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Innovations to Slow Antibiotic Resistance

CDC Invests in Innovative Solutions

Alongside academic investigators, CDC is looking for new ways to identify and evaluate strategies to combat antibiotic resistance. Antibiotic resistant infections can be deadly for humans and is a growing global threat jeopardizing modern medicine and the healthcare, veterinary, and agriculture industries. CDC is collaborating with multiple researchers to understand antibiotic resistance in healthcare facilities and outside healthcare facilities (including nearby surface water and soil), as well as the human microbiome, to determine the potential impact on human health.

Additionally, the CDC and FDA Antibiotic Resistance Isolate Bank supports innovation in diagnostics and drug development. A collection of organisms uncovered during outbreak and surveillance activities, the AR Isolate Bank provides the latest and highest quality samples of resistant organisms to microbiologists, lab directors, drug and diagnostic manufacturers, and academic researchers. These organisms can be used to meet lab testing needs; fulfill FDA approval requirements; and detect new, unusual, and timely public health resistance threats.

This work complements broader CDC efforts to support known strategies for protecting people and slowing antibiotic resistance, collectively known as CDC’s Antibiotic Resistance Solutions Initiative.


Healthcare Settings

CDC is investing in projects to discover and evaluate new strategies to protect patients from antibiotic resistance in healthcare settings.

People receiving medical care can get serious infections called healthcare-associated infections (HAIs), which may lead to sepsis or death. HAIs can be caused by bacteria that are resistant to antibiotics, making them difficult or, in some cases, impossible to treat, and the germs causing these deadly infections can spread. CDC works with networks of trusted partners to discover, implement, and evaluate innovative prevention strategies to improve healthcare quality and patient safety.

In collaboration with investigators, CDC aims to determine:

  • How Antibiotic Stewardship Programs Can Protect Patients. CDC and investigators will assess how programs focused on improving antibiotic use will improve patient safety.
  • How Enhancing Infection Control Actions can Prevent Spread of Infections. CDC and investigators will evaluate new strategies to limit the spread of infections through enhanced cleaning methods or use of specific disinfectants. This work guides CDC’s infection control and prevention and guidelines for U.S. healthcare facilities. Other CDC mechanisms and programs focused on innovation in healthcare settings include SHEPheRD, MInD – Healthcare, and Prevention Epicenters.
  • How to Obtain Better-Quality Data for Action. CDC and investigators will gather more and stronger infection data from healthcare facilities to better measure the challenges influencing healthcare quality and patient safety, and implement solutions.


Human Microbiome

CDC is investing in projects to expand our understanding of the gut-drug relationship.

Antibiotics can disrupt (unbalance) your microbiome, a community of naturally-occurring germs in and on our bodies, the way a wildfire can destroy a forest. Antibiotics impact the microbiome by wiping out the natural composition of both good and bad bacteria. With a disrupted microbiome, resistant bacteria can take over and the body is less able to defend against infection, putting people at risk for potentially untreatable illnesses. These patients can carry drug-resistant bacteria and can easily spread bacteria to other people, especially those who also have a disrupted microbiome. CDC is conducting applied research on the microbiome to identify effective public health approaches that protect people, their microbiomes, and the effectiveness of antibiotics.

In collaboration with investigators, CDC aims to determine:

  • How Antibiotics Disrupt a Healthy Microbiome. CDC and investigators will study novel strategies that can protect and restore the microbiome, and determine how exposure to antibiotics early in life affects microbiome development.
  • How a Disrupted Microbiome Puts People at Risk. CDC and investigators will develop a predictive index that identifies a patient’s risk of disruption from a specific antibiotic, a patient’s likelihood of becoming a carrier of antibiotic-resistant bacteria, and their risk of becoming infected with one. CDC and investigators will also work to develop and test microbiome measurements that monitor a patient’s risk for transmitting antibiotic-resistant bacteria and assess enhanced infection control triggers.
  • How Improving Antibiotic Use Can Protect the Microbiome. CDC and investigators will improve strategies to tailor antibiotic stewardship to a patient’s individual microbiome, as well as assess how to fit antibiotic stewardship to a specific population of patients (e.g., hospital unit, nursing home, doctor’s office).


Healthcare, Agriculture, and the Environment (i.e., surface water and soil)

CDC is investing in projects to fill knowledge gaps about antibiotic resistance and potential impact on human health.
CDC recognizes the One Health concept that the health of people is connected to the health of animals and the environment (e.g., surface water and soil), which includes resistant bacteria. It is not well understood if humans can get sick due to antibiotic resistant germs in water or soil. However, bodies of water can act as reservoirs, a place where germs grow and multiply without hindrance, including resistant bacteria. A body of water contaminated with resistance elements can contribute to antibiotic resistance CDC will explore how these resistance elements may contaminate and contribute to further resistance, and its impact on human health.

In collaboration with investigators, CDC aims to determine:

  • How Antibiotic Use Can Impact Aquatic Ecosystems and Human Health. CDC and investigators will detect and determine the amount of antibiotic resistant determinants (elements like a gene that can share resistance) in aquatic ecosystems where wastewater is discharged or runoff can leach into the soil and water. CDC and investigators will also look at how this can affect human health.
  • Data to Understand the Risk to Human Health. CDC and investigators will work towards identifying antibiotic residue and resistance elements in aquatic ecosystems near healthcare and agriculture settings, and quantifying concentrations at which resistance might emerge. This work could be used to understand the risk posed to humans.


List of Projects

Innovations to Slow Antibiotic Resistance

The below includes a list of projects focused on healthcare settings, the microbiome, and the non-healthcare environment.

Baylor College of Medicine
Cross-validation of human fecal minibioreactor arrays and humanized microbiota mice as complementary pre-clinical models of the GI (gastrointestinal) microbiome

This project will evaluate in vitro and mouse models of human gut microbiomes to help create a pre-screening tool to evaluate potential therapies. 

Children’s Hospital Oakland Research Institute (CHORI) at the University of California San Francisco
Rapid assays to detect Neisseria gonorrhea antibiotic resistance at the point of care

Investigators will develop and evaluate new diagnostics tools that can determine the antibiotics to which a patient’s strain of gonorrhea is susceptible (slowed or killed). This fast and efficient test, once available, will help guide individual patient management and can be used to identify antibiotic-resistant strains of gonorrhea. It can also be used to support outbreak investigations of resistant gonorrhea in the community. 

Cleveland VA Medical Research and Education Foundation
Natural history of Clostridium difficile colonization

Researchers will use data to show how C. difficile germs spread and to develop more effective control measures. This project will grow our understanding of C. difficile colonization and infection.

Department of Research & Evaluation, Kaiser Permanente Southern California
Prenatal antibiotic use and body weight in children

The goal of this study is to examine the potential relationship between antibiotic use during pregnancy and pediatric weight problems. 

Emory University
Computational methods for culture-independent disambiguation of wgMLST types in biological samples with multiple related bacterial strains

Investigators will develop computational tools to differentiate and analyze different types of DNA mixed in one sample. This project will help laboratories better understand the make-up of a mixture and its threat level. 

Georgia Tech Applied Research Corporation (GTARC) (2 projects)
Antibiotic resistance in concentrated poultry feeding operations: Impacts on environmental waters

This project will assess the types of antibiotic-resistant organisms in poultry houses, in addition to the amount of these organisms in a poultry house and further downstream in environmental waters. Researchers will also measure the amount of veterinary antibiotic residues in downstream environmental waters.

Optimization of therapeutic strategies to manage polymicrobial CF lung infections: Clinical assessment

Researchers will continue this project from last year to identify novel probiotic and antibiotic intervention strategies for patients with cystic fibrosis. The project will validate and improve new treatment strategies by implementing them in a small group of patients.

Infectious Diseases Society of America (IDSA)
The Leaders in Epidemiology, Antimicrobial stewardship and Public health, or LEAP, Fellowship are Infectious Diseases Fellowships to drive innovative education and approaches in antibiotic resistance, antibiotic stewardship and public health

This project establishes a fellowship for infectious disease physicians to bridge clinical infectious disease and public health work in the areas of antibiotic resistance and antibiotic stewardship. 

J. Craig Venter Institute (JCVI)
Improved bioinformatics tools for detection and characterization of antimicrobial resistance in public health

Researchers will develop a comprehensive gene and protein database and web-based resource that public health experts can use to quickly detect and identify antibiotic resistance genes as they emerge. 

OpGen, Inc.
Highly accessible system for infection control and antimicrobial stewardship in resource limited settings

This project will modify a commercial cloud and mobile-based software platform, which integrates electronic patient data and local treatment guidelines, to support antibiotic stewardship and infection control in low- and middle-income countries. Investigators will translate the software to Spanish and use it in up to three medical sites internationally. Implementers will assess factors such as cost, clinical impact, and feasibility. 

Regents of the University of Michigan
Microbiome disruption and Enterobacteriaceae dominance as a risk factor for sepsis in intensive care patients

Antibiotics can change the intestinal microbiome, which may increase the risk of sepsis. Researchers will extend previous CDC-funded work to assess intestinal microbiome disruption and dominance by the Enterobacteriaceae family of bacteria as risk factors for sepsis.  

Rutgers, the State University of New Jersey
Rapid identification and analysis of transmission of the emerging pathogen Candida auris

Researchers will validate a new rapid diagnostic platform to detect the multidrug resistant fungal pathogen Candida auris, and they will analyze C. auris transmission patterns in healthcare facilities by applying advanced genetic fingerprint methods. 

The Children’s Hospital of Philadelphia (CHOP)

Perinatal antibiotics and weight gain in childhood

Researchers will examine if antibiotics given to mothers immediately before birth, or to newborns right after birth, can increase the weight gain of children in the first 5 years of life. 

The Ohio State University
Preventing the dissemination of CRE from healthcare facilities into surface waters in the US (continuation request)

The study will evaluate potential discharge of antibiotic resistant bacteria from hospital sewage and test a technology to prevent it. 

The Rector and Visitors of the University of Virginia
Understanding the microbiologic dynamics of Carbapenemase-producing organisms in hospital wastewater premise plumbing

This project will track carbapenemase-producing organisms in healthcare facilities, in part by using a controlled sink lab to recreate a healthcare facility setting, to help guide facilities experiencing the transmission of these organisms from the healthcare environment or plumbing. 

The University of Georgia
The prevalence and diversity of antibiotic resistant bacteria in a mixed-use watershed

Investigators will sample surface water to analyze it for human and agricultural waste and antibiotic-resistant bacteria. This project will help to determine how antibiotics, pathogens, and resistance elements move across environments and potentially pose a risk to human health.  

Translational Genomics Research Institute (TGen)
Considering homologous and non-homologous recombination in outbreak analysis

Researchers are developing computational tool to improve analysis of bacterial DNA sequences, particularly from pathogen samples that are very closely related. 

University of Alabama at Birmingham
Sentinel surveillance for Macrolide-resistant Mycoplasma pneumoniae at select sites in the United States

Using samples from eight hospitals, researchers will determine the prevalence of macrolide antibiotic resistance in Mycoplasma pneumoniae, how it spreads, and how it affects patients. 

University of Arizona
Reducing antibacterial use in patients with coccidioidomycosis

This project will study the delay in diagnosis of Valley Fever (coccidioidomycosis) in Tucson, Arizona where this disease is endemic (very common). To some clinicians, Valley Fever looks like community acquired pneumonia. The University of Arizona will collect the diagnostic codes for Valley Fever in its hospital computer system.  Researchers will also analyze the health care cost due to delay in diagnosis and determine the unnecessary antibiotic usage for better antibiotic stewardship practices.

University of Georgia Research Foundation, Inc.
Azole resistance in agricultural settings

Researchers will collect and characterize azole-resistant fungal strains from agricultural and horticultural sites. Azoles are used to protect crops from fungi, but azole-resistant fungi can infect people and cause disease that is difficult to treat and can lead to death.

University of Maryland, Baltimore
Implementation of a novel strategy to prevent Staphylococcus aureus (SA) acquisition in community-based nursing homes to prevent invasive SA infection: Feasibility and pilot to guide a multicenter stepped wedge cluster trial

Researchers will conduct a pilot study (small-scale study that helps design larger studies) on the use of additional gowns and gloves in nursing homes to prevent the spread of Staphylococcus aureus infections. 

University of Mississippi Medical Center
Comparison of methods for detecting recombination in bacterial whole genome sequences

Investigators will compare genome analysis methods that determine the source of genetic material. This project will help researchers to understand the relationships and transmission of antibiotic-resistant bacteria.

Washington University
Double blinded, randomized controlled Trial of Oral vancomycin versus placebo in hospitalized patients with diarrhea and stool toXin NEGative but nucleic acid amplification test positive for toxigenic Clostridium difficile (TOX NEG trial)

Researchers will assess the risks and benefits of C. difficile treatment compared to a placebo treatment. Researchers will determine the impact of oral antibiotics on the microbiome, antibiotic resistance, C. difficile, and colonization of a multi-drug resistant organism, healthcare environment contamination, duration of diarrhea, and outcomes.

Microbiome Infographic Details

Antibiotic Resistance (AR) Solutions Initiative: Microbiome

CDC’s applied research on the human microbiome aims to identify effective public health approaches to protect people, their microbiomes, and the effectiveness of antibiotics. Bacteria, fungi, viruses, and other microbes (germs) live naturally on our skin and in our gut and other places within our body. These microbes make up a community called the microbiome. Antibiotics can destroy your microbiome the way a wildfire can destroy a forest.

  • A healthy microbiome helps protect you from infection because your body needs bacteria to function normally.
  • When you take antibiotics to treat an infection, the antibiotics not only kill the infection-causing bacteria, but the bacteria that keep you healthy can also be destroyed for several months. This can disrupt, or unbalance, a healthy microbiome.
  • With a disrupted microbiome, the body is less able to defend against infection, putting people at risk for infections from deadly germs like difficile and MRSA.
  • When drug-resistant bacteria take over, patients can carry these germs and spread them to other people, especially if those people have a disrupted microbiome.

When antibiotics are needed, the benefits outweigh the risks of side effects or antibiotic resistance. When antibiotics aren’t needed, those risks come with no benefits. By only using antibiotics when needed, we can avoid unnecessary microbiome disruption and risk for getting or spreading infections.

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