Patients admitted to our respiratory intensive care unit (RICU) due to respiratory failure provided written informed consent to undergo bronchoscopy and mNGS between September 2017 and October 2018; they were then examined via bedside bronchoscopy by experienced physicians. The safety of bronchoalveolar lavage (BAL) was enhanced by following a standard safety protocol [5 (link)].
BALF samples were harvested, of which 5 mL of the specimen was placed in a sterile sputum container, stored at − 20°C, and then sent to BGI-Huada Genomics Institute (Shenzhen, China) for detection. The remaining specimens were sent to our microbiological laboratory for bacterial and fungal smear and culture, Pneumocystis jirovecii (PC) smear (Grocott methenamine staining), acid-fast stain, Xpert MTB/RIF detection of DNA sequences specific for Mycobacterium tuberculosis and rifampicin resistance by PCR, and real-time PCR for cytomegalovirus (CMV), influenza A/B virus, PC, Mycobacterium tuberculosis, Mycoplasma spp., and Chlamydia spp.
BALF samples were harvested, of which 5 mL of the specimen was placed in a sterile sputum container, stored at − 20°C, and then sent to BGI-Huada Genomics Institute (Shenzhen, China) for detection. The remaining specimens were sent to our microbiological laboratory for bacterial and fungal smear and culture, Pneumocystis jirovecii (PC) smear (Grocott methenamine staining), acid-fast stain, Xpert MTB/RIF detection of DNA sequences specific for Mycobacterium tuberculosis and rifampicin resistance by PCR, and real-time PCR for cytomegalovirus (CMV), influenza A/B virus, PC, Mycobacterium tuberculosis, Mycoplasma spp., and Chlamydia spp.
