The human host has several mechanisms that nonspecifically protect the respiratory tract from infection: the nasal hairs, convoluted passages, and the mucous lining of the nasal turbinates; secretory IgA and nonspecific antibacterial substances (lysozyme) in respiratory secretions; the cilia and mucous lining of the trachea; and reflexes such as coughing, sneezing, and swallowing. These mechanisms prevent foreign objects or organisms from entering the bronchi and gaining access to the lungs, which remain sterile in the healthy host.

Aspiration of minor amounts of oropharyngeal material, as occurs often during sleep, plays an important role in the pathogenesis of many types of pneumonia. Once particles escape the mucociliary sweeping activity and enter the alveoli, alveolar macrophages ingest them and carry them to the lymphatics.

In addition to these nonspecific host defenses, normal flora of the nasopharynx and oropharynx help prevent colonization by pathogenic organisms of the upper respiratory tract. Normal bacterial flora prevent the colonization by pathogens by competing for the same space and nutrients as well as production of bacteriocins and metabolic products that are toxic to invading organisms. Some of the bacteria that can be isolated as part of the indigenous flora of healthy hosts, as well as many species that may cause disease under certain circumstances and are often isolated from the respiratory tracts of healthy persons, are listed in Box 1. Under certain circumstances and for unknown reasons, these colonizing organisms can cause disease—perhaps because of previous damage by a viral infection, loss of some host immunity, or physical damage to the respiratory epithelium (e.g., from smoking). Differentiation of normal flora of the respiratory tract is important for determining the importance of an isolate in the clinical laboratory. Colonization does not always represent an infection. It is important to differentiate colonization from infection based on the specimen source, number of organisms present, and presence or quantity of white blood cells. (Organisms isolated from normally sterile sites in the respiratory tract by sterile methods that avoid contamination with normal flora should be definitively identified and reported to the clinician.)

Box1.  Organisms Present in the Nasopharynx and  Oropharynx of Healthy Humans

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Definition of Sepsis

Types of Bloodstream Infections

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Human Prion Diseases

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Clinical Manifestations of Aging and Hematopoiesis

Reactions of Blood Vessels in Acute Inflammation