Maintaining the Microbiome: The Art of Balancing Colonization & Infection

Author: Deva Rea, MPH, BSN, BS, RN, CIC

Categories: Decolonization July 8, 2019
Intestinal microbiome, bacteria colonizing small intestine

Conventionally, we only think about the microbes on our skin and bodies when we become sick with an infection. Yet in reality, our microbial friend inhabitants have a much greater effect on our overall health and well-being than once understood. There is a significant relationship between our environment and the interaction with others on our body’s microbial flora. And now there is an increased focus on our “microbiome” and how it relates to our health. So what is our microbiome? And, what happens when it is altered and why would we purposefully remove some of these bugs (decolonization)?

The National Human Genome Research Institute describes the human microbiome “as the collective genomes of the microbes (composed of bacteria, bacteriophage, fungi, protozoa and viruses) that live inside and on the human body.”[1] The human microbiome is diverse and vast; consisting of 10 times more microbial cells than human cells.¹ This equates to 1-2% of our body mass.[2] Understanding the impact of our immense microbiome has on our health and illness is an important research focus.

Researchers are now evaluating the genetic contribution from the microbes in our microbiome. The contribution could be “many hundreds of times greater than the genetic contribution from the human genome.”¹ Our microbiome’s composition has been linked to cancers, heart disease, gastrointestinal diseases, obesity, antibiotic resistance, etc. Conversely, when our microbiome is balanced, microbes function in our benefit by assisting with digestion, detoxification, metabolism, cell renewal, and more; thus helping our immune system thrive.¹

Maintenance of our microbiome is important, but there are times when we may need to alter our microbiome somewhat in order to keep us safe and healthy. This would occur when we are admitted to a hospital and have to undergo a surgical procedure, or when we are given a central venous catheter (CVC) for intravenous medications. The goal of decolonization is to reduce the amount of microbes on the skin or other colonized areas so that our risk of infection is lessened. Historically, we have used skin washes and antibiotic nasal ointments to decolonize the body. Now, with the understanding of antimicrobial resistance, there is more focus on antiseptic decolonization strategies. Additionally, new evidence of antibiotic resistance continues to be explored with a keen focus on our microbiome.[3] Research has been predominately focused on how the human microbiome acts as an antibiotic resistance reservoir primarily in gut associated microbial communities. However, newer studies are showing more widespread microbial colonization with other organs as well.[4] With this understanding, it’s important to look at more decolonization strategies that will not encourage antimicrobial resistance.

The most prominent pathogens targeted for decolonization are methicillin-resistant and methicillin-susceptible Staphylococcus aureus (MRSA/MSSA). A recent Centers for Disease Control and Prevention (CDC) Vital Signs report described “an estimated 119,247 S. aureus bloodstream infections with 19,832 associated deaths” in 2017.⁵ Although there has been a decrease in hospital-onset MRSA bloodstream infections since 2005, this decline has slowed since 2012. Additionally, hospital-onset MSSA has not changed significantly, and community MSSA infections continue to increase annually.[5] New strategies to reduce MRSA/MSSA infections have been proposed to include targeted decolonization practices in addition to current infection prevention practices.

The updated strategies from the CDC include core and supplemental decolonization strategies. The focus is on higher risk patients in intensive care units, patients with central venous catheters or midline catheters, and pre-operative surgical patients. The decolonization recommendation is to use “topical chlorhexidine gluconate (at least 2%) along with an intranasal antistaphyloccal antibiotic/antiseptic (e.g. mupirocin or iodophor).”[6] Traditionally, the use of an antibiotic for intranasal decolonization has been standard practice. But, now the use of an iodophor antiseptic has become an acceptable alternative based on efficacy evidence and the promotion of antimicrobial stewardship.⁶

Our health and well-being is directly linked to our microbiome. It’s important to keep our microbiome in mind when it’s altered due to hospitalization or surgery. By incorporating decolonization strategies that help promote antimicrobial stewardship, we can hypothesize that we are keeping our microbiome more stable. It is a balancing act, but with proper strategies and interventions, we can continue to promote good health and outcomes in our medical facilities and within our communities.

[1] Yang, J. (2012). The Human Microbiome Project: Extending the definition of what constitutes a human. National Human Genome Research Institute.

[2] National Institutes of Health. Human Microbiome Project’s Health Relevance. Available at:

[3] Casals-Pascual, C., Vergara, A., & Vila, J. (2018). Intestinal microbiota and antibiotic resistance: Perspectives and solutions. Human Microbiome Journal, 9, 11-15.

[4] Burcham, Z. M., Schmidt, C. J., Pechal, J. L., Brooks, C. P., Rosch, J. W., Benbow, M. E., & Jordan, H. R. (2019). Detection of critical antibiotic resistance genes through routine microbiome surveillance. PloS one, 14(3), e0213280.

[5] Kourtis, A. P., Hatfield, K., Baggs, J., Mu, Y., See, I., Epson, E., … & Ray, S. M. (2019). Vital Signs: Epidemiology and Recent Trends in Methicillin-Resistant and in Methicillin-Susceptible Staphylococcus aureus Bloodstream Infections—United States. Morbidity and Mortality Weekly Report, 68(9), 214.

[6] Centers for Disease Control and Prevention (CDC). Strategies to Prevent Hospital-onset Staphylococcus aureus Bloodstream Infections in Acute Care Facilities. Available at:


Deva Rea MPH, BSN, BS, RN, CIC
deva Clinical Science Liaison, PDI Ohio Valley Region


Deva Rea’s passion for infection prevention and epidemiology began while studying for her MPH. Prior to her role in epidemiology at a local health department, she worked a nurse in various specialties.

While in infection prevention, Deva cultivated her skills and combined her vast educational background to help improve patient outcomes and advance the practice of infection prevention. She has been in the healthcare industry for over 15 years, speaking at many conferences, including national APIC. Deva is dedicated to spreading knowledge and will continue to be a strong advocate for patients and the field of infection prevention/ epidemiology.

Deva is currently a Clinical Science Liaison (CSL) supporting the Ohio Valley Region.


Phone: 702-283-5417
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University of South Florida
Master of Public Health in Tropical Public Health/ Communicable Diseases (Epidemiology)
Graduate Certificate in Infection Control

University of Central Florida
Bachelor of Science in Nursing
Bachelor of Science in Microbiology and Molecular Biology

Registered Nurse
Certification Board of Infection Control (CBIC)- CIC

Why I love what I do

‘Bugs’ are pretty cool! How microbes operate and survive has always amazed me. Understanding how this microbial world exists and our role in it has been a lifelong passion. From biofilms to the microbiome, the complexity of something we can’t see with the naked eye is a remarkable phenomenon. Being able to offer guidance and support to others in infection prevention and epidemiology is wonderful. Overall, helping prevent infections in healthcare is why I love doing what I do!

Areas of Expertise

Infection prevention and control
Micro/ molecular biology
Infectious diseases and transmission
Environmental disinfection
Healthcare associated infections

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