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Pulmonary or lung complications are significant causes of morbidity and mortality after stem cell transplant. Infectious and non-infectious causes of pneumonitis or lung inflammation after transplantation are well characterized. Pathogens that cause lung infections include bacterial, fungal and viral organisms. Weekly screening measures can be done to monitor patients for early reactivation of certain infectious agents, such as cytomegalovirus (CMV). Prophylactic medication is administered to recipients of allogeneic stem cell transplants at many centers along with weekly monitoring.