Primary atypical pneumonia is most often caused by Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella pneumophila. These organisms are termed "atypical" because they do not present with the classic lobar consolidation seen in typical bacterial pneumonia and are not detected on routine Gram stain or culture. They cause a more insidious onset of symptoms such as dry cough, low-grade fever, and malaise, often affecting younger patients. These pathogens require specialized diagnostic methods and are treated differently than typical bacterial pneumonias. Their significance lies in the need for specific antimicrobial agents like macrolides or fluoroquinolones.

Reference: Medical Microbiology, Murray et al., 9th Edition.