Antibiotic treatment for COVID-19 complications could fuel resistant bacteria

Science ’s COVID-19 reporting is supported by the Pulitzer Center.

In her regular job, Priya Nori runs Montefiore Medical Center’s antibiotic stewardship program, and spends most of her time ensuring that the Bronx-based hospital doesn’t overuse the drugs and allow bacteria resistant to them to thrive. But like many physicians, Nori is now spending all of her time helping treat COVID-19 patients at her New York City hospital, which like other medical centers in the pandemic hot spot, is crowded with 50% more patients than normal. As part of that care, she and other doctors are administering many more antibiotics than normal, which is a recipe for the rapid rise or spread of resistant bacteria, especially given the crowded conditions.

Antibiotics do not directly affect SARS-CoV-2, the respiratory virus responsible for COVID-19, but viral respiratory infections often lead to bacterial pneumonia. Physicians can struggle to tell which pathogen is causing a person’s lung problems. “We tend not to hold back on antibiotics in these patients,” Nori says, especially when that decision could mean life or death. “Is that a bad thing right now? I have trouble saying that it is.” But she and others worry the surge of COVID-19 patients could ultimately lead to a surge in antibiotic-resistant bacteria—a concern serious enough that the U.S. Department of Defense (DOD) is assembling a group of at least 10 medical centers to study “secondary” bacterial and fungal infections in these patients and the antibiotics being used to prevent them.

Hospitals, particularly intensive care units, are hotbeds of antimicrobial resistance, and they have long been struggling to rein in the use of antibiotics. But COVID-19 has put many such efforts on hold. Although the U.S. Centers for Disease Control and Prevention requires medical centers to report their antibiotic use and the rates of infections acquired in the facility, Nori and other physicians say compliance has fallen off in the pandemic.

Some researchers suggest the pandemic could slow the spread of both bacteria and antibiotic resistance within hospitals. Surgeries, which account for many hospital-acquired infections, have largely been canceled to keep beds open for COVID-19 patients, and hospital staff routinely wear robes, masks, and other personal protective equipment (PPE) during patient care. “Nothing gets people’s attention like a new pathogen that has the risk to be spread within a hospital,” says Neil Clancy, an infectious disease physician at the University of Pittsburgh.

But Bo Shopsin, an infectious disease physician at New York University’s Langone Health Center who is involved in DOD’s planned study, notes that some hospitals are being forced to reuse PPE and share ventilators between patients. “It’s quite clear that COVID is transmitting in hospitals and if it is, [resistant bacteria are] too.”

More important, antibiotic use appears to be surging. Several recent studies from China suggest that nearly all serious cases of COVID-19 are treated with antibiotics, and anecdotally, many U.S. and European physicians say the same. But often the antibiotics are necessary, researchers say. Many COVID-19 patients die of secondary infections rather than the virus itself, growing evidence suggests. A recent paper in The Lancet detailing the outcomes of 247 hospitalized COVID-19 patients in Wuhan, China, found that 15% of them—and half of those who died—acquired bacterial infections. Major outbreaks of other respiratory viruses illustrate the concern: up to half the 300,000 people who died of the 2009 H1N1 flu and the majority of deaths from the 1918 flu actually died of bacterial pneumonia.

“We do have some guidelines on when to treat and when not to treat,” says Leopoldo Segal, a pulmonologist at Langone.” But in the current situation, it’s hard to imagine those guidelines are totally applicable.” Several of his COVID-19 patients, he says, have antibiotic-resistant infections, and nearly all are receiving azithromycin: a widely used antibiotic that kills both of the two major classes of bacteria.

In combination with the antimalarial drug hydroxychloroquine, azithromycin has become a popular treatment for COVID-19 patients after President Donald Trump and others highlighted small, uncontrolled studies that appeared to show the combination was effective. It is impossible to know how often the combination is prescribed, but the rate is high enough to have caused an azithromycin shortage in the United States.

Infectious disease physician Marisa Holubar of Stanford University says it’s still too early to know the extent to which COVID-19 will affect global antibiotic resistance rates. But in some parts of the United States, 30% to 40% of some common types of bacteria were already resistant to the class of drugs that includes azithromycin, and overuse could render those or other antibiotics even less effective. “In terms of a nightmare scenario, it’s quite scary,” Clancy says.

The DOD study will investigate just how widely antibiotics are being given to COVID-19 patients, and how often they have secondary infections that warrant antibiotic use. The results should help experts develop guidelines for when and how doctors should prescribe antibiotics to COVID-19 patients, as well as provide a data set on potentially thousands of patients to help researchers better understand how infections spread in hospitals and why bacterial and viral infections are linked. “People have been studying [secondary] infections for decades with flu,” Shopsin says. “Things will move faster with COVID.”