de circulación en Antioquia.

Introduction: Psittacosis is a zoonotic disease caused by Chlamydia psittaci, a bacterium classified as an agent with bioterrorist potential. It has caused multiple outbreaks in exposed poultry workers around the world. Colombia has no epidemiological follow-up of the infection and a big knowledge gap. Objectives: To determine the antibodies' frequency against C. psittaci in workers with occupational exposure to birds and to review the literature on studies conducted in Colombia. Materials and methods: We conducted a cross-sectional descriptive study with analytical intent on workers in contact with birds and reviewed the related literature in Colombia. IgM and IgG serum antibodies against C. psittaci were detected by microimmunofluorescence. The sociodemographic and exposure characteristics were expressed as frequencies and summary measures. Associated factors were explored by bivariate and multivariate analysis. The scientific and gray literature review was done with a structured search. Results: We analyzed 54 workers in contact with birds. Antibody prevalence was 31.5%. Slaughtering and evisceration by non-veterinarians was a risk factor for antibody presence. There are only four previous studies on C. psittaci in Colombia. Conclusions: Here, we present the first evidence of C. psittaci circulation among workers exposed to birds in Antioquia and the second report in the country. These findings contribute to the "One Health" public health strategy.

Introducción: La psitacosis es una enfermedad zoonótica causada por Chlamydia psittaci. Esta bacteria es catalogada como un agente con potencial bioterrorista y ha causado múltiples brotes en trabajadores con exposición laboral a aves en diferentes lugares del mundo. En Colombia, no se hace seguimiento epidemiológico de la infección y existe una gran brecha en el conocimiento. Objetivos: Determinar la frecuencia de anticuerpos contra C. psittaci en trabajadores con exposición laboral a aves y sus factores asociados. Además, revisar la literatura en relación con los estudios sobre el tema realizados en Colombia. Materiales y métodos: Se llevó a cabo un estudio descriptivo, transversal, con intención analítica, en trabajadores en contacto con aves y se revisó la literatura científica relacionada en Colombia. Se detectaron anticuerpos IgM e IgG contra C. psittaci en suero por microinmunofluorescencia. La descripción de las características sociodemográficas y de exposición se hizo con frecuencias y medidas de resumen. Se exploraron factores asociados por análisis bivariados y multivariados. La revisión de la literatura científica y gris se hizo con búsqueda estructurada. Resultados: Se analizaron 54 trabajadores en contacto con aves y se encontró una prevalencia de anticuerpos del 31,5 %. El ejercer funciones de sacrificio y faenado de las aves sin ser médico veterinario fue un factor de riesgo para la presencia de anticuerpos. Solo se encontraron cuatro estudios previos sobre C. psittaci hechos en Colombia. Conclusiones: Este estudio constituye la primera evidencia de la circulación de C. psittaci en trabajadores en contacto con aves en Antioquia y el segundo reporte en el país. Estos hallazgos aportan desde la salud pública a la estrategia One Health.

Epidemiological and clinical characteristics of psittacosis among cases with complicated or atypical pulmonary infection using metagenomic next-generation sequencing: a multi-center observational study in China.

BACKGROUND: Chlamydia psittaci (C. psittaci) causes parrot fever in humans. Development of metagenomic next-generation sequencing (mNGS) enables the identification of C. psittaci. METHODS: This study aimed to determine the epidemiological and clinical characteristics of parrot fever cases in China. A multi-center observational study was conducted in 44 tertiary and secondary hospitals across 14 provinces and municipalities between April 2019 and October 2021. RESULTS: A total of 4545 patients with complicated or atypical pulmonary infection were included in the study, among which the prevalence of C. psittaci was determined to be 2.1% using mNGS. The prevalence of C. psittaci was further determined across demographic groups and types of specimens. It was significantly higher in patients with senior age (2.6% in those > 50 years), winter-spring (3.6%; particularly in December, January, and February), and southwestern (3.4%) and central and southern China (2.7%) (each P < 0.001). Moreover, the prevalence was the highest in bronchoalveolar lavage fluid (BALF) (2.9%), compared with sputum (1.1%) and peripheral blood specimens (0.9%). Additionally, co-infection of principal microorganisms was compared. Certain microorganisms were more likely to co-infect in parrot fever cases, such as Candida albicans in BALF (26.7%) and peripheral blood (6.3%), compared with non-parrot fever cases (19.7% and 1.3%); however, they did not significantly differ (each P > 0.05). CONCLUSION: Parrot fever remains low in patients with complicated or atypical pulmonary infection. It is likely to occur in winter-spring and southwestern region in China. BALF may be the optimal specimen in the application of mNGS. Co-infection of multiple microorganisms should be further considered.

Case Report: Clinical analysis of a cluster outbreak of chlamydia psittaci pneumonia.

Objective: To explore the clinical characteristics and prognosis of clustered cases of psittacosis pneumonia. Method: We retrospectively analyzed the clinical data of a cluster outbreak of psittacosis pneumonia. The analysis included epidemiological data, clinical symptoms, laboratory results, and prognosis. The diagnosis was made using mNGS and nested PCR technology. Result: Of the four cases, two had direct contact with diseased poultry while the other two did not. All cases presented with more than 39.5 °C fever and chills. Additionally, significant increases in C-reactive protein, ferritin, creatine kinase, and lactate dehydrogenase were observed in all cases, while absolute lymphocyte count decreased. Case 2 also had increased calcitonin levels. Acute respiratory failure occurred during the treatment of case 1 and case 2, leading to tracheal intubation and ventilator-assisted ventilation. Unfortunately, case 2 passed away due to sepsis and multiple organ dysfunction, while the other cases had a positive prognosis. Conclusion: mNGS facilitated the early diagnosis of psittacosis pneumonia. It is important to note that there is still a substantial risk of human-to-human transmission in psittacosis pneumonia. Absolute lymphocyte count and calcitonin levels can predict the severity and prognosis of the disease.

Case Report: A case of Chlamydia psittaci infection in an HIV patient.

Chlamydia psittaci is the pathogen of psittacosis and infects a wide range of birds and even humans. Human infection occurs most commonly in those with a history of contact with birds or poultry. We describe a case of psittacosis in a human immunodeficiency virus infected patient in Zhejiang Province for the first time. C. psittaci infection was confirmed by nested polymerase chain reaction (PCR) and Real-Time PCR. Phylogenetic analysis revealed that the sequences from the patient's samples clustered with genotype A in the same branch. Our study highlights the possibility of diagnosing psittacosis in patients with a chronic disease such as HIV-infected patients, and should increase awareness and surveillance of psittacosis in China.

Determining the Prevalence of Avian Chlamydiosis in Wild Amazona Species From Brazil Using Molecular Testing and Clinical Signs.

Avian chlamydiosis is a disease that occurs in birds, especially parrots, and is caused by the Gram-negative bacterium Chlamydia psittaci. Wild Animal Screening Centers in Brazil receive, maintain, treat, and place (preferably to nature) wild animals recovered from illegal trafficking. We performed molecular testing for avian chlamydiosis in parrots from the genus Amazona that were presented to these centers. Cloacal swab samples were collected from 59 parrots (Amazona species) and transported in aqueous or culture medium. The samples were subsequently submitted for DNA extraction by the boiling method, polymerase chain reaction (PCR) amplification using CPF/CPR primers, and agarose gel electrophoresis. Conjunctivitis, nasal discharge, and poor body condition were the clinical signs associated with a differential disease diagnosis of avian chlamydiosis. Transport medium did not have an effect on the test results. The prevalence of C psittaci in the samples was 37% (22/59, 95% confidence interval: 25-49). There was a significant (P = 0.009) association between the PCR test results and clinical signs. Follow-up testing was conducted on a subgroup of 14 individuals that initially tested negative on PCR; 50% (7/14) of these birds were found to be positive within 24 days of the first test. The results of this study confirm the feasibility of using the CPF/CFP primer-based PCR to detect C psittaci in Amazona species, describe a less costly method of transporting biological material for DNA extraction, and evaluate the temporal aspect for obtaining positive results through molecular testing for C psittaci in Amazona species.

Prevalence of asymptomatic infections of Chlamydia psittaci in psittacine birds in Korea.

Avian chlamydiosis is an acute or chronic bacterial disease of birds. Chlamydia psittaci is the primary agent of the disease. It is also an important zoonotic pathogen. Chlamydia avium and Chlamydia gallinacea have also been recognized as potential causative agents of the disease. Clinical signs of this disease can vary in severity. Asymptomatic infections of Chlamydia have commonly been reported in various birds worldwide. In this study, we investigated the distribution of Chlamydia species in healthy psittacine birds in Korea. A total of 263 samples (pharyngeal/cloacal swabs and faeces) were collected from psittacine birds of 26 species in five zoos, five parrot farms and seven parrot cafes between 2020 and 2021. Ages of these birds had a wide range (1 month to 30 years). During sample collection, no bird showed any clinical signs indicating diseases such as chlamydiosis. Samples were tested for the presence of Chlamydia spp. using real-time PCR assays. Chlamydia spp. were detected in 168 (63.9%) samples and C. psittaci was detected in 96 (36.5%) samples. However, C. avium and C. gallinacea were not detected. There were no significant differences in the prevalence of asymptomatic infections in birds among three types of housing environments. Regarding ompA genotypes, 87 C. psittaci-positive samples had genotype A based on sequence analysis (n = 28) and genotype-specific real-time PCR (n = 59). Other positive samples were untyped (n = 9). Overall findings showed high prevalence of asymptomatic infections of C. psittaci in psittacine birds in Korea, posing a significant hazard to public health.

Prevalence and Risk Factors of Avian Chlamydiosis Detected by Polymerase Chain Reaction in Psittacine Birds in Thailand.

This study surveyed avian chlamydiosis, with the aim to estimate the prevalence and potential risk factors associated with Chlamydia psittaci infection in psittacine birds kept as domestic pets in Thailand. Oropharyngeal swabs were collected from 120 psittacine birds that were randomly selected from hospitals in the central (Bangkok) and northeastern regions (Khon Kaen) of Thailand between 2019 and 2021. The oropharyngeal swabs were subject to polymerase chain reaction testing to detect the C psittaci ompA gene. The prevalence of C psittaci was 2.5% (3/ 120, 95% confidence interval = 0.3-5.3). Of the 3 positive birds, 1 was a Forpus parrot (Forpus species)(CP43TH) and 1 was an African grey parrot (Psittacus erithacus)(CP49TH) from Bangkok; both were juvenile birds with clinical signs of disease. The third positive bird (CP12TH) was a subclinical adult sun conure (Aratinga solstitialis) from Khon Kaen. Two sequences of samples that were previously identified in human psittacosis cases (accession numbers MK032053.1 and HM450409.1) were also examined. Since there was a low number of infected birds, potential associations between C psittaci infection and various environmental variables (eg, cage cleaning, synanthropic birds, quarantine of new birds, and overcrowding) were assessed by Fisher exact tests. This study provides estimates of the prevalence and potential risk factors associated with C psittaci infection in psittacine birds from central (Bangkok) and the northeastern regions (Khon Kaen) of Thailand. The detection of C psittaci in captive psittacine birds demonstrates that there is a possibility for bird-to-bird transmission as well as some zoonotic potential for the human caretakers of these birds. Furthermore, larger-scale studies should be conducted to confirm these findings.

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.

A cluster of two psittacosis cases among women farmers exposed to Chlamydia psittaci-infected domestic poultry in Zhejiang Province, China.

A cluster of Chlamydia psittaci (C. psittaci) cases was reported in Zhejiang Province, China, 2019. This study evaluates the extent of the outbreak and determines the source of infection. Real-time PCR and sequencing of the ompA gene of C. psittaci were performed to identify the cases, the domesticated poultry and close contacts. The index patient was a 76-year-old woman with chronic vertigo, and Case 2 was a 64-year-old female farmer with herpes zoster. Both women bought psittaci-infected chickens or ducks from the same mobile street vendor and raised them for 10 days and 23 days before fever onset. There were no direct contact between the two women. C. psittaci test was positive for the two patients, one sick chicken, three healthy ducks and the vendor's chicken cage. Phylogenetic analysis showed that all seven C. psittaci positive samples carried identical ompA genotype A of C. psittaci. Of all of the patients' 148 close contacts, none tested positive for C. psittaci, or developed acute respiratory symptoms. Both patients were discharged after a 4-week hospital stay. In conclusion, the source of this cluster was the poultry infected with C. psittaci, which occasionally cause infections in farmers, but inter-human transmission seems unlikely.

Psittacosis contagion in 1930: an old story in a new era of zoonotic disease.

The SARS-CoV-2 pandemic has highlighted the importance of zoonotic diseases. Psittacosis, a human disease resulting from infection spill-over from Chlamydia psittaci-infected birds, is a lesser-known example of a zoonosis. Psittacosis was responsible for numerous outbreaks in the 1930s, characterised by significant human mortality and disruption to the global trade in parrots. This paper describes the epidemiological and clinical details of one family group impacted by the purchase of an infected, imported parrot. Findings are discussed in the context of a growing awareness of the health risks of global disease outbreaks, as well as social and economic impacts. Health information recorded for cases of psittacosis associated with the 1930 cluster was reviewed using contemporary knowledge of disease symptoms and epidemiology. Case details and autopsy reports were examined. Public health investigation deduced that the cluster of infections was chronologically and physically connected to the purchase and subsequent death of an imported parrot. Disease symptoms were consistent with C. psittaci infection. Epidemiological data supported the diagnoses and causes of death, despite the presenting symptoms sharing significant overlap with other common respiratory diseases. There is growing awareness of the risks of epidemiological bridges in transmitting animal diseases to humans. Historical cases are a strong reminder of the fundamental role of scientific and public health responses in the face of such contagion.

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.

A Chlamydia psittaci Outbreak in Psittacine Birds in Sardinia, Italy.

Chlamydia psittaci is an intracellular bacterium belonging to the Chlamydiaceae family. It is the ethiologic agent of psittacosis, an occupational zoonotic disease that mainly concerns people who work in close contact with birds that represent the main infection route for human transmission. In Italy, information about this disease is lacking. This study is the first case of avian chlamydiosis reported from a pet shop in Sardinia, Italy. Chlamydia psittaci detected in psittacine birds by molecular analysis, direct immunofluorescence test together with anatomo-pathological observed lesions, highlighted the importance of focusing the attention over this underestimated zoonosis in a "One Health" prospective.

Severe community-acquired pneumonia caused by Chlamydia psittaci genotype E/B strain circulating among geese in Lishui city, Zhejiang province, China.

Between November 2021 and January 2022, four patients of community-acquired pneumonia were admitted to the hospitals in Lishui city, Zhejiang province, China. Their main clinical manifestations were fever and dry cough as well as radiographic infiltrate, but the empiric antimicrobial therapy or traditional Chinese medicine was not effective for their illness. Clinical specimens from the patients as well as environmental and poultry specimens were collected for the determination of the causative pathogen. The ompA gene and seven housekeeping genes of Chlamydia psittaci were successfully amplified from all the patients, and the sequences of each gene were identical to one another, suggesting that they were infected by the same strain of C. psittaci. A novel strain of C. psittaci (LS strain) was isolated from the bronchoalveolar lavage fluid of patient 2 and its whole genome was obtained. Phylogenetic analyses based on the whole-genome sequences showed that the isolate is most closely related to the strain (WS/RT/E30) identified as genotype E/B. In addition, The ompA gene and four housekeeping genes of C. psittaci were also amplified from two of four faeces samples of geese at the home of patient 2, and the sequences from geese were 100% identical to those from the patients. Accordingly, these cases could be attributed to a circulating C. psittaci strain of genotype E/B in the local geese. Therefore, there is an urgent need to strengthen the regional surveillance on C. psittaci among poultry and humans for prevention and control of the outbreak of psittacosis in the city.

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.

Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pneumonia Caused by Chlamydia psittaci.

Psittacosis is an uncommon disease which mainly presents as community-acquired pneumonia (CAP). We aim to apply metagenomic next-generation sequencing (mNGS) as a promising tool in the diagnosis of psittacosis pneumonia and to describe its clinical spectrum to provide physicians with a better understanding and recognition of this disease. Thirteen cases of psittacosis pneumonia were diagnosed by using mNGS. A retrospective analysis of the data on clinical manifestations, laboratory data, computed tomography (CT) images, new diagnosis tools, treatments, and outcomes was summarized. These patients had common symptoms of fever and weakness; some had poor appetite, cough, myalgia, and headache. Ten patients developed acute respiratory distress syndrome (ARDS), among which six patients were severe pneumonia cases and needed ventilator therapy. Most patients got psittacosis pneumonia during the cold season. Ten cases were sporadic, but three were family clustering. All of the 13 patients were traced to an exposure history to birds, cat, or poultry, among which 2 only touched the innards of killed poultry before cooking, which may be an atypical exposure history not been reported before, to our knowledge. Most patients had various degrees of liver dysfunction. Air-space consolidations, along with ground-glass opacities and reticular shadows, were detected on chest CT scan. mNGS takes 48 to 72 h to provide results and helps to diagnose psittacosis. After being diagnosed by mNGS, with effective medicines, all patients finally had complete recoveries. The use of mNGS can improve the diagnostic rate of psittacosis pneumonia and shorten the course of disease control. IMPORTANCE Psittacosis pneumonia is easily underdiagnosed and misdiagnosed. In this study, we use mNGS in the diagnosis of psittacosis pneumonia. We found this disease is prone in the cold season, and touching the innards of killed poultry during cooking may be an atypical exposure history which has not been reported before to our knowledge. There are sporadic cases and family outbreak cases as well. Except for typical symptoms of fever and weakness, headache may be the main and only symptom in some patients. The rate of severe pneumonia is high among inpatients with psittacosis pneumonia, and the incidence of hepatic involvements is also high. Psittacosis pneumonia can be cured if the diagnosis is accurate and in time, even if it is severe pneumonia on admission. Some problems worthy of our attention about psittacosis pneumonia were put forward, such as its sick season, special exposure history, the rate of severe disease, and the high cure rate. mNGS can quickly and objectively detect more rare pathogenic microorganisms in clinical specimens without the need for specific amplification and has an advantage in the diagnosis of rare pathogenic bacteria in difficult cases such as psittacosis pneumonia. The use of mNGS can improve the accuracy and reduce the delay in the diagnosis of psittacosis, which shortens the course of disease control.

Atypical pneumonia caused by Chlamydia psittaci during the COVID-19 pandemic.

OBJECTIVES: Here, we retrospectively described the diagnosis and treatment of 32 cases diagnosed with Chlamydia psittaci pneumonia during the COVID-19 pandemic. METHODS: Clinical information was collected from all the patients. Reverse transcription-PCR and ELISAs were conducted for the detection of COVID-19 using nasal swabs and bronchoalveolar lavage fluid (BALF) samples. Metagenomic next-generation sequencing (mNGS) was performed for the identification of causative pathogens using BALF, peripheral blood and sputum samples. End-point PCR was performed to confirm the mNGS results. RESULTS: All 32 patients showed atypical pneumonia and had infection-like symptoms that were similar to COVID-19. Results of reverse transcription-PCR and ELISAs ruled out COVID-19 infection. mNGS identified C. psittaci as the suspected pathogen in these patients within 48 hours, which was validated by PCR, except for three blood samples. The sequence reads that covered fragments of C. psittaci genome were detected more often in BALF than in sputum or blood samples. All patients received doxycycline-based treatment regimens and showed favorable outcomes. CONCLUSION: This retrospective study, with the highest number of C. psittaci pneumonia enrolled cases in China so far, suggests that human psittacosis may be underdiagnosed and misdiagnosed clinically, especially in the midst of the COVID-19 pandemic.

The Application Value of Metagenomic and Whole-Genome Capture Next-Generation Sequencing in the Diagnosis and Epidemiological Analysis of Psittacosis.

Background: To evaluate the value of metagenomic next-generation sequencing (mNGS) for the early diagnosis of psittacosis, and to investigate its epidemiology by whole-genome capture. Methods: Twenty-one bronchoalveolar lavage fluid (BALF) and blood samples of 16 psittacosis patients from multiple centers during August 2019 to September 2021 were analyzed retrospectively. mNGS with normal datasets (10 M 75-bp single-end reads after sequencing) and larger datasets (30 M 150-bp paired-end reads after sequencing) as well as quantitative real-time polymerase chain reaction (qPCR) were used to detect the pathogen. Also, whole-genome capture of Chlamydophila psittaci was applied to draw the phylogenetic tree. Results: mNGS successfully detected the pathogen in all 16 cases (100%), while qPCR was positive only in 5 out of 10 cases (50%), indicating a significantly higher sensitivity of mNGS than qPCR (p < 0.01). BALF-mNGS performed better than blood-mNGS (16/16 versus 3/5, p < 0.05). In addition, larger datasets (the read counts have tripled, and the base number was 12-fold larger compared to clinical mNGS with a normal dataset) of mNGS showed significantly increased contents of human DNA (p < 0.05) and decreased reads per million of the pathogen, suggesting no improvement. Whole-genome capture results of five samples (>60% coverage and >1 depth) were used to construct the phylogenetic tree. Conclusion: Significant advantages of mNGS with normal datasets were demonstrated in early diagnosing psittacosis. It is the first study to use whole-genome capture to analyze C. psittaci epidemiological information.

The prevalence of Chlamydia psittaci in confiscated Psittacidae in Colombia.

Chlamydia psittaci is a highly zoonotic bacteria distributed worldwide; it is responsible for psittacosis, one of the most important infectious diseases affecting the Psittacidae, mostly parrots. This work was aimed at determining C. psittaci prevalence and genotype in 177 parrots confiscated in Colombia; cloacal swab (166) and faecal (177) samples were analysed from birds confiscated and housed in a Temporary Wildlife Reception Centre (Centro de Reception de Fauna Temporal). Conventional PCR was run on the samples for amplifying the MOMP gene and then the ompA gene. The C. psittaci genotype A was found in 81.3 % (144/177) of the birds analysed. Cloacal swabs accounted for 129/166 (77.7 %) positive samples and faecal matter for 53/177 (29.9 %), 38 birds proving positive for both types of sample; there was an 8.15 times greater probability of detection for cloacal swabs compared to faecal swabs (p < 0.05). Clinical examination findings were correlated with the animals' positivity for cloacal swabs, faecal matter or both, finding a statistically significant relationship with low respiratory rate (p < 0.05) and broken plumage for cloacal swab sample results (p < 0.1). Even though 85 % seroprevalence has previously been reported in Colombia using indirect ELISA, this study reports for the first time C. psittaci genotype A endemicity in psittacines in captivity in Colombia using molecular techniques, considering the zoonotic risk involved in having these birds as pets.