Antibiotic and Antifungal Resistance

Antibiotic and antifungal resistance is one of the world’s greatest public health challenges. Antibiotic and antifungal resistance occurs when bacteria or fungi develop the ability to survive or grow despite being exposed to the drugs designed to kill them. The Division of Foodborne, Waterborne, and Environmental Diseases (DFWED) is slowing the spread of resistance in enteric bacteria (bacteria that cause intestinal illness) and fungi through science, surveillance, and outreach aimed at improving the public’s health.

DFWED addresses drug resistance using a One Health approach, which recognizes the health of people is closely tied to the health of animals and our shared environment. The division’s efforts are part of CDC’s Antibiotic Resistance Solutions Initiative and are centered around the goals of the U.S. National Action Plan for Combating Antibiotic-Resistant Bacteria (National Action Plan).

Enteric Bacteria

Three common enteric bacteria—Salmonella, Campylobacter, and Shigella — cause around 740,000 antibiotic-resistant infections each year in the United States.[i] These bacteria are becoming more resistant to some clinically important antibiotics, limiting treatment options for severe infections.

DFWED applies research and innovation, surveillance, and laboratory analysis to combat antibiotic-resistant enteric bacteria in food, water, and the environment by:

  • Tracking antibiotic resistance in human illnesses caused by select enteric bacteria as part of the National Antimicrobial Resistance Monitoring System (NARMS), a tri-agency national surveillance system with the U.S. Food and Drug Administration (FDA) tracking resistance in retail meats and the U.S. Department of Agriculture (USDA) tracking resistance in food animals.
  • Supporting the important work of FDA and USDA to improve antibiotic useexternal icon in veterinary medicine and agriculture.
  • Responding to multistate outbreaks caused by resistant enteric bacteria by providing epidemiologic expertise and rapid laboratory analysis of resistance patterns. Some of these outbreaks are linked to contaminated food or contact with farm animals, pets, or pet food and treats.

Fungal Pathogens

Learn more and see recent data about resistance in C. auris and other Candida species.

Only three types of antifungal drugs exist, so antifungal resistance can severely limit treatment options. Some types of fungi, like Candida auris (C. auris), can become resistant to all three drug types. Each year among hospitalized patients in the United States, antifungal-resistant C. auris causes about 400 infections, and all other types of antifungal-resistant Candida cause about 35,000 infections.[i] The fungus Aspergillus, a type of mold, is increasingly resistant to antifungal drugs. Resistance can occur in the environment and in patients who are sick with an Aspergillus infection and have been taking antifungal drugs for a long time. Learn more about antifungal resistance.

DFWED scientists address the threat of antifungal resistance through surveillance, clinical and environmental research, laboratory innovations, outbreak response, and supporting stewardship initiatives. Find out more about how DFWED is tackling antifungal resistance.

AR Innovation Projects

CDC supports innovations and collaborations with investigators to identify and implement new ways to prevent antibiotic-resistant and anti-fungal resistant infections and their spread. Below includes select innovation projects covering enteric bacteria and fungi, including Broad Agency Announcements (BAA). Click on project titles to learn more. To see all projects, visit CDC’s antibiotic resistance website.

Enteric Bacteria

2020—Innovation Projects
University of South Carolina: SARS-CoV-2 and antibiotic resistance genes within municipal sewage treatment facilities

The Ohio State University: Resistance genes in food animal populations through livestock and poultry feed, pet food, and treats

CDC-designated Food Safety Centers of Excellence: Integrated Food Safety Centers of Excellence One Health and Antimicrobial Resistance Projects


Instituto de Biomedicina y Biotecnología de Cantabria: Structure and dynamics of Salmonella plasmids

University del Desarrollo: Human exposure to MDR organisms in environmental waters in a Chilean community


California Department of Public Health: Patients infected with Shigella with elevated ciprofloxacin MIC values

Iowa State University: Campylobacter burden testing in dogs

Texas Tech University: MCR-harboring Salmonella and Escherichia coli in food products, food animals, and their environments in the Dominican Republic

The Ohio State University: Salmonella Heidelberg in the dairy calf production chain

The Ohio State University: Antimicrobial stewardship education for calf producers

University of Chicago: Design of a highly multiplexed targeted sequencing panel for the detection and characterization of antimicrobial resistance determinants from complex metagenomic samples

University of South Carolina: AMR and resistant pathogens in bioaerosols generated during wastewater treatment

University of Virginia: Outcomes in patients treated for MDR Shigella infections in Bangladesh

Virginia Tech: Critical barriers to AMR during water reclamation and reuse

Virginia Tech: Optimizing in-building disinfection of antibiotic-resistant opportunistic pathogens


2020—Innovation Projects

University of California, Los Angeles, David Geffen School of Medicine & Fielding School Public Health: Determining the Incidence of Secondary Aspergillus Infections in Influenza positive patients


Case Western Reserve University: Improving Environmental Control of Candida auris


Rush University: Candida auris, an emerging fungal pathogen of high concern

University of Georgia: Azole-resistant Aspergillus fumigatus strains from agricultural sites

[1] 2019 Antibiotic Resistance Threats Report: