Clinical diagnosis and etiology of C. psittaci pneumonia patients based on metagenomic next-generation sequencing
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PROVIDER: PRJEB55126 | ENA |
REPOSITORIES: ENA
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Project description:Pneumocystis carinii pneumonia Diagnosis via Metagenomic Next-Generation Sequencing
| PRJEB43652 | ENA
Project description:Pneumonia stands as the primary cause of death among children under five, with its onset attributed to a broad spectrum of microorganisms. Diagnosis poses an ongoing challenge, relying on clinical or microbiological criteria, often resulting in delayed and inaccurate treatment and unnecessary therapy. Our research focuses on identifying host transcriptomic biomarkers in the blood of children affected by viral and bacterial pneumonia, alongside healthy controls. The main goal is to establish a gene-expression signature enhancing disease diagnosis and management. We conducted an analysis of a total of 192 whole blood samples, comprising 38 controls and 154 viral and bacterial pneumonia patients recruited through the EUCLIDS clinical network. Our investigation identified 5,486 differentially expressed genes (DEGs) when comparing blood RNA from pneumonia patients with healthy controls. Functional enrichment analysis highlighted pathways related to the immune system response, encompassing neutrophil degranulation, humoral immune response, and various inflammatory pathways. In the comparative analysis of gene expression between viral and bacterial pneumonia patients, we identified 272 DEGs. Gene set analysis revealed a significant difference in pathway enrichment for the immune response, contingent on the over-regulation of gene sets in viral or bacterial pneumonias. Furthermore, we identified a 5-transcript host signature specifically designed to distinguish between viral and bacterial pediatric pneumonia (FAM20A, BAG3, TDRD9, MXRA7 and KLF14; AUC: 0.95 [0.88–1.00]), pseudo-validated in a cohort including probable bacterial and viral patients (AUC: 0.87 [0.77–0.97]). This signature holds the potential to enhance the accuracy of previously described general transcript-based signatures for viral and bacterial infections.
2024-12-09 | GSE261482 | GEO
Project description:DNAseq of pathogens identified from C. psittaci pneumonia patients Raw sequence reads
| PRJNA955318 | ENA
Project description: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.
| S-EPMC9431268 | biostudies-literature
Project description:To clarify the host inflammatory response in psittacosis,we compared transcriptome data and concentrations of serum cytokines and chemokines in pneumonia and bronchitis cases.
2022-05-16 | GSE202947 | GEO
Project description:BackgroundThis is a retrospective cross-sectional study aiming to explore the clinical and imaging manifestations of Chlamydia psittaci pneumonia (CPP), thus improving its diagnosis, guiding its early clinical treatment, and reducing its mortality rate.MethodsFifty cases of CPP diagnosed by hospitals across the country with metagenomics next-generation sequencing (mNGS) from January 2019 to March 2021 were collected. Its clinical symptoms, laboratory test results, and computed tomography (CT) features were discussed.ResultsForty patients had a history of poultry exposure; 37 experienced respiratory symptoms, 48 had a fever, 14 experienced gastrointestinal symptoms, and 12 experienced neurological symptoms; 34 patients had normal blood cell counts, 49 patients had elevated C-reactive protein, and 24 showed decreased serum sodium. Imaging manifestations: (I) Distribution: lesions were limited to a single lung in 31 patients, lesions were distributed in bilateral lungs in 19 patients; (II) Signs: 37 patients developed the "fine mesh sign". Necrosis, cavity and "tree-in-bud" were not observed. Pleural effusion occurred in 33 patients, mediastinal lymphadenopathy in 18, and splenomegaly in 15 patients.ConclusionsPatients with CPP often have a history of poultry exposure and present with fever and increased C-reactive protein. White blood cells may be slightly increased or completely normal. Hyponatremia may occur in some patients, and multiple systems may be clinically involved. The imaging can show lesions with unilateral or bilateral lung distribution and a rapid progression. Both the lung parenchyma and the interstitium are involved. Fine mesh sign is the most common sign. Necrosis, cavitation, and tree-in-bud signs are not observed. In conclusion, imaging examinations are helpful for the early diagnosis of this disease and the evaluation of the treatment effect.
| S-EPMC10102789 | biostudies-literature
Project description:A 5-transcript signature for discriminating viral and bacterial etiology in pediatric pneumonia
| PRJNA1087273 | ENA
Project description:Rationale: Patients in the intensive care unit (ICU) are frequently exposed to unnecessary antibiotics. Markers of the host response to infection may aid pneumonia diagnosis and avoid antibiotic-induced complications. Objective: To assess the host response to suspected bacterial pneumonia through assessment of alveolar neutrophilia and transcriptomic profiling of alveolar macrophages. Methods: We determined the test characteristics of BAL neutrophilia for the diagnosis of bacterial pneumonia in 3 cohorts of mechanically ventilated patients. In one cohort, we also isolated alveolar macrophages from BAL fluid and used the transcriptome to identify signatures of bacterial pneumonia. Finally, we developed a humanized mouse model of Pseudomonas aeruginosa pneumonia to determine if pathogen-specific signatures can be identified in human alveolar macrophages. Measurements and Main Results: BAL neutrophilia was highly sensitive for bacterial pneumonia in both the retrospective (N = 851) and validation cohorts (N = 76 and N = 79) with a negative predictive value of over 90% when BAL neutrophil percentage was less than 50%. A transcriptional signature of bacterial pneumonia was present in both resident and recruited macrophages. Gene signatures from both cell types identified patients with bacterial pneumonia with test characteristics similar to BAL neutrophilia. Conclusions: A BAL neutrophil percentage of less than 50% is highly sensitive for bacterial pneumonia. Informative transcriptomic signatures can be generated from BAL fluid obtained during routine clinical care in the ICU. The identification of novel host response biomarkers is a promising approach to aid the diagnosis and treatment of pneumonia.
2018-11-06 | GSE121871 | GEO
Project description:Host inflammatory response is the major factor in the progression of Chlamydia psittaci pneumonia
| PRJNA837877 | ENA