Sample Collection and Etiological Diagnosis

BALF was collected according to previous consensus and guideline (Meyer et al., 2012; Diseases CSoR, 2017). After eliminating contraindications, all patients underwent bronchoscopy under intravenous combined anesthesia or 2% lidocaine topical anesthesia. After an equal volume of normal saline was fractionally injected into the affected bronchial segments, BALF was aspirated under negative pressure for related testing.

All patients were subject to pathogen detection using BALF-mNGS and conventional methods at the same time. BALF and peripheral blood specimens were simultaneously submitted for microscopic examination. Lavage fluid was centrifuged to collect the sediment for pathogen identification under the microscope after staining. The fully automated medical PCR analysis system GeneXpert Dx System (Cepheid, Sunnyvale, CA, USA) was used for pathogen nucleic acid detection. A microbial culture (BACT-ALERT; bioMérieux, France) and automated microbial identification systems (VITEK 2 Compact and VITEK MS; bioMérieux, France) were employed.