The COVID-19 Pandemic’s Impact on Antimicrobial Resistance in the U.S.

October 12, 2022

In nearly all elements of the United States healthcare industry there were setbacks during the COVID-19 pandemic, including the fight against antimicrobial resistance. Antimicrobial resistance has emerged as an urgent global public health threat that has the potential to affect people at any stage of life, as well as the healthcare, veterinary, and agriculture industries. If antibiotics and antifungals lose their effectiveness, then we lose the ability to treat infections and control these public health threats. 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 which being resistant to antibiotics. Antifungal-resistant threats also rose, with Candida auris increasing 60% overall.

During the first year of the pandemic, more than 29,400 people died from antimicrobial-resistant infections commonly associated with healthcare. Of these, nearly 40% of the people got the infection while they were in the hospital. The pandemic resulted in more resistant infections, increased antibiotic use, less data, and less prevention actions. This setback can and must be temporary. If properly resourced, the U.S. can continue to build resilient public health and healthcare systems to keep our nation safe from antimicrobial resistance.

Detection of MDRO

For several reasons there is a lack of data pertaining to antimicrobial resistant infections during the pandemic. In some instances, healthcare facilities cutback on services or reduced access to care and testing; while also public health resources were forced to shift from tracking antimicrobial resistance to tracking COVID-19 cases.

Since 2016, the Antimicrobial Resistance Laboratory Network (AR Lab Network) has been used by the CDC to detect known and emerging antimicrobial resistance in every state, and in 2020 submissions were down almost 21%. During the COVID-19 pandemic, identifying and reporting data decreased dramatically because of changes in patient care, supply challenges, and the overload on health departments.

Currently, CDC is missing data for nine of the 18 pathogens listed in its 2019 AR Threats Report. Data we do has shown an alarming increase in resistant infections resulting from hospitalization, growing at least 15% from 2019 to 2020. CDC’s 2019 estimates are still the strongest 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.

More resources are needed to continue establishing a resilient public health system that can maintain capacity to respond to antimicrobial resistance while also responding to other threats. Without an infrastructure and supply chains grounded in preparedness, critical antimicrobial resistance data will be delayed again when the next threat emerges. We must address gaps identified before the COVID-19 pandemic, including expanding the public health workforce, increasing local access to the best detection tools and technology, and expanding laboratory capacities.

Impact on Infection Prevention & Control

Pandemic-related challenges hindered many infection prevention and control practices like routine cleaning and disinfection of equipment, separating patients, and properly using personal protective equipment (PPE). This is partly because 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 visits

Candida auris is just one out of 18 antimicrobial-resistant bacteria or fungi that is a current threat in healthcare facilities. C. auris is resistant to all three major antifungal drug classes and primarily identified in acute care facilities pre-pandemic. C. auris clinical cases significantly increased in 2020, due to staffing and supply shortages, an increased number of sicker patients, and changes in infection prevention and control practices (e.g., re-use or extended use of gowns and gloves).

The COVID-19 pandemic likely intensified spread of C. auris and hindered detection of additional cases. The rapid rise in cases is concerning and emphasizes the need for continued surveillance, expanded lab capacity, quicker diagnostic tests, and robust infection prevention and control.


The threat of antimicrobial-resistant infections is not only still present but has gotten worse over the past two years. The total national burden of deaths from antimicrobial resistance may be much higher, but data gaps caused by the pandemic hinder that analysis. More investments are needed to continue addressing antimicrobial resistance while simultaneously responding to COVID-19 and other health threats. Emphasis on infection control and delegating antimicrobial usage will be need to be implemented across the healthcare industry to protect people from antimicrobial-resistant infections and their spread. Solid infection control and prevention procedures are the greatest tools for combating antimicrobial resistance and reducing healthcare costs. 

Click here to schedule a customized consultation with Shari Solomon, President of CleanHealth Environmental, and discuss how antimicrobials are used in your operations and proper environmental hygiene procedures. 

In addition, we invite you to learn more about our Infection Prevention Services.