Pathogen Reduction & Decolonization to Prevent Infections

Pathogens (harmful germs) cause infections. People receiving medical care in healthcare facilities like hospitals and nursing homes can get serious infections called healthcare-associated infections (HAIs). People can get HAIs during or after procedures like surgery, or from devices like catheters or ventilators. Sometimes HAIs are caused by antimicrobial-resistant pathogens, making them difficult to treat.

People can also be colonized with pathogens without symptoms of an infection. Colonization means the germs are present on or in a person’s body and are alive and growing.

Colonization can increase a person’s risk for infection. Also, people who are colonized can unknowingly spread these germs to others through person-to-person contact or contaminated surfaces in shared settings.

Some people are at even higher risk for infection when they are colonized. These include patients who are critically ill, had surgery, received transplants, are in intensive care units, and have compromised immune systems.

Healthy microbial communities with beneficial bacteria help our body protect against pathogen colonization and growth. Healthcare providers and infection preventionists can use intervention strategies to reduce or eliminate colonized pathogens in people to protect them from infection and prevent the spread of the colonizing pathogens. These strategies include:

  • Pathogen reduction, a strategy that decreases the number of bacterial or fungal pathogens that might lead to infection.
  • Decolonization, a type of pathogen reduction that eliminates the colonizing pathogens. A primary goal of decolonization is to remove pathogens on specific places on our body, such as skin (e.g., surgery sites) and mucosal surfaces (e.g., nose, gastrointestinal tract). These specific body sites (skin, mouth, respiratory tract, urinary tract, gut) are home to microbiomes, communities of naturally occurring germs.

Endogenous vs. Exogenous Infection 

Endogenous: When a person gets an infection caused by a pathogen that is already colonizing a part of their body (e.g., S. aureus in their nose).

Exogenous: When a person gets an infection from a germ that recently spread to them from another person or from a shared contaminated surface.

Learn more microbial ecology terms.

How Colonization Can Cause Infections

Germs can cause infection by entering the body through various body sites and via medical devices. Additionally, when a microbiome is disrupted, pathogens can take over, or dominate, including antimicrobial-resistant pathogens.

Dominance of one or several pathogens puts people at increased risk for infection, including recurring C. difficile infection, multidrug-resistant infections, skin infections, or sepsis. This is especially true for vulnerable people and critically ill patients, such as surgical patients and newborns in the intensive care unit. For example, a 2019 CDC-funded study found that patients who had a high number of antibiotic-resistant Klebsiella pneumoniae in their microbiomes were at higher risk for K. pneumoniae bloodstream infections, which can be life-threatening.

When a person is colonized and it leads to infection, it often happens like this:

  • Lucy is colonized with antibiotic-resistant Pathogen A.
    Lucy goes to the hospital for surgery. Lucy is either already colonized with antibiotic-resistant Pathogen A, which is not causing an infection, or she becomes colonized with Pathogen A soon after admission. This could happen by person-to-person spread or from contaminated surfaces. Lucy and her healthcare providers do not know that Lucy is colonized.

    Lucy is at higher risk for an infection following her procedure and can spread these germs to others. Because Pathogen A is a resistant germ, it may cause an infection that is difficult or impossible to treat.
  • Lucy’s microbiome becomes disrupted, allowing Pathogen A to dominate her microbiome.
    Lucy is given antibiotics through an IV to help prevent infections that could happen following her surgery. Her gut’s beneficial germs are wiped out by the antibiotics in addition to some pathogens, resulting in an unbalanced microbiome.

    However, Pathogen A is not killed and remains. It now outcompetes and outnumbers the beneficial germs, becoming dominant in the microbiome.
  • Pathogen A starts to invade the body, causing an infection.
    An unbalanced microbiome puts Lucy at higher risk for infection because her body’s defense is low. Pathogen A starts to invade and causes a skin infection at the IV site. Pathogen A also continues to spread to the surrounding environment and to other people.

Using Pathogen Reduction and Decolonization Methods

When a healthcare facility identifies certain multidrug-resistant pathogens within their facility, CDC recommends colonization screening. Colonization screening is an infection prevention method using laboratory testing to identify patients who are colonized with resistant pathogens. Checking patients who are at risk for colonization helps guide infection control to prevent spread.

Traditional therapeutic strategies or medical interventions to decolonize people include:

These decolonization strategies help avoid the loss of beneficial germs and disrupting microbiomes by

  • Limiting application to a certain body site/individual microbiome (e.g., in the gut or the nasopharynx, the top part of throat) or targeting specific pathogens
  • Decreasing the use of antibiotics and antifungals needed to treat infections, which can help slow antimicrobial resistance
  • Implementing across larger populations of patients at increased risk for infection or only the subset who are colonized

Newer, less frequently used strategies include microbiome therapeutic strategies to reduce the number of pathogens colonizing a person, such as fecal microbiota transplantation for recurrent Clostridioides difficile infection. Pathogen reduction and decolonization in the future may involve the use of bacteriophages (phages), viruses that only infect bacteria, and other live biotherapeutic products (e.g., ingesting beneficial germs). Phage and live biotherapeutic products have not been approved for this use by the U.S. Food and Drug Administration (FDA). As part of the National Action Plan for Combating Antibiotic-Resistant Bacteria, CDC and FDA are working together to discuss approaches to evaluate the safety and efficacy of these products.

More Research Needed

Pathogen reduction and decolonization strategies can prevent infections and stop the spread of pathogens and their genes. CDC invests in innovative research projects to identify and implement new ways to respond to antimicrobial resistance. CDC funds research on pathogen reduction and decolonization, but more research is needed to develop new therapeutic strategies to address colonization, microbiomes, and healthcare-associated and antimicrobial-resistant infections.

Examples of CDC research include:

Data from these projects help CDC better protect people by, for example, uncovering places resistant germs live and spread, improving outbreak response, and strengthening infection prevention practices.