Germs Lead the Way: Exploring Microbial Ecology to Elevate the Fight Against Antimicrobial-resistant Healthcare-associated Infections

Posted on by Melia Haile, Christopher Elkins, Cliff McDonald, Alison Laufer Halpin, Mihnea Mangalea, and Lacey Avery

Three to four billion years ago, microbes (germs) were the first life on earth. They have thrived for millions of years longer than humans have existed. Much like humans, microbes have complex social and physical communities and are always evolving. These microbial communities are home to helpful germs and pathogens (harmful germs). Better understanding the ecology of microbes—relationships within and across these communities—is just the beginning of public health’s scientific journey. We are working to better understand what microbes and their surrounding environments can teach us about preventing infections, including antimicrobial-resistant infections.

CDC knows there is an important connection between microbial ecology and the health and wellbeing of people. We all have our own microbial communities, called microbiomes, on our skin and in our gut that help us maintain good health. We have a better chance of fighting infections when our microbiomes are in balance—a mix of “good” beneficial germs to help keep the “bad” pathogens in check.

However, when we take antibiotics, antifungals, or other therapeutics, these drugs kill all germs—both the harmful and helpful. This disrupts our microbiome, allowing the surviving pathogens, which are often resistant to the treatment, to dominate our microbiome. This can lead to infection.

Our risk for infection increases when we are colonized, meaning we have a threatening pathogen in our body but do not have symptoms of an infection. Our risk of infection is even higher when we are colonized and have a disrupted microbiome.

Leveraging microbial ecology to advance and protect our health involves a cross-cutting and dynamic effort from diverse collaborators, including public health experts, academic researchers, private industry, and regulatory experts. Expanding our microbial ecology knowledge at the intersection of public health will lead us to new strategies to prevent infections and combat antimicrobial resistance, especially in healthcare settings.

healthy biome
Everyone carries germs, including resistant germs. Balanced microbiomes keep harmful germs (pathogens) from taking over.
drug intervention
Antibiotics, antifungals, and other therapeutics kill germs—both the harmful & helpful. This disrupts a balanced microbiome.
pathogens dominate
Some of the surviving pathogens are often resistant to the treatment. They begin to grow, take over, & dominate our microbiome. This can lead to infection, including a resistant infection.

Leveraging Microbial Ecology to Protect Patients

Although scientists know that microbial ecology plays an important role in maintaining human health, there are remaining scientific questions. CDC invests in microbial ecology research to study the interactions of microbes among people, animals, plants, food, and surfaces (e.g., counter tops), all of which can serve as sources of microbes that can lead to infection.

When a healthcare facility identifies certain multidrug-resistant pathogens within their facility, CDC recommends colonization screening—using laboratory test to identify patients who are colonized. When patients are colonized, a unique patient safety intervention called pathogen reduction and decolonization can remove the colonized pathogens in a patient’s microbiome, such as skin, nose, or gut.

Healthcare providers are already using traditional therapeutic strategies to decolonize people, such as antiseptic agents like chlorhexidine gluconate. These strategies help avoid the loss of beneficial germs and disrupting microbiomes because they can:

  • Limit application to a certain body site/individual microbiome or specific pathogens
  • Decrease the use of antibiotics and antifungals to treat infections, which can help slow antimicrobial resistance
  • Focus on colonized individuals or larger populations of patients who are at increased risk for infection

However, more research is needed in the field of microbial ecology to expand upon and develop new therapeutic strategies that address colonization, healthcare-associated infections (HAIs), and antimicrobial resistance, all while considering patient safety and the implications for a patient’s microbiome. This innovative work helps us better understand how to develop and implement life-saving tools.

To expand our patient safety toolbox, CDC needs public health experts, academic researchers, private industry, and regulatory experts to develop preventative products or strategies that:

  1. Prevent colonization recurrence and do more than “decontaminate,” such as protecting and/or restoring the microbiome
  2. Reduce pathogen burden (load) and/or eliminate pathogens completely, especially if there is a targeted application (e.g., body site, pathogen)
  3. Benefit both individuals (individual patients or “source”) and populations

We also need more conversations to continue identifying challenges that arise and form new paths forward as public health and scientific experts explore this untraversed landscape.

How You Can Help

4 Ways Healthcare Providers Can Help

4 Ways Healthcare Providers Can Help

1 Consider the impact of antibiotics, antifungals, & other therapeutics on microbiomes when implementing antimicrobial stewardship practices.

2 Incorporate pathogen reduction & decolonization into clinical practice when appropriate.

3 Learn about the importance of protecting microbiomes.

4 Reduce your & your patient’s risk of HAIs from water in healthcare facilities.

As leaders in public health and patient safety, CDC and the Food and Drug Administration (FDA) are co-sponsoring a public virtual workshop on August 30, 2022, on developing therapeutic drugs for HAIs and the role microbial ecology can play in this effort.

The workshop is the first of its kind to focus on the

  • Current state of pathogen-directed products to prevent HAIs
  • Decolonization as a strategy to prevent HAIs and their spread
  • Targeting antimicrobial-resistant pathogens
  • Challenges and approaches to developing drugs and registering products to prevent HAIs

Can’t make the meeting? You can still help!

Let’s Talk! Register for the upcoming CDC & FDA Public Virtual Workshop on Aug. 30, 2022.

From policy, industry, academics, funding institutions, and researchers, to healthcare personnel, patients, and advocacy groups—we can all contribute to incorporating microbial ecology into our prevention work. We look forward to working with you and having more conversations together as we enter this new terrain together.
Melia Haile, Christopher Elkins, Cliff McDonald, Alison Laufer Halpin, and Mihnea Mangalea, Division of Healthcare Quality Promotion, and Lacey Avery, Antimicrobial Resistance Coordination and Strategy Unit, National Center for Emerging and Zoonotic Infectious Diseases at the Centers for Disease Control and Prevention (CDC)

Posted on by Melia Haile, Christopher Elkins, Cliff McDonald, Alison Laufer Halpin, Mihnea Mangalea, and Lacey AveryTags , , , , , , ,

6 comments on “Germs Lead the Way: Exploring Microbial Ecology to Elevate the Fight Against Antimicrobial-resistant Healthcare-associated Infections”

Comments listed below are posted by individuals not associated with CDC, unless otherwise stated. These comments do not represent the official views of CDC, and CDC does not guarantee that any information posted by individuals on this site is correct, and disclaims any liability for any loss or damage resulting from reliance on any such information. Read more about our comment policy ».

    The subject is highly relevant in the context of infections by antibiotic resistant organisms.
    The starry eyed wonder and confidence that bacterial infections were on the way out has given way to a despondence. It is now realised that antibiotic resistance is inevitable and a serious matter. Novel efforts are needed, the role of resident flora is a subject that has to be pursued. The success of normal faecal transplants in cases C. difficile colitis is a pointer.

    As documented over 25 years ago, most bacterial and fungi form biofilm – an extracellular shield to protect the growing colony against threats – sterilization, UV, physical removal, immune responses, antimicrobial disinfectants and antibiotics. Not surprisingly, every antimicrobial-resistant (AMR) pathogen today is a biofilm-former and 90% of hospital-acquired infections are associated with biofilm. Biocides and antibiotics have failed.
    Aequor has discovered over 70 small molecules that remove biofilm in minutes and prevent its formation for days Some potentiate ineffective antibiotics, including Penicillin, to kill AMR pathogens at sub-MIC doses (too low to trigger resistance). Biofilm is at the center of the issues regarding microbial ecosystems and HAIs.

    Thanks for this. I need latest guidelines and protocol to help me in applying antimicrobial stewardship at my work in hospital.

    An excellent article, thank you. We have found in our research, lab work and field trials the simple act of keeping reusable personal items ( such as nasal cannula, HHN, or toothbrush … ) clean and dry dramatically reduces bacteria and pathogen growth which confirmed an equal reduction in respiratory infections when applied. See articles :
    Kent M. Collins

    NORMAL FLORA IMPACT ON HEALTH AND DISEASE – We the humans and many little creatures too are diverse, it was though in the past Genes alone made the difference to species, and differentiated to many Phyla and families, we are familiar with Major histocompatibility complex, and the understanding was better when we started doing transplantation and more thinking started with cancer biology. Today the thinking on human disease, survival, and cure of many diseases is changing towards understanding the little one as we call as normal flora (Microbiota) colonizing the humans. Justin Sonnenburg, a microbiologist at Stanford, suggests that we would do well to begin regarding the human body as “an elaborate vessel optimized for the growth and spread of our microbial inhabitants.” This humbling new way of thinking about the self-has large implications for human and microbial health, which turn out to be inextricably linked. The word microbiota represents an ensemble of microorganisms that reside in a previously established environment. The human body is colonized by a vast number of microbes, collectively referred to as the human microbiota. The link between these microbes and our health is the focus of a growing number of research initiatives, and new insights are emerging rapidly Human beings have clusters of bacteria in different parts of the body, such as in the surface or deep layers of skin (skin microbiota), the mouth (oral microbiota), the vagina (vaginal microbiota), and so on. Microbes associated with the human body include eukaryotes, archaea, bacteria, and viruses, with bacteria alone estimated to outnumber human cells within an individual by an order of magnitude. Our gut microbiota contains tens of trillions of bacteria – ten times more cells than in our body. Our knowledge of these communities and their gene content referred to collectively as the human microbiome, The US NIH-funded Human Microbiome Project Consortium (HMP) brought together a broad collection of scientific experts to explore these microbial communities and their relationships with their human hosts. Human health today is guided by normal flora as is defined today as Microbiota which has a greater influence on health and disease, the human gut is the greatest colonizer of many bacteria, is home to trillions of microorganisms, and there is vast diversity within this gut microbiota. Research into the association of the gut microbiota with health and disease (including, among others, diet and nutrition, obesity, IBD, and cancer) continues to expand, with the field advancing at a rapid pace. The complex microbial communities that reside on or within the human body have a vital role in health and disease. Interest in the gut microbiota—arguably the highest density of micro-organisms in the human body—has rapidly increased in the past few years. It contains tens of trillions of microorganisms, including at least 1000 different species of known bacteria with more than 3 million genes (150 times more than human genes). Microbiota can, in total, weigh up to 2 kg. One-third of our gut microbiota is common to most people, while two-thirds are specific to each one of us. In other words, the microbiota in your intestine is like an individual identity card. Furthermore, the advent of advanced Meta genomic sequencing has finally enabled the diversity within the gut microbiota to be fully appreciated; the majority of bacteria resident in the gut are not easily cultured using traditional microbiological techniques. A testament to the importance of the gut microbiota in human disease is the growing number of conditions now linked to dysbiosis of the resident microbiota, including, amongst others, IBD, cancer, obesity, neurological diseases and cardiovascular disease. As we come to accept the gut microbiota as a human microbial ‘organ’ central to human health and disease, understanding the host–microbiota relationship is vital, and targeting the gut microbiota is likely to become a future therapy for a number of conditions. Just how we can manipulate the resident gut microbiota to our benefit is yet to be fully determined, but new insights are emerging rapidly, and ongoing research is needed. More than 1,000 different known bacterial species can be found in the human gut microbiota, but only 150 to 170 predominate in any given subject. The changing composition of the human microbiota is linked to alterations in human behavior and the rising prevalence of immune allergic and metabolic disorders. The composition of our microbiota evolves throughout our entire life, from birth to old age, and is the result of different environmental influences. Gut micro biota’s balance can be affected during the aging process and, consequently, the elderly have substantially different microbiota to younger adults. Although it can adapt to change, a loss of balance in gut microbiota may arise in some specific situations. This is called dysbiosis. Dysbiosis may be linked to health problems such as functional bowel disorders, inflammatory bowel disease, allergies, obesity, and diabetes. The use of Antibiotics has a counterproductive effect on the Gut flora. However, the effect of antibiotics on the intestinal microbiota has not been extensively scrutinized other than in studies on the induction of antibiotic resistance in commensal bacteria following treatment. The studies show that microbiota imbalance predisposes the host to more severe enteropathogenic infections including Pseudo membranous colitis. The peer-reviewed observations could be part of the explanation for the high rates of nosocomial infections when antibiotics are abundantly used, making many venerable to morbidity and mortality. In the past, only Immunology was thought as an important factor in protecting humans, however, the current science is changing that Immunology with normal Microbiota makes the difference in human survival.
    Dr.T.V.Rao MD former professor of Microbiology Frellancing clinical Microbiologist

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Page last reviewed: September 19, 2022
Page last updated: September 19, 2022