What Is Bacterial Colonization?

Bacterial Colonization of the Lungs With Cystic Fibrosis

image of a brain scan in a patient with cystic fibrosis
What is the importance of bacterial colonization in people with cystic fibrosis?. Credit: Medic Image

You may have heard about bacterial colonization if you are living with cystic fibrosis. What does this mean?

What is Colonization?

Colonization occurs when microorganisms live on or in a host organism but do not invade tissues or cause damage. Colonization refers to the presence of microorganisms which can cause infection, but not to infection itself. Having these microorganisms present, however, increases the risk of infection if the right environment for an infection occurs.

Importance of Colonization in Cystic Fibrosis

People with cystic fibrosis (CF) are often colonized with bacteria, especially in the mucus and airways. If the organisms begin to invade tissues and cause damage or make the person sick, the colonization becomes an infection.

Respiratory Tract Changes in People With Cystic Fibrosis

In people with cystic fibrosis, excess secretion of mucus and chronic bacterial infection result in a special type of chronic obstructive pulmonary disease. People with cystic fibrosis eventually develop bronchiectasis wherein the airways become badly damaged and scarred.

Bronchiectasis is a condition in which the bronchi and bronchioles (smaller branches of the airways) become thickened, widened and scarred. Mucous accumulates in these widened airways predisposing to infection. Infection then results in further thickening, widening, and scarring of the airways repeating a vicious cycle.

Beyond the bronchi and bronchioles lie the alveoli, the small air sacs through which the exchange of oxygen and carbon dioxide occurs. When the bronchioles leading to these smallest of airways lose their elastic recoil (from the thickening and scarring) and become clogged with mucous, oxygen inhaled into the lungs cannot reach the alveoli for this gas exchange to take place.

Why Do the Lungs in People With Cystic Fibrosis Produce Excess Mucus?

It's somewhat unclear whether people with cystic fibrosis initially produce excess viscid mucus or do so because of bacterial colonization. However, examination of the lungs in newborns with cystic fibrosis who have yet to be colonized with bacteria shows excess production of mucus. These findings suggest that the mucus predisposes people with cystic fibrosis to colonization with bacteria.

What Types of Bacteria Colonize the Lungs of People With Cystic Fibrosis?

Many types of aerobic bacteria (bacteria which grow in the presence of oxygen), anaerobic bacteria (bacteria which grow without oxygen) and opportunistic pathogens like fungus colonize the lungs of people with cystic fibrosis. The term opportunistic pathogens is used to describe microorganisms which do not ordinarily cause infections in healthy people, but may cause infections when the "opportunity" arises, such as when lung disease is present.

Here are some organisms that colonize lungs of people with cystic fibrosis:

Most Common Type of Pathogens Which Colonize Airways in People with CF

Of the above organisms, colonization with Pseudomonas typically predominates and about 80 percent of adults with cystic fibrosis are colonized with this type of bacteria.

Multidrug-Resistant Organisms and Cystic Fibrosis

In addition to the above pathogens, people with cystic fibrosis are more likely to be colonized with "superbugs" or multidrug-resistant organisms. Multidrug-resistant organisms (organisms which are resistant to many antibiotics) take hold in the lungs after a person with cystic fibrosis receives antibiotic treatment for lung infections, such as Pseudomonas. Colonization and infection with multidrug-resistant organisms is scary because these organisms resist treatment with conventional antibiotics.

Why Does Colonization With Pseudomonas Predominate?

Experts have plenty of thoughts or hypotheses as to why the lungs of people with cystic fibrosis are predominantly colonized with Pseudomonas, including the following:

  • Reduced mucociliary clearance combined with the malfunction of antibacterial peptides
  • Impaired defense of the lungs due to low levels of glutathione and nitrous oxide
  • Reduced ingestion of bacteria by lung cells
  • Increased numbers of bacterial receptors

We don't know exactly which of these mechanisms is most important in establishing colonization of Pseudomonas. Nevertheless, it's apparent that once Pseudomonas takes hold, chronic infection persists.

People with cystic fibrosis who are colonized with Pseudomonas require daily maintenance therapy as well as periodic aggressive intravenous antibiotic therapy when infection sets in. Unfortunately even with such treatment, Pseudomonas infection results in progressive loss of lung function and leads to eventual death in most people with cystic fibrosis. Learn more about Pseudomonas in people with cystic fibrosis.)


Boutin, S., and A. Dalpke. Acquisition and Adaptation of the Airway Microbiotia in the Early Life of Cystic Fibrosis Patients. Molecular and Cellular Pediatrics. 2017. 4(1):1.

Huang, Y., and J. LiPuma. The Microbiome in Cystic Fibrosis. Clinical Chest Medicine. 2016. 37(1):59-67.

Voynow JA, Mascarenhas M, Kelly A, Scanlin TF. Cystic Fibrosis. In: Grippi MA, Elias JA, Fishman JA, Kotloff RM, Pack AI, Senior RM, Siegel MD. eds. Fishman's Pulmonary Diseases and Disorders, Fifth Edition. New York, NY: McGraw-Hill; 2015. Accessed January 23, 2016.

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