The Pandemic Fueled a Superbug Surge. Can Medicine Recover?


As Covid swept ICUs, doctors prescribed antibiotics to ward off secondary infections. Now bacteria have evolved resistance—but hospitals are fighting back.

The desperate need to save the lives of Covid patients during the pandemic’s first waves, coupled with shortages of hospital personnel and protective equipment, drove a shocking reversal in progress against deadly superbugs, according to a new analysis by the US Centers for Disease Control and Prevention.
The report, released July 12, synthesizes lab and hospital-admission data to reach a grim conclusion: From 2019 through 2020, the number of antibiotic-resistant infections occurring in hospitals, and resulting deaths, each increased by at least 15 percent. For some of the most hard-to-treat pathogens, the increases shot up 26 percent to 78 percent. And those figures are even worse than they appear, because in the years immediately preceding the pandemic, resistant infections in hospitals across the US had been forced down by almost a third—meaning that Covid wiped out years of progress in reducing one of health care’s most stubborn threats to patients.
“The pandemic created the perfect storm for this to happen,” says Arjun Srinivasan, a physician and associate director of the CDC’s health-care-associated infection-prevention programs. “You had large numbers of patients needing very advanced care, oftentimes in intensive care units—needing central lines, needing urinary catheters, needing mechanical ventilation; all of those increasing risks for infection, all of those increasing risks for infections with antibiotic-resistant organisms.”
But medical experts say that hidden within the dismaying trend—and this isn’t present in the CDC’s report—is a surprising bright spot. Some US hospitals managed to reduce their patients’ vulnerability to superbugs because they kept supporting prevention programs they had set in motion before the pandemic started, and especially because they kept those programs’ personnel from being diverted to different tasks.
Any use of an antibiotic carries the possibility of provoking resistance, because bacteria adapt to defend themselves. So hospitals run programs, broadly known as antibiotic stewardship, that monitor which drugs are being used and reserve the most precious compounds as last-report options. Simultaneously, they maintain infection-prevention teams to protect patients against infections that can arise when medical devices accidentally conduct bacteria inside the body, or drug treatments suppress the immune system, or pathogens are carried between patients on staffers’ gowns or hands.
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When masks and protective equipment ran short during the first waves, health care workers couldn’t swap out their gear as they normally would have. In deluged wards, they may have skipped safety steps to try to save lives. And as desperately ill patients overwhelmed ICUs, clinicians preemptively put them on antibiotics—not to control Covid, because the virus isn’t affected by these drugs, but to ward off other infections. The CDC analysis finds that in 2020 almost 80 percent of Covid patients received at least one antibiotic during their hospital stay, a far higher percentage than normal.
Uneasy predictions during the past two years suggested this might happen. In the first months of the pandemic, multiple experts, including a former CDC director, published warnings that broad use of antibiotics among the earliest Covid patients was lighting the fuse on a time bomb. In March 2021, a project of the Pew Charitable Trusts predicted that resistance rates were sure to rise, because so many Covid patients were receiving antibiotics. And by the end of that year, evidence began to arrive that they were right. A CDC analysis last September revealed that Covid’s pressures on health care reversed years of progress in reducing infections in already-hospitalized people. This May, researchers from pharmaceutical giant Merck and medical-technology company Becton Dickinson presented preliminary data showing that rates of resistant infections in 271 US hospitals rose in 2020 and 2021—in patients with and without Covid—compared to 2019.
So the CDC’s findings this week ought to come as no surprise. They confirm spikes in incidence of dangerous bacteria and fungi, including carbapenem-resistant Acinetobacter (up by 78 percent), multidrug-resistant Pseudomonas aeruginosa (up by 32 percent), and the multi-drug-resistant fungus Candida auris (up by 60 percent).
Some stewardship and infection-prevention programs were dented by Covid care because their specialists possessed expertise that easily could be redeployed. “People who work in stewardship have logistical and organizational skills and understand infrastructure and health care systems, so a lot of time they simply got moved over to the Covid response,” says Cornelius J. Clancy, a physician and professor of medicine at the University of Pittsburgh who researches antibiotic utilization. “Likewise, there’s only so many people working in infection prevention in a given hospital, and there’s only so many hours in the day—and all the time they were spending scouring for PPE and putting protocols together got diverted from other hospital [infection prevention].”
“A lot of personnel—the pharmacists, the infectious disease physicians—were diverted to the frontline response, and that’s a representation of how thin resources were to begin with,” agrees David Hyun, a physician who leads the Pew Trusts’ resistance project. “But we’ve also heard, anecdotally, of hospital leadership and administrations that had invested in stewardship programs and protected their time.”
A few examples: The University of Michigan Health System managed to keep its stewardship program supported by protecting them as a research team. In the earliest days, when antivirals weren’t available and treatment pathways weren’t clear, the group chased historical data on bacterial and viral co-infections. They also compared notes with health care workers at other institutions, and then developed their own protocols.
“We didn’t want a cookie-cutter thing,” says Payal Patel, a physician and assistant professor who is also medical director of antimicrobial stewardship at the VA Ann Arbor Healthcare System. “So every person who came in with Covid got a consult with an infectious disease physician, looking at the patient, looking at the care, and then giving advice. Oh, I see that they're on antibiotics. You know, you probably don't need those.” Within three months, the Michigan team helped reduce the hospitals’ Covid antibiotic use, cutting short misuse that could lead to the emergence of superbugs.
The University of Maryland Medical Center in Baltimore took a similar tack, making sure the advice of its stewardship team—three pharmacists and a physician focused on infectious disease—was consulted at the start of any Covid patient’s care. “We have long-standing institutional antimicrobial use guidelines—we have them on a web platform, and they're also in a mobile app,” says Emily Heil, pharmacy director for its antimicrobial stewardship program and an associate professor of medicine and pharmacy. “So we built our Covid treatment recommendations right into that platform, where physicians are already used to going to get real-time information.”
That meant the teams treating pandemic patients were served advice about restricting antibiotics at the same moment that they received the newest recommendations about Covid care. It also meant that, once scarce antivirals arrived, clinicians could order them through the same system they would use to request last-resort antibiotics, so prioritization and triage processes were already familiar.
Among hospitals and at the CDC, there’s no confidence that this episode of superbug resurgence has ended, though the Covid pandemic has morphed from a full-on emergency into a wearying slog. New hospital admissions are at the same level they were in July 2020, yet there are fewer health care workers; between the start of 2020 and the end of 2021, 18 percent quit, according to one survey. One of the challenges of the recovery will be to coach more institutions into making stewardship and infection prevention central to care.
“You get what you pay for, and we have paid for not-the-best system when it comes to antimicrobial-resistance monitoring and prevention,” Srinivasan says. “We have underinvested in both the public health side, to have the data and the expertise to help health care facilities monitor these trends. And we underinvested in the health care side, making sure that they had systems in place to provide safe care, even when the system is strained.”
Just restoring what existed pre-pandemic won't work, because that didn’t keep programs from being cannibalized when institutions were under stress. “It's not sufficient to go back to how it was before,” Hyun says. “As we're rebuilding, we need to think about: How do we make all this more resilient, so that it can be sustainable during the next public health emergency?”

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