Formulations have been developed to treat or reduce the spread of respiratory infections, especially chronic or drug resistant infections, particularly tuberculosis (TB), severe acute respiratory syndrome (SARS), meningococcal meningitis, Respiratory syncytial virus (RSV), influenza, and small pox. Formulations include a drug or vaccine in the form of a microparticle, nanoparticle, or aggregate of nanoparticles, and, optionally, a carrier, which can be delivered by inhalation. Giving the drugs via an inhaler sidesteps the problems associated with oral or injectable drugs by bypassing the stomach and liver, and delivering the medication directly into the lungs. In one embodiment, the particle containing the agent is a large porous aerosol particle (LPPs). In another embodiment, the particles are nanoparticles, which can be administered as porous nanoparticle aggregates with micron diameters that disperse into nanoparticles following administration. Optionally, the nanoparticles are coated, such as with a surfactant or protein coating. The formulation may be administered as a powder or administered as a solution or via an enteral or non-pulmonary parenteral route of administration. The formulation is preferably administered as a pulmonary formulation. In the preferred embodiment for treatment of TB, the vaccine is a BCG vaccine that is stable at room temperature, or is an antibiotic effective against TB, such as capreomycin or PA-824, loaded at a very high percentage into the microparticles or nanoparticles. In one embodiment, a patient is treated with formulations delivering both antibiotic and vaccine.