Sixteen cases of severe pneumonia caused by Chlamydia psittaci in South China investigated via metagenomic next-generation sequencing

Psittacosis pneumonia with the reversed halo sign: a case report and literature review

BACKGROUND

Chlamydia psittaci is a rare pathogen that causes community-acquired pneumonia. The reversed halo sign (RHS) is a computed tomography (CT) finding that is commonly observed in diseases such as cryptogenic organizing pneumonia, invasive fungal infections, tuberculosis, sarcoidosis, and pulmonary thromboembolism, but has seldom been described in association with psittacosis pneumonia.

CASE PRESENTATION

We report a case in which a 26-year-old man with a history of close contact with pigeons and chicken manure presented with fever and cough for 6 days. A CT examination revealed the RHS in the right lower lobe of the lung. Psittacosis pneumonia was diagnosed by metagenomic next-generation sequencing of the patient's bronchoalveolar lavage fluid. Treatment with omadacycline abolished his symptoms. We also discuss six other cases of psittacosis pneumonia with the RHS identified by literature search.

CONCLUSIONS

When clinicians encounter patients with atypical pneumonia with the RHS and a history of contact with poultry, psittacosis should be considered.

Clinical characteristics of Chlamydia psittaci pneumonia and predictors analysis of severe patients: a retrospective observational study

Background

With this study, we aimed to explore the clinical features, laboratory examinations, imaging features, and severe predictors of Chlamydia psittaci pneumonia to identify the disease early, shorten the course of illness, and improve prognosis.

Methods

We retrospectively reviewed the clinical data of 39 patients diagnosed with Chlamydia psittaci pneumonia and 39 patients with non-psittacosis community-acquired pneumonia at the Third Xiangya Hospital of Central South University from December 2018 to April 2021. We collected the remaining medical serum to analyze cytokines that are associated with disease-related inflammation. We used the R software to perform statistical analysis.

Results

Compared to the non-psittacosis community-acquired pneumonia group, the common Chlamydia psittaci pneumonia group exhibited more severe symptoms, including a longer duration of hyperthermia. Most patients experienced dyspnea, as well as extrapulmonary symptoms such as fatigue, muscle soreness, and diarrhea. There were also significant increases in levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), lactate dehydrogenase (LDH), C-reactive protein, and procalcitonin, while hemoglobin (Hb) and albumin (ALB) levels decreased significantly. Primary lung imaging features included consolidation and exudation, with nodules and cavities being rare. These changes were even more severe in the severe Chlamydia psittaci pneumonia group, with further increased levels of myoglobin and a larger spread of lesions in the lungs. Additionally, the Th1 inflammatory factor INF-γ was elevated in the Chlamydia psittaci pneumonia group.

Conclusion

Fatigue, myalgia, low Hb, low ALB, high ALT, and high AST are predictors of Chlamydia psittaci pneumonia. Fast respiratory rates, low Hb, high LDH, significant involvement of multiple lobes, high Sequential Organ Failure scores, and high Acute Physiological and Chronic Health scores are predictors of severe Chlamydia psittaci pneumonia. The increase of INF-γ may be related to the condition.

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.

Distinction of clinical features and microbiological methods between Chlamydia psittaci and Legionella pneumophila pneumonia confirmed by metagenomic next-generation sequencing

OBJECTIVES

Detection and diagnosis of Chlamydia psittaci (C. psittaci) pneumonia is often overlooked due to conventional methods limitations and similarity to other atypical community acquired pneumonia (CAP). Using mNGS, we aimed to distinguish psittacosis from legionellosis for early C. psittaci pneumonia diagnosis and better prognosis.

METHODS

Thirty-seven patients diagnosed with atypical CAP were enrolled in this retrospective study, including 14 C. psittaci pneumonia and 23 Legionella pneumophila (L. pneumophila) pneumonia. We collected and compared baseline, lab results, radiology imaging, conventional microbiological methods and more importantly, mNGS results of clinical samples, as well as the treatments and prognosis between psittacosis and legionellosis.

RESULTS

Patients with C. psittaci and L. pneumophila had similar symptoms and were presented with high levels of inflammatory markers. However, patients with C. psittaci pneumonia were more likely to have exposure to birds or parrots [11 (78.6%) vs. 2 (8.7%), p < 0.001], had higher proportions of fever and chill (p = 0.015 and 0.035), higher levels of hemoglobin and albumin (p = 0.002 and 0.018) compared with those with L. pneumophila. Of 14 C. psittaci patients, only one had positive IgM antibody, with no positive cultures. Early identification of pathogens by mNGS method contributed to timely antibiotics' adjustment and better outcomes then, yet with similar hospital mortality between two groups [7.1% (1/14) vs. 34.8% (8/23), p = 0.112].

CONCLUSION

Early mNGS detection of atypical pathogens in multiple samples improves on traditional methods, promptly adjust empirical antimicrobial treatment to pathogen-targeted antibiotics, further improve prognosis.

Analysis and Perception of Chlamydia psittaci Pneumonia: Novel Insights of the Rare Disease in Infectiology

OBJECTIVE

To investigate and analyze the clinical features, diagnosis and treatment, and prognosis of rare Chlamydia psittaci pneumonia, and to improve the understanding of this rare disease.

METHODS

A retrospective analysis and exploration was performed for 33 cases of patients with Chlamydia psittaci pneumonia in the First Affiliated Hospital of Gannan Medical University from January 2017 to March 2024, and the clinical features, diagnosis, treatment and key points for differential diagnosis were summarized and analyzed. Meanwhile, the latest literature from PubMed was retrieved to systematically discuss the research progress in Chlamydia psittaci pneumonia.

RESULTS

A total of 33 patients with Chlamydia psittaci pneumonia were included in this study, including 21 males (63.64%) and 12 females (36.36%), with a median age of 59 (32-79) years. There were 27 cases (81.82%) of patients accompanied with a history of poultry contact, 22 patients (66.67%) had underlying diseases. In our study, patients with Chlamydia psittaci pneumonia were mainly affected in Autumn (21.21%) and Winter (54.55%). All patients had undergone bronchoscopy and obtained bronchoalverolar lavage fluid (BALF) for metagenomic next-generation sequencing (mNGS) detection, and mNGS results showed that all patients (100%) were co-infected with multiple pathogens including Chlamydia psittaci. All patients were given antimicrobial therapy after diagnosis, and no treatment-related adverse reactions or adverse events were observed in our study, the average length of hospitalization was 11.09 days. Fortunately, no death was observed in our study, and patients were all discharged from hospital after recovery and in favourable physical and psychological conditions after discharge.

CONCLUSION

Chlamydia psittaci pneumonia lacks specific clinical features or manifestations and tends to develop into severe exacerbation. mNGS could help to achieve an accurate diagnosis. Early administration of antibiotics can improve the prognosis of patients to the greatest extent.

A novel variant of Chlamydia psittaci causing human psittacosis in China

From January 2022 to November 2022, sporadic psittacosis occurred in Lishui city, China. The patients were presented with fever, cough, and pulmonary infiltration. Their clinical symptoms were not relieved after receiving cephalosporin, penicillin, beta-lactamase inhibitors, and quinolones. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid samples from the patients revealed Chlamydia psittaci infection. Then, three C. psittaci strains were isolated from the patients. Their whole genome sequences (WGSs) were obtained, and a core genome multilocus sequence typing (cgMLST) method was developed to study the population structure of C. psittaci. Using the constructed cgMLST method, 72 WGSs were divided into four related groups and ten sub-clusters. The Lishui strains formed a unique population of C. psittaci, which might represent a new variant of C. psittaci. In vitro antimicrobial susceptibility testing suggested that the Lishui strains were sensitive to tetracycline, macrolides, quinolones, and no drug-resistance was observed.

CRISPR/Cas9-edited duck enteritis virus expressing Pmp17G of Chlamydia psittaci induced protective immunity in ducklings

Chlamydia psittaci is threatening to the animal industry and human beings. Live attenuated duck enteritis virus (DEV) is considered a good vaccine vector. In the present study, the Pmp17G antigen of C. psittaci was expressed in DEV to construct a recombinant DEV-Pmp17G vaccine. The growing curve of the rDEV-Pmp17G vaccine was comparable to the parental DEV strain, and Pmp17G protein expression was detected in the cytosol and membrane of the infected host cells. A total of 30 ducklings assigned to 5 groups were used to evaluate the vaccine efficacy. The birds in the vaccine groups received 15 000 plaque forming units of the rDEV-Pmp17G vaccine via hypodermic injection. In contrast, the control groups received intramuscular inoculation with 1 × 103 embryo lethal dose of DEV vector or 50 µg of commercial recombinant major outer membrane protein (MOMP) vaccine. The rDEV-Pmp17G vaccine induced significantly higher levels of IgG antibodies than the commercial MOMP did on day 14, and the IgG antibodies persisted for 28 days. Moreover, the rDEV-Pmp17G vaccine also induced higher levels of lymphocyte proliferations compared to the DEV vector. The vaccinated animals significantly reduced lesions and enhanced bacterial clearance in the lungs and throats compared to the MOMP immunization. Thus, the rDEV-Pmp17G vaccine induced persistent IgG antibodies and lymphocyte proliferation against C. psittaci infection.

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.

Clinical features and outcome of eight patients with Chlamydia psittaci pneumonia diagnosed by targeted next generation sequencing

INTRODUCTION

The clinical symptoms of Chlamydia psittaci pneumonia are still poorly understood. This study was designed to summarize the clinical features and outcome of eight C. psittaci pneumonia patients diagnosed by targeted next generation sequencing (tNGS).

METHODS

We included eight C. psittaci pneumonia patients admitted to our hospital from January 2021 to July 2022. The tNGS was performed to the samples collected from bronchoalveolar lavage fluid of each patient. Their clinical data were analysed, including baseline features, clinical symptoms, chest radiographic findings and laboratory examinations.

RESULTS

The tNGS sequence number for C. psittaci was in a range of 10 to 1722. The radiographic characteristics were mainly featured by patchy consolidation shadows, ground-glass density shadows, air bronchogram and slight pleural effusion. Within 1-3 days after hospitalization, most patients showed increased neutrophil ratio, C-reactive protein and erythrocyte sedimentation rate, and decreased lymphocyte count, total protein, albumin and prealbumin. Some patients showed increased glutamic-pyruvic transaminase, glutamic-oxaloacetic transaminase and lactate dehydrogenase levels. Three critically ill patients showed increased creatine kinase, creatine kinase isoenzyme and high-sensitivity troponin T (hs-TnT) levels.

CONCLUSIONS

A poultry or bird contact history, typical flu-like symptoms, patchy consolidation, ground-glass density shadow and air bronchogram may contribute to the diagnosis and treatment of C. psittaci pneumonia. Increase in creatine kinase, creatine kinase isoenzyme and hs-TnT may indicate a severe condition. Moxifloxacin and minocycline were effective in the management of C. psittaci pneumonia.

Distribution of drug-resistant genes in alveolar lavage fluid from patients with psittacosis and traceability analysis of causative organisms

Background

Chlamydia psittaci is a small bacterium often found in birds, including poultry, and domesticated mammals, which causes psittacosis (or parrot fever) in humans. Different strains of C. psittaci respond variably to antibiotics, suggesting a possible risk of antibiotic resistance. In general, different genotypes of C. psittaci have relatively stable hosts and different pathogenicity.

Methods

Macrogenomic sequencing was performed using nucleic acids extracted from psittacosis patients' alveolar lavage fluid samples and analyzed for genetic variability and antibiotic resistance genes. Nucleic acid amplification sequences specific to the core coding region of the C. psittaci ompA gene were used, and a phylogenetic tree was constructed with C. psittaci genotypic sequences from other sources, including Chinese published sources. The C. psittaci found in each patient were genotyped by comparing ompA gene sequences. In addition, to better illustrate the relationship between genotype and host of C. psittaci, 60 bird fecal samples were collected from bird-selling stores for screening and C. psittaci typing.

Results

Macrogenomic sequence alignment revealed the presence of resistance genes in varying abundance in samples from all three patients, including C. psittaci resistance gene sequences from two patients that matched those previously published on NCBI. Based on ompA genotyping, two patients were infected with C. psittaci genotype A and one patient was infected with genotype B. All five C. psittaci-positive samples obtained from bird-selling stores were genotype A. Both genotypes are reported to be infectious to humans. The host origin of the samples and the previously reported main sources of each genotype suggested that all but one of the C. psittaci genotype A in this study were derived from parrots, while genotype B was probably derived from chickens.

Conclusion

The presence of bacterial resistance genes in psittacosis patients may affect the efficacy of clinical antibiotic therapy. Focusing on the developmental progression of bacterial resistance genes and differences in the therapeutic efficacy may facilitate effective treatment of clinical bacterial infections. Pathogenicity genotypes (e.g., genotype A and genotype B) are not limited to one animal host, suggesting that monitoring the development and changes of C. psittaci may help prevent transmission to humans.

Gestational psittacosis causes severe pneumonia and miscarriage: A case report and literature review

Psittacosis is an uncommon zoonotic illness, and gestational psittacosis is even rarer. The clinical signs and symptoms of psittacosis are varied, often overlooked, and swiftly identified by metagenomic next-generation sequencing. We recorded the case of a 41-year-old pregnant woman with psittacosis where the disease was not detected early on, resulting in severe pneumonia and fetal miscarriage. The clinical symptoms, diagnosis, and treatment of psittacosis in pregnancy are the subject of this case study.

Rapid detection of pulmonary nocardiosis by metagenomic next generation sequencing

We retrospectively analyzed 3 cases of pulmonary nocardiosis. Patients were identified by metagenomic next generation sequencing (mNGS) in the First Affiliated Hospital of Soochow University, from January 2019 to April 2022. All patients had underlying diseases, and were in immunocompromised state, with membranous nephropathy, acute lymphoblastic leukemia (ALL), and systemic lupus erythematosus (SLE), respectively. Symptoms common to all cases included fever, cough and expectoration. Chest computed tomography (CT) presented patchy shadows or nodules, with or without cavitation lesions, or pleural effusion. mNGS detected Nocardia spp. via bronchoalveolar lavage fluid (BALF) or blood samples from patients. All the patients were discharged with recovery after using the trimethoprim-sulfamethoxazole (TMP-SMX) and remained without evidence of disease during regular follow-ups. mNGS may be a tool for rapid and accurate detection and identification of pulmonary nocardiosis, but interpreting the mNGS results should be more cautious because the mNGS assay can also detect colonization.

Clinical Characteristics of Six Patients with Chlamydia psittaci Infection Diagnosed by Metagenomic Next-Generation Sequencing: A Case Series

The incidence of psittacosis infection has gradually increased in recent years. Metagenomic next-generation sequencing (mNGS) can be used to comprehensively identify the total DNA and RNA content of the microbiome, as well as identify both known and unexpected pathogens within 24 hours. We diagnosed and treated six patients with psittacosis infection using mNGS, two of whom developed severe disease and most of whom presented with pulmonary symptoms. One of the young female patients also presented with irregular vaginal bleeding and myocarditis. Patients with underlying gastric disorders first showed gastrointestinal symptoms, which is a rare manifestation in patients with psittacosis. Older patients with underlying disease usually showed more severe symptoms. However, rare complications can also occur in immunocompetent young people and develop into severe disease. All patients showed significant congestion at bronchial lumen lesions, which may be associated with a severe inflammatory response to mucosal Chlamydia psittaci (C. psittaci) infection. Overall, mNGS is a rapid and effective tool for the clinical diagnosis of psittacosis caused by C. psittaci, and early diagnosis and treatment can prevent psittacosis from developing into a serious illness.

Physiological analysis of severe chlamydia psittaci pneumonia and clinical diagnosis after doxycycline-based treatment

Objective: To describe the clinical spectrum of severe Chlamydia psittaci pneumonia in order to understand the disease better. Methods: Retrospective analysis was made on 31 patients with severe Chlamydia psittaci pneumonia diagnosed in ICU by next-generation sequencing of metagenome Metagenomic next-generation sequencing(mNGS) from January 2019-November 2022, including clinical characteristics, laboratory examination results, imaging characteristics, treatment, and prognosis. Results: We included 31 patients with severe Chlamydia psittaci pneumonia, 15 of whom had a history of virus exposure. There were 12 cases with multiple bacterial infections, and the common symptoms included fever (31/31,100%), dyspnea (31/31, 100%), cough (22/31, 71.0%), and myalgia (20/31, 64.5%). Laboratory data showed that white blood cells were average or slightly increased, but the levels of C-reactive protein and neutrophils were high. CT findings of the lung were consolidation (19/31, 61.3%) and pleural effusion (11/31, 35.5%). Only one lobe was involved in 11 patients (35.5%). Before diagnosis, 22 patients (71.0%) did not have atypical pathogens in their antimicrobial regimen. After diagnosis, 19 patients (61.3%) received single drug treatment, of which doxycycline or moxifloxacin were the most commonly used drugs. Among 31 patients, three died, nine improved, and nineteen were cured. Conclusion: The clinical manifestations of severe Chlamydia psittaci pneumonia are non-specific. The application of mNGS can improve the diagnostic accuracy of Chlamydia psittaci pneumonia, reduce the unnecessary use of antibiotics, and shorten the course of the disease. Doxycycline-based treatment is effective for severe chlamydia psittaci pneumonia, but it is necessary to understand the secondary bacterial infection and other complications in the course of the disease.

Omadacycline for the Treatment of Severe Chlamydia psittaci Pneumonia Complicated with Multiple Organ Failure: A Case Report

Psittacosis is a rare zoonotic disease caused by Chlamydia psittaci infection, and tetracyclines are the preferred treatment. Omadacycline is a novel tetracycline that has a strong in vitro antibacterial activity against atypical pathogens, including C. psittaci; however, clinical data for its usage are lacking. We report a patient with severe C. psittaci-induced pneumonia presenting with a high fever, muscle aches, severe hepatic and renal insufficiency, and acute respiratory failure requiring tracheal intubation and mechanical ventilation. The condition was diagnosed using metagenomic next-generation sequencing. The patient was discharged after treatment with omadacycline. The findings of this study suggest that metagenomic next-generation sequencing is valuable for the rapid and accurate diagnosis of psittacosis. With its good safety profile and no requirement for dose adjustment in special populations, omadacycline is a new option for the treatment of severe C. psittaci pneumonia. However, additional case reports are needed to support this conclusion.

Etiology of Severe Community Acquired Pneumonia in Adults Identified by Combined Detection Methods: A Multi-center Prospective Study in China

Severe Community Acquired Pneumonia (SCAP) challenges public health globally. Considerable improvements in molecular pathogen testing emerged in the last few years. Our prospective study combinedly used traditional culture, antigen tests, PCR and mNGS in SCAP pathogen identification with clinical outcomes. From June 2018 to December 2019, we conducted a multi-centre prospective study in 17 hospitals of SCAP patients within 48 hours of emergency room stay or hospitalization in China. All clinical data were uploaded into an online database. Blood, urine and respiratory specimens were collected for routine culture, antigen detection, PCR and mNGS as designed appropriately. Aetiology confirmation was made by the local attending physician group and scientific committee according to microbiological results, clinical features, and response to the treatment. Two hundred seventy-five patients were included for final analysis. Combined detection methods made identification rate up to 74.2% (222/299), while 14.4% (43/299) when only using routine cultures and 40.8% (122/299) when not using mNGS. Influenza virus (23.2%, 46/198), S. pneumoniae (19.6%, 39/198), Enterobacteriaceae (14.6%, 29/198), Legionella pneumophila (12.6%, 25/198), Mycoplasma pneumoniae (11.1%, 22/198) were the top five common pathogens. The in-hospital mortality of patients with pathogen identified and unidentified was 21.7% (43/198) and 25.9% (20/77), respectively. In conclusion, early combined detection increased the pathogen identification rate and possibly benefitted survival. Influenza virus, S. pneumoniae, Enterobacteriaceae was the leading cause of SCAP in China, and there was a clear seasonal distribution pattern of influenza viruses. Physicians should be aware of the emergence of uncommon pathogens, including Chlamydia Psittaci and Leptospira.