How the COVID-19 Pandemic Altered the Course of Antimicrobial Resistance

Anne Meneghetti, MD, discusses the effects of the COVID-19 pandemic on inappropriate antibiotic use in both the inpatient and outpatient setting.

There are 2 sides to the story of how the COVID-19 pandemic affected antibiotic use and its impact on antimicrobial resistance (AMR) — the inpatient and outpatient side.

On the inpatient side, COVID-19 flooded hospitals with severely ill patients who endured prolonged lengths of stay. Many patients hospitalized with fever and pneumonia were treated with antibiotics. Trained as an intensivist, I understand the impulse to treat patients with pneumonia in the intensive care unit with broad-spectrum antibiotics — especially early in the pandemic when little was known about the course of severe COVID-19 infection. Later, it was discovered that the estimated rate of bacterial coinfection was less than 9%, according to study findings comprising data captured from more than 30,000 patients.1 According to a report from the Centers for Disease Control and Prevention (CDC), resistant hospital-acquired infections (HAIs) and deaths both increased by at least 15% during the first year of the pandemic, despite years of steady reductions in HAIs prior to the pandemic.2

In the outpatient setting, there’s a different story. Unlike the inpatient setting, there are less public data available to directly assess changes in resistance. During the pandemic, health care-seeking behavior and access to care were limited; stay-at-home orders, masking, and social distancing intended to reduce COVID-19 transmission likely reduced the spread of other respiratory infections such as influenza and the common cold. Although upper respiratory tract viral infections are often inappropriately treated with antibiotics, antibiotic prescriptions for these infections dropped from pre-pandemic levels. Overall, data on antibiotics prescriptions in the outpatient setting have trended favorably, though data from 2021 show a possible rebound. In addition, infections caused by Streptococcus pneumoniae, as well as gonorrhea, tuberculosis, and other infections that warrant antibiotics, may have gone undiagnosed and untreated during the pandemic.

The Fundamentals of Antibiotic Stewardship

The future of AMR hangs on the decisions that antibiotic prescribers make today and with the care teams accountable for infection control and prevention. To reverse some of the lost ground during the pandemic, the following fundamentals of antibiotic stewardship and infection control need to be revisited:

  • Prevent infections with routine and catch-up vaccinations. The COVID-19 pandemic significantly affected preventive vaccination uptake rates across multiple patient populations. Pneumonia caused by methicillin-resistant Staphylococcus aureus and other bacteria is a leading cause of death in patients with influenza, and influenza vaccination may reduce the risk for bacterial superinfection.
  • Do not use antibiotics for viral infections. The use of viral diagnostics and procalcitonin measurements might help identify patients for whom antibiotics may be discontinued. For suspected viral infections, acknowledge the patient’s symptoms, offer symptom relief, and provide education on the risks associated with inappropriate antibiotic use. It is also important to follow specialty society guidance for the treatment of viral infections.
  • Tailor treatment to the antibiotic spectrum. In decision-making, reference the most current and local data available on antimicrobial susceptibility. If obtaining blood cultures, take care to avoid contamination and narrow the spectrum based on results. Critically evaluate the validity of documented antibiotic allergies, especially those associated with penicillin.3
  • Follow the latest specialty society guidance on antibiotic treatment durations and use the shortest possible durations to minimize unnecessary antibiotic exposures.
  • Antibiotic stewardship and infection control programs.A sharpened focus on infection control procedures stemming from the COVID-19 pandemic has the potential carryover benefit of reducing other HAIs.

Antibiotic stewardship is our most powerful weapon against AMR and warrants high prioritization and investment by health care systems. Decreasing diagnostic uncertainty about bacterial infections, avoiding inappropriate use and improper durations of antibiotic treatment, rapid de-escalation based on results, rapid-cycle research and education efforts, and controlling the spread of infections are all core to the effort. A reliance on new antibiotics will not solve this problem. The pipeline of antimicrobial agents with novel mechanisms of action is limited, and the pace from research to market is slow. A report published in 2019 by the CDC concluded that the “post-antibiotic era” has already begun, owing to the gap between AMR rates and the development of novel antibiotics. Resistance will surely develop with new agents as well. Research is underway for novel treatment approaches, such as antibody therapy, bacteriophages, and fecal microbiota transplantation. 

Course Correction

During the pandemic, some of the CDC’s inpatient AMR tracking programs were repurposed. The CDC is now organizing to simultaneously handle emerging outbreaks while providing surveillance on AMR infections. Fortunately, hospitals have the capacity to track AMR and susceptibility within their own walls. However, in the outpatient setting, public data about bacteria prevalence and local susceptibility patterns are limited. The epocrates team was awarded a software patent for geography-based AMR tracking. This software, powered by athenahealth data, represents locality-centered patterns based on data largely captured from the outpatient setting. The epocrates team is working to make this software available for use in clinical practice.

Patient education is vital to antibiotic treatment adherence. Years ago, there was an emphasis on “taking the full course” of antibiotics. Now, the focus has shifted to the shortest and clinically appropriate effective duration of therapy. Each additional day of antibiotic treatment increases the risk for patient harm. Optimizing the duration of antibiotic therapy at the time of hospital discharge is key; for example, most excess antibiotic use for community-acquired pneumonia occurs following discharge.

As current data suggest that patients with bacterial coinfection comprise less than 9% of those with COVID-19 infection, the impulse to prescribe antibiotics to patients with COVID-19 infection will decrease.1 During the first 2 years of the COVID-19 pandemic, hard lessons were learned about prioritizing surveillance for COVID-19 transmission at the expense of decreased AMR surveillance. A report published by the CDC in 2022 outlines the agency’s plans to organize for the simultaneous handling of emerging outbreaks as well as the surveillance of AMR bacterial infections.2

Anne Meneghetti, MD, is the physician executive who leads the Medical Information Team at Epocrates. After training in internal medicine, pulmonary, and critical care specialties, she worked in health care policy before joining the Epocrates team in 2006. Her team creates and curates clinical decision support tools for the moments of care.


1. Langford BJ, So M, Raybardhan, et al. Antibiotic prescribing in patients with COVID-19: rapid review and meta-analysis. Clin Microbiol Infect. Published online January 5, 2021. doi:10.1016/j.cmi.2020.12.018

2. Centers for Disease Control and Prevention. COVID-19: U.S. impact on antimicrobial resistance, special report 2022. Updated February 25, 2022. Accessed August 5, 2022.

3. Centers for Disease Control and Prevention. Blood culture contamination: an overview for infection control and antibiotic stewardship programs working with the clinical laboratory. Accessed August 5, 2022.

4. Centers for Disease Control and Prevention. Core elements of hospital antibiotic stewardship programs. 2019. Updated April 7, 2021. Accessed August 5, 2022.