Metagenomic next-generation sequencing for the diagnosis of Chlamydia psittaci pneumonia

Exploring the pathogen diagnosis and prognostic factors of severe COVID-19 using metagenomic next-generation sequencing: A retrospective study

Background

This study aimed to identify pathogens and factors that predict the outcome of severe COVID-19 by utilizing metagenomic next-generation sequencing (mNGS) technology.

Methods

We retrospectively analyzed data from 56 severe COVID-19 patients admitted to our hospital between December 2022 and March 2023. We analyzed the pathogen types and strains detected through mNGS and conventional microbiological testing and collected general patient information.

Results

In this study, 42 pathogens were detected using mNGS and conventional microbiological testing. mNGS had a significantly higher detection rate of 90.48% compared to 71.43% for conventional testing (P=0.026). A total of 196 strains were detected using both methods, with a significantly higher detection rate of 70.92% for mNGS compared to 49.49% for conventional testing (P=0.000). The 56 patients were divided into a survival group (33 cases) and a death group (23 cases) based on clinical outcomes. The survival group had significantly lower age, number of pathogens detected by mNGS, number of pathogens detected by conventional testing, APACHE-II score, SOFA score, high-sensitivity troponin, creatine kinase-MB subtype, and lactate dehydrogenase compared to the death group (P<0.05). Multivariate logistic regression analysis showed that these factors were risk factors for mortality in severe COVID-19 patients (P<0.05). In contrast, ROC curve analysis revealed that these factors had diagnostic values for mortality, with AUC values ranging from 0.657 to 0.963. The combined diagnosis of these indicators had an AUC of 0.924.

Conclusions

The use of mNGS technology can significantly enhance the detection of pathogens in severe cases of COVID-19 and also has a solid ability to predict clinical outcomes.

Clinical features and risk factors of liver injury in patients with Chlamydia psittaci pneumonia- a retrospective analysis

Background

Research into the effects of Chlamydia psittaci pneumonia on the liver has emerged in the last few years. However, no studies have systematically described liver injury in patients with psittacosis. We present the first report on the clinical features and risk factors of liver injury in patients with Chlamydia psittaci pneumonia.

Methods

We retrospectively collected the clinical parameters for 46 patients with Chlamydia psittaci pneumonia admitted to Jinhua Central Hospital from January 2019 to February 2023. We analyzed the liver function parameters and summarized the clinical characteristics and risk factors of liver injury.

Results

Among the 46 patients, 39 (84.8%) had abnormal liver function, and 23 (50.0%) had liver injury. The ratio of patients with a history of alcohol consumption (39.1% vs. 4.3%, P =0.004) or severe pneumonia (56.5% vs. 26.1%, P =0.036) was higher in the liver injury group compared with the non-liver injury group. Laboratory tests showed higher lactate dehydrogenase (LDH) levels in the liver injury group (P <0.001). The optimal cut-off LDH level associated with liver injury was 473 IU/L as determined by ROC curve analysis. Furthermore, multivariate logistic regression analysis demonstrated that a history of alcohol consumption (odds ratio [OR] = 11.251; 95% confidence interval [CI] = 1.022 ~ 123.897, P =0.048) and an LDH level of ≥ 473IU/L (OR = 11.635, 95% CI = 1.832 ~ 73.869, P =0.009) were independent risk factors for liver injury.

Conclusions

A history of alcohol consumption and an LDH level of over 473 IU/L are independent risk factors for Chlamydia psittaci pneumonia-related liver injury. It is recommended that particular attention be given to monitoring and evaluating liver function parameters when treating patients with Chlamydia psittaci pneumonia who have a high LDH level and history of alcohol consumption.

Chlamydia psittaci Pneumonia-Induced Pulmonary Thrombosis: A Case Report

Chlamydia psittaci pneumonia frequently leads to various extrapulmonary complications; however, reports of C. psittaci-pneumonia complicated by pulmonary thrombosis are uncommon. We report a case of severe C. psittaci pneumonia in a patient with a history of poultry contact and clinical manifestations including hyperpyrexia, dyspnea, and respiratory failure, which necessitated tracheal intubation for assisted ventilation. C. psittaci in bronchoalveolar lavage fluid was detected with metagenomic next-generation sequencing. Following targeted antibiotic therapy, the fever subsided, although dyspnea persisted without significant improvement, and chest pain developed. Compared to previous measurements, the D-dimer level increased, and CT pulmonary angiography revealed thromboses in the pulmonary artery trunk and left pulmonary artery. The symptoms improved after anticoagulant treatment, and the patient was discharged subsequently. This study suggests that C. psittaci infection may be associated with the formation of pulmonary thrombosis. Additional clinical data are required to support this inference. Following targeted antibiotic therapy, if persistent dyspnea, chest pain, and increased D-dimer level are present, pulmonary thrombosis should be considered, and pulmonary artery angiography can confirm the diagnosis.

Acute abdominal pain as the first symptom of Chlamydia psittaci pneumonia complicated by acute pancreatitis: a case report

Background

Chlamydia psittaci infections primarily cause damage to the lungs but may also affect the cardiovascular system, gastrointestinal tract, liver, kidney, and brain, resulting in a variety of extrapulmonary complications. However, reports regarding C. psittaci infection-associated pancreatitis are rare. In this report, a patient with C. psittaci pneumonia complicated by acute pancreatitis is presented.

Case description

The patient presented with acute upper abdominal pain and developed severe pyrexia and dyspnoea one day later. A chest computed tomography image revealed patchy consolidation in the left lung. The disease progressed rapidly, and the patient exhibited liver and kidney damage and type 1 respiratory failure within a short period of time. Metagenomic next-generation sequencing of alveolar lavage fluid revealed the presence of C. psittaci. The patient was administered doxycycline and moxifloxacin, after which the patient's abdominal pain and lung infection significantly resolved.

Conclusion

This case report demonstrates that extrapulmonary C. psittaci infections due to secondary acute pancreatitis can manifest as abdominal pain, although the exact mechanisms of C. psittaci caused by acute pancreatitis remain unclear. Timely diagnoses and treatments of such infections are necessary to achieve favorable clinical outcomes.

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.

A Case Report of Cutaneous Anthrax Diagnosed by Using a Metagenomic Next-Generation Sequencing (mNGS) Approach

Anthrax is caused by Bacillus anthracis. Humans are mainly infected through contact with the fur and meat of livestock. The cutaneous form is the most common form. The skin lesions of typical cutaneous anthrax are characterized by shallow ulcers with black crusts, surrounded by small blisters and nonpitting edema of nearby tissues. Metagenomic next-generation sequencing (mNGS) is a new pathogenic detection method which is rapid and unbiased. We reported the first case of cutaneous anthrax diagnosed by mNGS. Ultimately, the man received prompt antibiotic therapy and had a good prognosis. In conclusion, mNGS is proved to be a good method for etiological diagnosis, especially for rare infectious diseases.

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.

Case Report: Chlamydia psittaci pneumonia complicated by Guillain-Barré syndrome detected using metagenomic next-generation sequencing

Psittacosis and Guillain-Barré syndrome are both rare clinical diseases with low incidence, and their combination has rarely been reported. Here, we report a case of Chlamydia psittaci pneumonia combined with Guillain-Barré syndrome. The patient initially presented with high fever, difficulty breathing, and fatigue. Chest computerised tomography indicated large consolidation opacities in both lungs. Metagenomic next-generation sequencing clearly identified the pathogen as C. psittaci. The patient's fever subsided after targeted antibiotic treatment, but difficulty breathing and fatigue worsened, and the patient developed symmetric limb numbness and weakness. Lumbar puncture, electrophysiological examination, and clinical characteristics were suggestive of Guillain-Barré syndrome, and the symptoms improved after treatment with human immunoglobulin. The results of this study suggest that metagenomic next-generation sequencing is useful for the rapid diagnosis of pulmonary infectious agents. Psittacosis is closely associated with the development of Guillain-Barré syndrome; however, more cases are needed to support this conclusion, and early targeted antibiotic treatment, immunotherapy, and basic supportive treatment are essential for improving outcomes.

Case report: A clinical case study of six patients with Chlamydia psittaci pneumonia

Objective

To investigate the clinical features, diagnosis, and treatment of Chlamydia psittaci (C. psittaci) pneumonia.

Methods

We retrospectively analyzed the clinical data of six patients with C. psittaci pneumonia who were admitted to the Division of Pulmonary and Critical Care Medicine of the Second Hospital of Jiaxing from December 2021 to September 2022.

Results

All patients reported a fever and other accompanying symptoms, including cough (5/6), chest tightness (1/6), fatigue (2/6), and headache (1/6). Laboratory results showed that all patients had high levels of C-reactive protein (CRP≥70 mg/L), procalcitonin (PCT; 2 patients with PCT levels ≥0.5 ng/L), and erythrocyte sedimentation rate (ESR). Lactate dehydrogenase (LDH) and aspartate aminotransferase (AST) levels were elevated in 3/6 and of 2/6 patients, respectively. Chest computed tomography (CT) of most patients showed patchy, high-density shadows with partial consolidation, accompanied by air bronchogram signs and pleural effusion. Six patients were diagnosed with C. psittaci pneumonia using metagenomic next-generation sequencing (mNGS). They showed favorable outcomes following immediate adjustment of the regimen to doxycycline-based therapy and hydration, nutrition, and other follow-up treatments. In the imaging findings obtained at one-two month, the lesions were completely cleared, suggesting a favorable prognosis.

Conclusion

Patients with C. psittaci pneumonia commonly present sepsis and rapidly progressing disease. Early diagnosis is critical for C. psittaci pneumonia using mNGS, which can lead to favorable prognoses via immediate adjustment therapies.

Metagenomic next-generation sequencing for the diagnosis of Chlamydia psittaci pneumonia

The aim of this study was to investigate the clinical characteristics of Chlamydia psittaci pneumonia and evaluate the diagnostic value of Metagenomic Next-Generation Sequencing (mNGS). A total of 44 patients diagnosed with Chlamydia psittaci pneumonia using mNGS were retrospectively analysed. The demographic and clinical features, laboratory data, imaging findings and clinical outcomes were collected. Results showed that 65.91% of the patients had a history of exposure to poultry or birds. All patients presented with fever. Apart from systemic and respiratory symptoms, some patients also presented with digestive and neurological symptoms. Respiratory failure was common among patients. The key laboratory tests were normal white blood cell counts, slightly elevated PCT, changes in levels of cardiac enzymes, liver enzymes and hyponatremia. Chest imaging revealed that most of the lesions contained patchy exudation or lobar consolidation of one lobe, especially in the lower lobe. Consolidation of both lungs was seen in critically ill patients. Although quinolones were effective in most patients, tetracyclines should be the first choice of treatment. The overall prognosis was good; however, patients who developed severe pneumonia had poor prognosis. The incidence of chlamydia psittaci pneumonia may be underestimated due to the nonspecific clinical manifestations and lack of confirmatory testing methods. The use of mNGS has increased the number of patients diagnosed with chlamydia psittaci pneumonia. mNGS is an effective diagnostic method for chlamydia psittaci pneumonia.