Etiology of lower respiratory tract in pneumonia based on metagenomic next-generation sequencing: a retrospective study

Study ParticipantsPatients with pulmonary infection admitted to the first affiliated Hospital of Zhengzhou University from April 30th, 2018 to June 30th, 2020 were retrospectively selected as the object. All patients met the following inclusion criteria: (1) met the diagnostic criteria in the “Diagnosis and Treatment of Adults With Community-acquired Pneumonia 2016” [16] and “Management of Adults With Hospital-acquired and Ventilator-associated Pneumonia:2016 Clinical Practice Guidelines by the Infectious Diseases Society of America and the American Thoracic Society” . (2) during hospitalization, routine methods (sputum, pharyngeal swab or bronchoalveolar lavage fluid (BALF) bacterial smear, culture, and PCR detection of microorganisms in peripheral venous blood) and mNGS (BALF) were used to detect respiratory tract pathogenic microorganisms. Exclusion criteria: (1) complicated with other parts of infection. Exclusion criteria: those with incomplete clinical data. When a patient meets at least one of the following criteria, it is defined as low immune function: (1) hematopathy; (2) taking glucocorticoids or chemotherapeutic drugs for autoimmune diseases; (3) taking immunosuppressants for solid organ transplantation; (4) receiving chemotherapy or neutropenia for solid tumors in the past 3 months. (5) low immune function caused by other causes, such as congenital or hereditary low immune function.Microbiological Testing and Pathogenic AnalysisSputum, peripheral venous blood and pharyngeal swabs were collected from all patients, and BALF was collected by bronchoalveolar lavage. Routine methods (bacterial smear, PCR, culture, etc.) were used to detect pathogenic microorganisms. At the same time, mNGS was used to detect pathogenic microorganisms in BALF.Sputum, pharyngeal swabs and BALF samples were stained with routine Gram staining and bacterial smears and cultured (bacteria, fungi, etc.), and peripheral venous blood was collected for bacterial + fungal culture. Multiplex real-time polymerase chain reaction (RT-PCR) was used to detect viral nucleic acid in respiratory secretions.mNGS testing: immediately after taking BALF 5mL, store it in 4℃ refrigerator and submit it for inspection within two hours. MNGS testing is completed by a third party company.Clinical Data Collection and Antibiotic TreatmentClinical data of all patients were retrieved from the medical records, including demographics, laboratory test results and ICU special treatment data. Antibiotic treatment before ICU, initial antibiotic at ICU admission and adjustment later based on the pathogen results of mNGS were also been collected.