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.
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.
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.
Objective To explore the application value of metagenomic next-generation sequencing (mNGS) based on human sequencing in the clinical early diagnosis of lung cancer. Methods Four patients hospitalized with suspected lung infection were retrospectively analyzed, and the test results of bronchoalveolar lavage fluid (BALF) on mNGS of tumor metagenome, the routine clinical test results, and their clinical diagnosis and treatment information in between August 26, 2021, and December 18, 2021. Results Patient 1 was preliminarily diagnosed with lung cancer by referring to chest computed tomography (CT) imaging. Chest radiograph or CT in the other three patients showed bilateral lung CT and lamellar hyperintensities (patient 2), bilateral lung mass-like and lamellar hyperintensities (patient 3), and lung masses (patient 4), respectively. BALF samples from all 4 patients were detected with mNGS based on human tumor sequences, indicating tumor. In addition, the result in patient 3 also indicated white pseudofilamentous yeast infection consistent with clinical culture, and the result in patient 4 also showed infection of rhinovirus type A. Conclusion The second generation genome sequencing technology based on human sequence can not only assist clinical diagnosis of infection, but also provide detection datUM support for tumor early warning.
Objective To explore the clinical value of metagenomic next-generation sequencing (mNGS) in the diagnosis and treatment of severe and complex infection of malignant hematological disorder. Methods The mNGS test results, traditional etiology test results and general clinical data of inpatients with malignant hematological disorder in the Department of Hematology, the Affiliated Hospital of Southwest Medical University between June 2020 and February 2022 were retrospectively analyzed. To explore the clinical application value of mNGS in the diagnosis and treatment of severe complicated infection of hematological disorder. Results A total of 21 patients were included. The samples included 18 peripheral blood samples, 2 pleural fluid samples and 1 alveolar lavage fluid sample. In the included patients, through mNGS, pathogenic bacteria were directly detected in 17 patients, including 8 fungi, 9 bacteria and 10 viruses, of which 9 were mixed infections. The positive rate (81.0% vs. 33.3%, P=0.002), sensitivity (85.7% vs. 30.0%), granulocytopenia (9 vs. 3 cases, P=0.031) and the types of pathogen (Z=−3.416, P=0.001) detected by mNGS were all higher than those by traditional method. The infection control of 17 patients improved in varying degrees after adjusting the treatment plan according to the test results. ConclusionsmNGS has significantly higher detection rate and sensitivity for bacteria, fungi, viruses and mixed infections. Compared with the traditional method, mNGS has more efficient characteristics. Its clinical application can further improve the diagnosis and treatment efficiency of severe complicated infection of malignant hematological disorder, and thus improve the survival rate of patients.
Objective To analyze the differences in microbial communities in bronchoalveolar lavage fluid (BALF) from patients with simple pneumonia versus those with chronic obstructive pulmonary disease (COPD) combined with lower respiratory tract infection using metagenomic next-generation sequencing (mNGS). Methods Patients hospitalized for pulmonary infections at the First Affiliated Hospital of Xinjiang Medical University between December 2021 and March 2023 were included. Based on the presence of COPD, the patients were divided into two groups: those with simple pneumonia and those with COPD combined with lower respiratory tract infection. mNGS was employed to detect microbes in BALF, and the microbial community distribution characteristics of the two groups were analyzed. Results A total of 97 patients were included, of whom 80 (81.82%) had positive microbial detection results. The smoking index in COPD group with lower respiratory tract infection was significantly higher than that in the group with simple pneumonia (t= −3.62, P=0.001). Differences in microbial community distributions were observed between the groups. At the genus level, 19 species of microorganisms were detected in the simple pneumoniapulmonary infection group, including 8 bacteria (42.11%), 2 fungi (10.53%), 3 viruses (15.79%), and 6 other types of microorganisms (31.58%). In contrast, 22 types of microbes were detected in COPD group with lower respiratory tract infection, including 10 bacteria (47.62%), 3 fungi (14.29%), 4 viruses (19.05%), and 4 other types of microorganisms (19.05%). Differences were also noted in reads per million (RPM) values; bacterial RPM values at the genus level were significantly higher in the COPD group during non-severe pneumonia compared to the simple pneumonia group (Z=–2.706, P=0.007). In the patients with severe pneumonia, RPM values at the genus and species levels were significantly higher than those in non-severe pneumonia (Z=−2.202, P=0.028; Z=−2.141, P=0.032). In COPD combined with severe pneumonia, bacterial RPM values were significantly higher at the species level compared to non-severe pneumonia (Z=−2.367, P=0.017). ConclusionsThere are differences in the distribution of microbial communities at the genus and species levels in BALF from patients with COPD combined with lower respiratory tract infection compared to those with simple pulmonary pneumonia. Bacteria are the predominant microbial type in both groups, but the dominant bacterial species differ between them. Simple pneumonia are primarily associated with bacterial, viral, and other types of microbial infections, while COPD combined with lower respiratory tract infection is predominantly associated with fungal and bacterial infections. RPM values may serve as an indicator of the severity of pneumonia.
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.