The discovery of antibiotics by Sir Alexander Fleming in 1928 revolutionized medicine. However, antibiotics cannot differentiate between the beneficial bacteria that help keep us healthy and the pathogens that make us sick. Like a wildfire, antibiotics wipe out all bacteria. Consequently, we have been altering our microbiomes for almost a century, putting ourselves at risk for subsequent infections, most notably, infections due to antibiotic resistant pathogens and Clostridium difficile. Antibiotic resistant infections are a global crisis. Improving our knowledge of how we can prevent antibiotic resistant infections is key in the effort to save lives and prevent unnecessary hospitalizations and deaths.

The human microbiome is the collective genome of microbial communities that live in and on us. These microbial communities are found on our skin, and in our mouths, respiratory tract, urinary tract, and gut. Microbiota work symbiotically with our body to keep us from getting sick. One example of how they do this is through colonization resistance, meaning, for example, that the microorganisms living in our intestines take up all the available nutrients and places for organisms to bind so that pathogens cannot get a toehold long enough to cause infection.

The potential power of the microbiome represents an intersection of precision public health and precision medicine. Changes in composition and diversity of our gut microbiome are generally accepted as a risk factor for becoming carriers of antibiotic resistant pathogens and developing Clostridium difficile infection. The microbiome represents untapped data for us to leverage to improve patient health and protect the public. But first, we have to understand how the microbiome works in concert with our bodies to keep us healthy, as well as how each pathogen changes in our microbiome when it makes us sick. The rapid advancement of next-generation sequencing technology has provided a way to make leaps and bounds in microbiome research. CDC’s Division of Healthcare Quality Promotion is interested in harnessing the power of the microbiome to improve patient care and advance public health, specifically through infection prevention and control. To do this, we are working to develop Microbiome Indices that measure the health status of a person’s microbiome. We believe Microbiome Indices will have a positive impact on patient care, antibiotic stewardship, infection control, and drug development.

For an individual patient, similar to when a doctor orders bloodwork to check a patient’s health and to determine if they are at risk for a disease like diabetes, the goal of Microbiome Indices is to measure risk of colonization and/or infection – a literal “gut check.” Physicians could use Microbiome Indices to assist in selection of antibiotics to treat effectively an infection without putting the patient at increased risk of becoming a carrier of antibiotic resistant bacteria, thereby preventing additional risk to the patient. Microbiome Indices might also be used as a measure of whether an intervention to protect the microbiome (e.g., orally administered antibiotic-neutralizing enzymes or absorbents) is working for a patient, and to determine if treatment to restore a patient’s microbiome to a more healthy state (e.g., fecal microbiota transplant) is needed.

From a public health perspective, Microbiome Indices can serve as tools for infection prevention and control and antibiotic stewardship. By measuring patients’ Microbiome Indices, we can identify subsets of the population at risk for infection or for transmitting pathogens, to determine how to best implement infection control measures. This is how precision medicine intersects with precision public health.

Finally, for drug development, we anticipate Microbiome Indices could someday be used in early phase drug and therapeutic development to help select for compounds that have a neutral or positive impact on the microbiome.

A key for developing useful Microbiome Indices is developing a strong evidence base for using these new methods and technologies regarding their impact on patient health. In 2016, through the CDC Antibiotic Resistance Solutions Initiative, CDC initiated collaborations with and provided $34M in funding to academic institutions, nonprofit companies, and one commercial company to identify and implement novel approaches to preventing antibiotic resistance. Fourteen of the projects are focused on the role of the microbiome in human health. In 2017, we look forward to new projects that will support these efforts.

Only by working together to leverage novel technology and analyze the wealth of data available will we achieve optimal population health outcomes. We want to prevent people from getting sick with an antibiotic-resistant pathogen, not treat them after they get sick. Having the ability to do this will save lives and protect the public.