Addressing Antimicrobial Resistance Following COVID-19

By Matt Phillion

The pandemic has taken a toll on the healthcare industry’s battle against antimicrobial-resistant infections. Rates of these infections skyrocketed from 2019 to 2020 as more and more Americans found themselves hospitalized with COVID-19. To highlight this growing issue, the CDC is issuing a special report and discussing how the industry might turn these numbers around.

Before COVID-19, deaths from antimicrobial resistance were headed in the right direction, decreasing by nearly 30% in hospitals between 2012 and 2017. But in 2020, resistant hospital-onset infections and deaths both increased by 15% compared to 2019. These infections were linked to seven healthcare-associated pathogens:

  • Carbapenem-resistant Acinetobacter(78% increase in infections)
  • Carbapenem-resistant Enterobacterales (35% increase in infections)
  • Antifungal-resistant Candida(26% increase in infections)
  • ESBL-producing Enterobacterales (32% increase in infections)
  • Multidrug-resistant  aeruginosa (32% increase in infections)
  • Vancomycin-resistant Enterococcus (16% increase in infections)
  • Methicillin-resistant Staphylococcus aureus(13% increase in infections)

We have previously discussed the CDC’s work on antibiotic stewardship and the historic gains in this area that were reversed during the pandemic. Between March and October 2020, nearly 80% of patients hospitalized with COVID-19 received an antibiotic—and though we now know that antibiotics and antifungals are ineffective against COVID-19, this dramatic usage put patients on the path for side effects and enabled resistance to develop and spread.

The time is now, experts say, to reverse this upward trend.

New numbers for a known problem

The increase in antimicrobial resistance was already on the radar for experts, notes Arjun Srinivasan, MD, associate director for healthcare-associated infection prevention programs in the CDC’s Division of Healthcare Quality Promotion. Given the rise of patients with healthcare-associated infections (HAI) in hospitals and nursing homes during the pandemic, there was concern that the industry would see a concurrent rise in antimicrobial-resistant infections.

“We were worried we’d see antimicrobial resistance rise when we were able to get the data that would allow us to look at trends, and we saw increases among those pathogens commonly encountered in healthcare settings,” says Srinivasan.

One surprise when those numbers came in, though, was that researchers only had data for half the pathogens they wanted to track. “We have 18 pathogens we monitor in our threat report that we’re worried about, and during the pandemic, half of those are common outside the healthcare setting, like STIs, foodborne pathogens, and others.”

The pandemic drastically disrupted the infrastructure used to collect that information, which was something no one could have anticipated, says Srinivasan. “It’s not surprising given what happened, but in many senses the report is alarming in two ways: the increase in antimicrobial-resistant pathogens we have the data for, and [the fact that] we don’t have the data for the others.”

A return to what was working

For the pathogens with available numbers, specifically in healthcare environments, the next step is pretty clear: “We need to implement the actions that were working before the pandemic,” says Srinivasan.

The window from 2012 to 2017 demonstrated some impressive statistics: an 18% overall reduction in infections, almost 30% in healthcare specifically, with the industry doing a fantastic job bringing pathogens under control. But with the arrival of the pandemic, “we had more and sicker patients presenting for care—they needed catheters in place, ventilators, and we had a lot of those patients getting antibiotics,” says Srinivasan. “We didn’t know what to offer or what to do, and that drove antibiotic use.”

The shortage of personal protective equipment was also damaging, impeding the maintenance of best practices. “It was a whole host of factors that contributed to the increase,” says Srinivasan.

So how do we get back to the good place we were in? “We need to think about what was contributing to the success before the pandemic. We know COVID hasn’t gone away, but we also know that the healthcare system has gotten much better at managing COVID on top of everything else they deal with,” he says. “Now that systems are stabilizing, we need to turn our attention back to how we reimplement those best practices.”

There’s also the matter of getting data for the pathogens that the industry lacks numbers on. “We need to focus on our data infrastructure,” says Srinivasan. “Better systems that aren’t dependent on someone entering data into a system, better delivery, better testing infrastructure to ensure that when the next pandemic comes, we aren’t so disrupted.”

Leadership from everywhere

Making this happen will require a broad effort, says Srinivasan. “The CDC is at the forefront, but it takes everyone coming to the table,” he says.

Currently, multiple institutions are undertaking a data modernization initiative with the goal of transforming how we collect, share, and use public health data for the next decade and beyond. “It’s not a CDC-only thing. There are healthcare facilities [who are] collecting information and have the data, state and local health departments, vendors who make software programs and EHRs. There are tons of different groups” who should be involved in this initiative, he says. “The good news is those groups are at the table now because of the data modernization initiative, because of the gaps COVID helped identify.”

The pandemic spotlighted a lot of frustration with healthcare professionals’ inability to get the data they needed to protect patients from COVID-19. “It became clear those weaknesses existed before COVID and exist for other pathogens,” says Srinivasan.

COVID-19 created more urgency to fix a known issue in data collection, much as it helped highlight challenges in other areas.

“COVID illustrated the impacts a pandemic can have,” says Srinivasan. “Not just the people who got it, and the numbers who died from it, but also all these other incredible knock-on effects that COVID had that deteriorated the health of the nation: increases in HAIs, falls, pressure ulcers. A lot of clinics were closed, so patients weren’t getting routine cancer screenings, blood pressure medications, and we will be suffering the long-term consequences of COVID for years to come. And fundamentally, if we don’t learn from the mistakes of the past, we’re doomed to repeat them. If we don’t fix the things that went wrong with our system during COVID, we’ll be back here again with all the same challenges.”

The CDC issued its last national report on antimicrobial resistance threats in 2019, and while things were improving at that point, the numbers of infections and deaths were still staggering, says Srinivasan: three million antimicrobial-resistant infections every year, and more than 30,000 patients dying every year from them. “We were making progress, but this was still a cause for significant concern,” says Srinivasan. “We continue to emphasize that antimicrobial resistance is one of our major threats—that was true before the pandemic and continues to be true.”

Raising awareness of antimicrobial resistance and motivating action to reduce its severity continues to be of great importance, he says. “What I like to see as practices come back online are things that had stopped during the pandemic—getting data collection both inside and outside of healthcare back online and moving toward improvement so they’re more robust and don’t go offline during future pandemics,” he says.

Srinivasan says he’d like to see a more sustained investment in the infrastructure needed to tackle this problem. “In a sense, you get what you’ve paid for when it comes to prevention in public health,” he says. “We’ve underinvested in these systems in the past. The investments we’ve made have come to bear, but we need to see those sustained. This is not an issue solved by a one-time investment. They need to be made planning into the future.”

Matt Phillion is a freelance writer covering healthcare, cybersecurity, and more. He can be reached at