ObjectiveTo improve the understanding of psittacosis, the clinical data of 8 cases are reviewed. The application of pathogen metagenomics next-generation sequencing (mNGS) in the diagnosis of nocardiosis is also investigated.MethodsThe clinical data of eight patients with psittacosis diagnosed by mNGS in Nanjing Drum Tower Hospital from January 2018 to May 2020 were reviewed. The clinical characteristics, laboratory examination characteristics and imaging changes were analyzed, and the treatment outcome was followed-up.ResultsAmong the eight cases, there were six males and two females, aged 43～83 years old, with an average age of 64±12 years old. Six of them had a clear history of poultry exposure. The major clinical manifestations were fever, cough, dyspnea, etc. Chest high-resolution computed tomography (HRCT) may have solid shadow, ground glass like shadow. Chlamydia psittaci was detected by mNGS in eight patients’ bronchoalveolar lavage fluid. Minocycline or moxifloxacin were administrated, six patients were discharged after their condition improved, and two patients died.ConclusionsThe incidence of psittacosis is low, and its clinical manifestations lack specificity. In the course of the disease, there may be different degrees of fever, cough, sputum, dyspnea and other symptoms. The lungs can be heard with wet rales, chest HRCT can be seen ground glass shadow, consolidation shadow, accompanied by air bronchogram. Chlamydia psittaci can be detected in alveolar lavage fluid by mNGS. The patients need to be treated for a long time, lasting at least 10 to 14 days. Tetracycline drugs should be the first choice, and can be combined with other antibiotics with activity against gram-positive and gram-negative bacteria in critical patients.
In recent years, due to the extensive usage of immunosuppressant and the rise of patients with cancers and organ transplantation, the incidence rate of invasive fungal infection, especially invasive pulmonary fungal infection, has increased. Besides the clinical manifestations, medical history and imaging, the diagnosis of pulmonary mycosis mainly depends on pathogen detection methods in clinical microbiology laboratory. However, due to the difficulty in fungi culturing and the low sensitivity of smear microscopy, better molecular biology methods are needed. To date, the emergence of metagenomic next-generation sequencing (mNGS) has improved the identification rate of pulmonary fungal infections. mNGS is significantly superior to traditional detection methods in rapid, accurate, and comprehensive determination of fungi from various clinical specimens, especially atypical fungi. However, some problems in mNGS method have to be addressed including sample collection, report interpretation, and its combination with traditional microbiology methods. With the in-depth discussion and solution of the above problems, mNGS will be indispensable to the etiological diagnosis of pulmonary invasive fungal infection.
ObjectiveTo explore the clinical value of next-generation sequencing (NGS) in the diagnosis of Pneumocystis jirovecii pneumonia (PCP).MethodsTwo patients with Pneumocystis jirovecii pneumonia after lung transplantation were detected by NGS in the sputum and bronchoalveolar lavage fluid. The clinical data, imaging features, laboratory examination and treatment of the two patients were reported. A systematic literature review was performed for similar published cases in PubMed database, using the keywords "lung transplantation/solid organ transplantation" and "Pneumocystis jirovecii".ResultsThere were six references based on the keywords of "lung transplantation " and " Pneumocystis jirovecii ", of which three were case report. Sixty-six lung transplant patients were complicated with Pneumocystis jirovecii in total. The clinical manifestations of Pneumocystis jirovecii pneumonia were fever and dyspnea of different degrees. The diffuse "ground glass" infiltration could be shown on imaging. Computer tomography scan of chest was a sensitive method to detect PCP. Combined immunofluorescence microscope/PCR/serum 3-β-D-glucan could effectively improve the accuracy of microbiology detection. In addition, NGS could quickly and accurately identify pathogenic bacteria, give guidance for treatment and improve prognosis so as to benefit patients well. Trimethoprim/sulfamethoxazole (TMP/SMZ) was the preferred choice for the treatment of PCP patients.ConclusionsPneumocystis jirovecii pneumonia is more common in patients with immunodeficiency or immunosuppression. NGS can help rapid and accurate diagnosis, and the treatment should be early and sufficient.
ObjectiveTo study the application of non-real-time ultrasound bronchoscopy combined with Metagenomic Next-Generation Sequencing (mNGS) for diagnosis in focal pulmonary infectious diseases. MethodsProspective inclusion of patients with focal pulmonary infection were randomly divided into two groups, the experimental group used non-real-time ultrasound bronchoscopy positioning to collect bronchial alveolar lavage fluid (BALF), while the control group used chest CT position. BALF was subjected to mNGS and traditional microbial detection including traditional culture, the fungal GM test and Xpert (MTB/RIF). ResultThe positive rate of traditional culture (39.58% vs. 16.67%, P=0.013) and mNGS (89.58% vs. 72.92%, P=0.036) in experimental group was higher. The positive rate of Xpert MTB/RIF (4.17% vs. 2.08%, P=1) and fungal GM test (6.25% vs. 4.17%, P=0.765) was similar. The positive rate of bacteria and fungi detected by mNGS was higher than traditional culture (61.46% vs. 28.13%, P<0.001). Mycobacterium tuberculosis was similar to Xpert MTB/RIF (8.33% vs. 3.13%, P=0.21). Aspergillus was similar to GM test (7.29% vs. 5.21%, P=0.77). The total positive rate of traditional microbial methods was 36.46%, but 81.25% in mNGS (P<0.001). mNGS showed that 35 cases were positive and 13 kinds of pathogens were detected in control group, but 43 patients and 17 kinds of pathogens were detected in experimental group. The average hospitalization time [(12.92±3.54) days vs. (16.35±7.49) days] and the cost [CNY (12209.17±3956.17) vs. CNY (19044.10±17350.85)] of experimental group was less (P<0.001). ConclusionsNon-real-time ultrasound bronchoscopy combined with mNGS can improve the diagnostic rate of focal pulmonary infectious diseases which is worthy of popularization and application in clinical practice.
ObjectiveTo explore the application and clinical value of metagenomic next-generation sequencing (mNGS) combined with Omadacycline in the treatment of Refractory Mycoplasma pneumoniae pneumonia (RMPP).MethodsThe clinical data, relevant laboratory results, diagnosis and treatment process, and imaging outcomes of four patients diagnosed with Mycoplasma pneumoniae pneumonia through mNGS were analyzed. ResultsThe clinical symptoms at onset in all four patients were consistent with Mycoplasma pneumoniae pneumonia. After conventional treatment with macrolides, tetracyclines, or quinolone antibiotics, the symptoms showed no significant improvement, and there was a trend of radiological worsening. Following the confirmation of Mycoplasma pneumoniae infection through mNGS of bronchoalveolar lavage fluid, and due to various reasons preventing the use of the aforementioned drugs, omadacycline was ultimately chosen for treatment. Radiological improvements were observed in all cases, leading to a good prognosis and discharge. ConclusionsFor pneumonia cases where the infectious pathogen cannot be identified and conventional treatment has failed, mNGS can be utilized for early and accurate diagnosis. In cases of RMPP, Omadacycline can be employed as an alternative treatment to prevent delays in care and reduce the risk of complications.
Objective To explore the clinical characteristics of Chlamydia psittaci pneumonia. Methods From January 2020 to March 2023, 21 cases of Psittacosis from the First Affiliated Hospital of Nanjing Medical University were diagnosed via metagenomic next-generation sequencing (mNGS). They were divided into a severe group (n=10) and a non-severe group (n=11) based on diagnostic criteria for severe pneumonia, and the clinical presentation, secondary examination, treatment, and prognosis of the two groups were analyzed retrospectively. Results Among the 21 patients, there were 11 males and 10 females, with a mean age of (51.7±11.6) years. All patients had an acute onset and 12 had a confirmed history of exposure to poultry. The onset of the disease occurred in the autumn and winter seasons in 18 patients. All the patients were suffering from high fevers. Other symptoms included coughing, phlegm, tightness in the chest and fatigue. Laboratory examinations showed that the levels of leukocytes, neutrophil counts, C-reactive protein, procalcitonin, aminotransferase, creatine kinase, lactic dehydrogenase, brain natriuretic peptide precursors and D-dimer were significantly higher in the severe group than those in the non-severe group. Chest CT scans revealed varying levels of consolidation and spot shadowing with peripheral exudate in all patients. The patients in the severe group were more likely to have bilateral lung involvement, bilateral pleural effusion, cavity and mediastinal lymph node enlargement. Eleven patients received tetracycline alone, three received laudanum alone, two received respiratory quinolones alone, and five received a combination of two drugs including tetracycline. Chest CT at clinical follow-up showed absorption of lung lesions. Conclusions Chlamydia psittaci pneumonia usually occurs in the fall and winter, and most patients have a history of contact with poultry. Clinical presentation and imaging are not specified. The technology of mNGS enables early diagnosis of the disease, and neutrophil lymphocyte ratio, neutrophil-lymphocyte ratio and lactic dehydrogenase levels help assess the risk of severe disease.