In the intensive care unit, bronchoscopy can be used to clear the airways by removing phlegm and secretions that block the bronchi. Bronchoscopy to remove phlegm plugs does not replace conventional phlegm suction techniques or daily respiratory therapy such as percussion, turning, breathing exercises, etc.

Because of their lipid-rich cell wall structure, Mycobacteria cannot be detected by conventional Gram staining. Diagnosis of Mycobacteria infection can be made by using acid-fast bacillus (AFB) sputum staining to look for bacteria.