Other infections occasionally occur in the lung and some may be identified on transbronchial biopsy. Rickettsiae, obligate intracellular bacteria, occur in the United States most commonly with tick-transmitted Rocky Mountain spotted fever, caused by Rickettsia rickettsii, and flea-transmitted endemic typhus, caused by Rickettsia typhi. Because these infections target the endothelial lining of the microvasculature systemically, cerebral and pulmonary edema due to increased microvasculature permeability is generally the cause of morbidity and mortality. Ehrlichiae are also obligate intracellular bacteria. Ehrlichia chaffeensis and E. ewingii target cells in the mononuclear phagocytic system and target polymorphonuclear neutrophils, respectively, and they are systemic diseases that may cause lung injury. Histologically, both rickettsiae and Ehrlichiae are small Gram-negative bacilli. These infections are most often diagnosed by open biopsy; however, transbronchial biopsy may show features of diffuse alveolar damage with edema, hyaline membranes, and interstitial pneumonitis. Immunostains or immunofluorescent techniques may occasionally show rickettsiae within the endothelial cells of the microcirculation, or ehrlichiae as intracytoplasmic bacterial aggregates within intravascular monocytes or pulmonary macrophages and neutrophils.

A variety of parasites is found in the lungs, and they are generally diagnosed by open biopsy. Some parasitic infections are amenable to diagnosis by transbronchial biopsy, however. Strongyloides infection is endemic in some countries, and infection may result from travel there. Strongyloides stercoralis lung infection occurs when migrating larvae molt within alveolar capillaries. Within immunocompromised patients, various stages of the life cycle may be identified, including filariform and rhabditiform larvae and eggs. Transbronchial biopsy of an involved area of lung parenchyma may show a mixture of hemorrhage, acute inflammation, and necrosis. Granulomas may be present and granulomatous inflammation may involve airways. Definitive diagnosis on transbronchial biopsy requires identification of filariform or rhabditiform larvae or eggs. Only very rarely is an adult female worm identified in the lung, even on open biopsy.