COVID-19 & Antimicrobial Resistance

Key points

  • The U.S. lost progress in combating antimicrobial resistance (AR) in 2020 because of COVID-19.
COVID-19: U.S. Impact on Antimicrobial Resistance, Special Report 2022, is a publication of the Antimicrobial Resistance Coordination and Strategy Unit within the Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention

COVID-19 impacts on antimicrobial resistance

The U.S. lost progress in combating antimicrobial resistance (AR) in 2020 due, in large part, to effects of the COVID-19 pandemic. The CDC COVID-19: U.S. Impact on Antimicrobial Resistance, Special Report 2022, concluded that the threat of antimicrobial-resistant infections was not only still present but had gotten worse.

During the first year of the pandemic, more than 29,400 people died from antimicrobial-resistant infections commonly associated with health care. Of these, nearly 40% of the people got the infection while they were in the hospital.

The total national burden of deaths from antimicrobial resistance may be much higher, but data gaps caused by the pandemic hinder that analysis. In the 2022 report, CDC is missing data for nine of the 18 pathogens listed in its 2019 AR Threats Report. CDC's 2019 estimates are still the most robust data to show the U.S. burden of antimicrobial resistance—at least 2.8 million antimicrobial-resistant infections continue to occur in the U.S. each year and more than 35,000 people die as a result.


Antimicrobial-resistant infections and Clostridioides difficile—a bacterium that is not typically resistant but can cause deadly diarrhea and is associated with antibiotic use—cause more than 3 million infections and 48,000 deaths in the U.S. each year.

The pandemic undid much of the nation's progress on antimicrobial resistance, especially in hospitals. The U.S. must continue to invest in prevention-focused public health actions to combat antimicrobial resistance.

COVID-19 impact on healthcare facilities & community settings

U.S. healthcare facilities saw more healthcare-associated, antimicrobial-resistant infections, especially in hospitals. Hospitals treated sicker patients who required more frequent and longer use of medical devices like catheters and ventilators. Hospitals also experienced personal protective equipment supply challenges, staffing shortages and longer patient stays.

  • Resistant hospital-onset infections and deaths both increased at least 15% from 2019 to 2020 among seven pathogens.
  • A 2021 CDC analysis reported that after years of steady reductions in healthcare-associated infections (HAIs), U.S. hospitals saw significantly higher rates for four out of six types of HAIs in 2020. Many of these HAIs are resistant to antibiotics.
  • Antifungal-resistant threats rose in 2020, too, including Candida auris (C. auris), which increased 60% overall—and Candida species (excluding C. auris), with a 26% increase in infections in hospitals.

New AR threats data‎

In July 2024, CDC published Antimicrobial Resistance Threats in the United States, 2021-2022. These new data show that increased by a combined 20% during the COVID-19 pandemic compared to the pre-pandemic period, peaking in 2021, and remaining above pre-pandemic levels in 2022. In addition, the number of reported clinical cases of C. auris—a type of yeast that can spread in healthcare facilities, is often resistant to antifungal medications, and can cause severe illness—increased nearly five-fold from 2019 to 2022. These data show that additional action is critical to slow the spread and impact of antimicrobial resistance.

In communities, CDC has limited data for the spread of antimicrobial-resistant pathogens, like drug-resistant gonorrhea and foodborne germs.

  • Public health personnel nationwide were diverted to the pandemic response and people (potential patients) had reduced access to care and testing services.
  • Many clinics and healthcare facilities limited services, served fewer patients, or closed their doors entirely in the face of challenges from COVID-19.
  • Before the pandemic, many resistant infections often found in the community were increasing (2012-2017).1 CDC is concerned that resistant infections continued to spread in communities undetected and untreated in 2020.

COVID-19 impact on five core actions to combat resistance

CDC targets five core actions to better prepare the U.S. to combat antimicrobial resistance, integrating a One Health approach to comprehensively tackle new threats that will continue to emerge worldwide. The pandemic impacted these core actions.

Tracking and data: COVID-19 impact

Tracking AR‎

Tracking antimicrobial resistance, including detection and reporting data, slowed tremendously during the COVID-19 pandemic because of changes in patient care, testing, treatment and the staff availability of healthcare facilities and health departments.
  • Knowing where and how changes in resistance are occurring informs solutions (e.g., outbreak response) to prevent spread and slow resistance.
  • CDC's Antimicrobial Resistance Laboratory Network (AR Lab Network) received and tested 23% fewer specimens or isolates in 2020 than in 2019. It continued to collect isolates throughout 2020 using established processes, but some isolates remain untested due to testing backlogs. This may be because healthcare facility and public health staff had to shift focus to COVID-19.

Preventing infections: COVID-19 impact

Infection prevention and control - progress lost.‎

Unfortunately, pandemic-related challenges weakened many infection prevention and control practices in U.S. healthcare facilities, undoing some progress on combating antimicrobial resistance. Infection prevention and control practices includes hand hygiene, cleaning equipment, separating patients and appropriately using personal protective equipment.
  • It is vital to prevent infections before they start, including in our communities and when in a healthcare facility.
  • There were more and sicker patients during the pandemic who required more frequent and longer use of catheters and ventilators. This may have increased risk of HAIs and spread of pathogens, especially when combined with personal protective equipment and lab supply challenges, reduced staff and longer lengths of stay.

Antibiotic/antifungal use: COVID-19 impact

Antibiotics, antifungals and AR‎

Antibiotics were commonly prescribed to patients with COVID-19, even though antibiotics are not effective against viruses like the one that causes COVID-19. Antibiotics and antifungals can save lives, but any time they are used—for people, animals or plants—they can contribute to resistance.
  • Antibiotic use throughout the pandemic varied across healthcare settings. Almost 80% of patients hospitalized with COVID-19 received an antibiotic from March to October 2020.
  • In hospitals, approximately half of hospitalized patients received ceftriaxone, which was commonly prescribed with azithromycin. This likely reflects difficulties in distinguishing COVID-19 from community-acquired pneumonia when patients first arrive at a hospital for assessment.
  • In outpatient settings, antibiotic use significantly dropped in 2020 compared to 2019 due to less use of outpatient health care and less spread of other respiratory illnesses that often lead to antibiotic prescribing. Outpatient antibiotic use rebounded in 2021 but was still lower overall in 2021 compared with 2019. From 2020 through December 2021, most antibiotic prescriptions for adults were for azithromycin and increases in azithromycin prescribing corresponded to peaks in cases of COVID-19.
  • In nursing homes, antibiotic use spiked alongside surges of COVID-19 cases but remains lower overall. However, azithromycin use was 150% higher in April 2020 and 82% higher in December 2020 than the same months in 2019. Azithromycin prescribing remained elevated through October 2020. In 2021, antibiotic use overall was, on average, 5% lower than 2019. This decrease might be due to fewer nursing home residents during this time.

Environment and sanitation: COVID-19 impact

Wastewater research‎

Researchers leveraged an existing CDC AR Solutions Initiative funded-project that measured resistance genes in wastewater and in treatment plant workers to better understand the burden of COVID-19 in communities using wastewater (sewage).
  • In September 2020, CDC established the National Wastewater Surveillance System (NWSS) to provide community-level data on COVID-19 infection trends by looking for markers in wastewater that tell scientists when SARS-CoV-2 is present.
  • Antimicrobial resistance is a One Health issue, impacting the health of humans, animals, plants, and the environment. Efforts to identify antimicrobial-resistant germs, track the spread of resistance and measure the effect of antibiotic and antifungal use require surveillance across human, animal and plant populations and the environment.

Vaccines, therapeutics and diagnostics: COVID-19 impact

Prevention products and AR‎

Treatment after infection occurs is not the only solution and should not be the only option. The U.S. needs more prevention products, not just new drugs, to stop infections before they happen.
  • The COVID-19 pandemic highlighted the need to stop the spread of germs before they can cause an infection.
  • Prevention products include alternatives to new antibiotic and antifungal drugs, new vaccines to combat infections that can develop antimicrobial resistance and novel decolonizing agents to stop the spread of antimicrobial-resistant germs by people who may not know they are carriers.

What CDC is doing

Healthcare facilities & community settings

Many of the nation's efforts to combat antimicrobial resistance also helped prevent the spread of COVID-19. This includes CDC investments in infection prevention and control, training, surveillance and public health personnel, such as:

  • Providing COVID-19 testing and identifying antimicrobial-resistant outbreaks through CDC's AR Lab Network in 50 states and several cities/territories.
  • Supporting experts in infection prevention and control, including healthcare training programs like Project Firstline to help stop the spread of pathogens.
  • Developing and implementing antibiotic use patient education tools for frontline workers.
  • Working with partners and supporting projects to improve clinical and public health outcomes and control emerging infectious disease threats, such as antimicrobial resistance and COVID-19.

Tracking and data

CDC's AR Lab Network adapted to the pandemic.

Many of CDC's antimicrobial resistance programs were leveraged to support the nation's response to COVID-19, including for testing or surge capacity to overwhelmed labs. CDC's National Tuberculosis Molecular Surveillance Center used its AR Lab Network sequencing capacity to study SARS-CoV-2 (the virus that causes COVID-19). The lab sequenced more than 4,700 SARS-CoV-2 genomes in 2020 to support contact tracing and help stop the virus from spreading.

Preventing infections

CDC responds to antimicrobial-resistant infection outbreaks.

In 2020, there were healthcare outbreaks of antimicrobial-resistant Acinetobacter and Candida, including C. auris, in COVID-19 units. CDC and public health partners responded to more than 20 outbreaks caused by resistant germs in COVID-19 treatment and observation units. The long-term impact on the spread of antimicrobial-resistant germs in a region is uncertain.

From January through July 2020, CDC's investments to build capacity in state and local health departments allowed them to perform 14,259 consultations in response to potential COVID-19 outbreaks at healthcare facilities. Outbreak consultants frequently included infection control assessments. They completed 2,105 onsite and 4,151 remote assessments.

Antibiotic/antifungal use

Tracking antibiotic use to optimize prescribing practices.

Tracking antibiotic use in settings like nursing homes and long-term care facilities is often non-existent or difficult to implement. While more work is needed, the number of hospitals reporting antibiotic use data to CDC's National Healthcare Safety Network (NSHN) from 2018 through 2021 more than doubled. Beginning in 2024, the Centers for Medicare & Medicaid Services began requiring reporting from eligible acute care and critical access hospitals into the NSHN AUR Module. Thus, it is expected that the amount of data collected will continue to increase even more.

This helps CDC and facilities better monitor prescribing and use.

Environment and sanitation

Exploring new public health tools to slow resistance.

CDC is exploring how innovative solutions in wastewater surveillance can be used to improve detection and response for antimicrobial resistance. CDC supports projects to better understand how antibiotics, antifungals and antimicrobial-resistant pathogens can spread in water and soil.

Vaccines, therapeutics and diagnostics

CDC supports innovative research.

The U.S. National Action Plan supports innovative approaches to developing and deploying diagnostic tests and treatment strategies. Since 2016, CDC has invested more than $160 million in innovative research to address knowledge gaps with scalable, solutions such as vaccines, therapeutics, diagnostics and other prevention tools.

Explore more


Fact sheets and videos

Share these fact sheets and social graphics and watch an AMR Exchange webinar about how the COVID-19 pandemic has impacted five core actions to combat antimicrobial resistance.

AR in a changed world: building resilient systems for today and tomorrow.

In May 2021, CDC hosted its first AMR Exchange webinar featuring experts who address the challenges of antimicrobial resistance during the COVID-19 pandemic. The panel includes experts from CDC; the Center for Strategic & International Studies; and the Center for Disease Dynamics, Economics & Policy.

Suggested citation

CDC. COVID-19: U.S. Impact on Antimicrobial Resistance, Special Report 2022. Atlanta, GA: U.S. Department of Health and Human Services, CDC; 2022.

  1. CDC. Antibiotic Resistance Threats in the United States, 2019. Atlanta, GA: U.S. Department of Health and Human Services, CDC; 2019.
  • CDC. COVID-19: U.S. Impact on Antimicrobial Resistance, Special Report 2022. Atlanta, GA: U.S. Department of Health and Human Services, CDC; 2022.
  • Databases used for bacterial pathogens analyzed were the PINC-AI Healthcare Database and the BD Insights Research Database. CDC is working on a future publication that will include more detailed data analysis for bacterial pathogens discussed in this fact sheet. C. auris data was obtained by monthly reporting through jurisdiction public health departments.
  • The six bacterial antimicrobial-resistant hospital-onset infections include Carbapenem-resistant Enterobacterales (CRE), Carbapenem-resistant Acinetobacter, Methicillin-resistant Staphylococcus aureus (MRSA), Vancomycin-resistant Enterococcus (VRE), Extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales and Multidrug-resistant (MDR) Pseudomonas aeruginosa.