Upper Respiratory Tract Infections
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General Goal: To know the major mechanisms of defense in the URT, the major mechanisms invaders use to avoid the defenses of the LRT, the common modes of transmission and the most common microbes that infect a particular location of the respiratory tract.

Educational Objectives: The student should be able to:

The respiratory tract is the most common site of infection by pathogens. Each year, children acquire between two and five upper respiratory tract infections and adults acquire one or two infections. The respiratory tract is a frequent site of infection because it comes in direct contact with the physical environment and is exposed to airborne microorganisms. A wide range of organisms can infect the respiratory tract, including viruses, bacteria, fungi and parasites (Table R-1).


The anatomy of the upper respiratory tract contains several structures that help rid the system of particles and pathogens. The nasal cavity has a mucociliary lining similar to that of the lower respiratory tract. The inside of the nose is lined with hairs, which act to filter larger particles that are inhaled. The turbinate bones (“baffle plates”) are covered with mucus that collects particles not filtered by nasal hairs. The baffle plates cause the air as it passes to swirl forcing the particles to make contact with the mucus covering the nasal passages. Usually, particles 5–10 µm in diameter are either trapped by nasal hairs or impinge on the nasal mucosal surfaces.


After inhaled air moves through the nasal passages, the anatomy of the upper airway changes direction and causes many of the larger airborne particles to impinge on the back of the throat. The adenoids and tonsils are lymphoid organs in the upper respiratory tract that are important in developing an immune response to pathogens and are located in an area where many of these airborne particles make contact with the mucosal surface over the adenoids and tonsils.


A layer of mucus and ciliated cells covers the lower portion of the respiratory tract. Both single and subepithelial cells secrete mucus. Respiratory pathogens that reach the lower respiratory tract if trapped in the mucous layer can then be driven upwards by ciliary action (the mucociliary elevator) to the back of the throat. In addition, the sneeze and cough reflexes are important mechanisms for clearing material that accumulates in or irritates the respiratory tract.


Nearly all of the surfaces of the respiratory tract (nasal and oral passages, nasopharynx, oropharynx, trachea, bronchi, bronchioles, and alveolar sacs) are colonized by the host microbiota. These organisms are inhabitants of the respiratory tract and rarely, if ever, cause disease. The microbiota of the respiratory tract has two main functions important in maintaining the healthy state of the host: (1) These organisms compete with pathogenic organisms for potential attachment sites, and (2) they can produce substances that are bactericidal and prevent infection by pathogens.


At one time it was thought that there was no microbiota in the lower respiratory tract. However, recent studies have shown that there are from 10-100 bacterial cells per 1000 lung cells. Many of the organisms in the lower respiratory tract microbiota do not grow on media commonly used to grow bacteria. It appears that most of the lung microbiota comes from the oropharynx.


Pathogenic organisms inhaled or aspirated into the lower respiratory tract are usually eliminated by alveolar macrophages. Alveolar macrophages are considered the most important means of eliminating pathogenic organisms that enter the lungs.


Table R-1. Common Causes of Various Respiratory Diseases by Location

Disease Location


Group of Pathogen


Upper respiratory tract

Nasal passages

Common cold (nonspecific URI)


Most common cause rhinovirus

Nasal sinuses




Viruses are most common cause of rhinosinusitis




Viruses cause 90% of these infections Streptococcus pyogenes and Corynebacterium diphtheriae

Respiratory airways




Usually Haemophilus influenzae type b

Trachea and bronchi

Bronchitis, tracheobronchitis, croup, laryngitis


Usually caused by viruses




Most common cause is respiratory syncytial virus

Lower respiratory tract

Alveoli and alveolar sacs



Severe Acute Respiratory Syndrome- Coronavirus-2 (SARS-CoV-2) 

Most common cause in adults is Streptococcus pneumoniae

Send comments and email to Dr. Neal R. Chamberlain, nchamberlain@atsu.edu
Revised 8/20/21
©2010-2021 Neal R. Chamberlain, Ph.D., All rights reserved.