Mycobacterium tuberculosis is an acid-fast bacillus (AFB), 0.5 × 4 to 5 μm, and the etiologic agent of tuberculosis in debilitated individuals. M. tuberculosis infection produces necrotizing granulomas, with a few bacilli found in the necrotic center and within the epithelioid cells and Langerhans multinucleated giant cells. The bacilli are slender, often beaded, and stain bright red with carbol fuchsin. The bacteria also stain with Gomori methenamine silver, Gram, and periodic acid-Schiff (PAS) stains. Transbronchial biopsy may demonstrate the necrotizing granulomas; however, identification of the acid-fast bacilli often requires a diligent search under oil immersion.

Atypical mycobacteria are nontuberculous acid-fast bacilli, <1.0 μm × 4 to 6 μm, and etiologic agents of multisystem human infection in immunocompromised patients. Multiple strains include Mycobacterium avium-intracellulare complex (MAC), M. kansasii, M. scrofulaceum, and M. xenopi. Infection in immunocompetent individuals is uncommon and may show caseating or noncaseating granulomas in the transbronchial biopsy. In immunocompromised patients, the atypical mycobacteria often present as stacks of AFB-positive bacilli within the cytoplasm of histiocytes.