With All Eyes on Covid-19, Drug-Resistant Infections Crept In

The spread of other dangerous germs is surging — a result, in part, of the chaotic response to the pandemic.

As Covid-19 took hold over the last year, hospitals and nursing homes used and reused scarce protective equipment — masks, gloves, gowns. This desperate frugality helped prevent the airborne transfer of the virus.

But it also appears to have helped spread a different set of germs — drug-resistant bacteria and fungi — that have used the chaos of the pandemic to grow opportunistically in health care settings around the globe.

These bacteria and fungi, like Covid-19, prey on older people, the infirm and those with compromised immune systems. They can cling tenaciously to clothing and medical equipment, which is why nursing homes and hospitals before the pandemic were increasingly focused on cleaning rooms and changing gowns to prevent their spread.

That emphasis all but slipped away amid an all-consuming focus on the coronavirus. In fact, experts warn, the changes in hygiene and other practices caused by the Covid-19 fight are likely to have contributed to the spread of these drug-resistant germs.

“Seeing the world as a one-pathogen world is really problematic,” said Dr. Susan S. Huang, an infectious disease specialist at the University of California at Irvine Medical School, noting that the nearly singular focus on the pandemic appears to have led to more spread of drug-resistant infection. “We have every reason to believe the problem has gotten worse.”

A few data points reinforce her fears, including isolated outbreaks of various drug-resistant infections in Florida, New Jersey and California, as well as in India, Italy, Peru and France. Overall figures have been hard to track because many nursing homes and hospitals simply stopped screening for the germs as resources were diverted to Covid-19.

When even modest screening picked up again early in the summer, the results suggested that certain drug-resistant organisms had taken root and spread. Particularly troublesome have been growing case counts of a fungus called Candida auris, which authorities had tried to fight before the pandemic with increased screening, isolation of infected patients and better hygiene.

Cultured Candida auris in a petri dish. Some strains of C. auris are resistant to all three major classes of antifungal drugs. 
Centers for Disease Control and Prevention

These intensive efforts had limited the spread of C. auris to a handful of cases in Los Angeles County. Now there are around 250, said Dr. Zachary Rubin, who leads the county’s infection control efforts at health care facilities.

“We saw a blooming in Candida auris,” said Dr. Rubin, who attributed the change to a handful of factors, notably the challenges in testing for the germ when so many testing resources went toward Covid-19.

Noxious drug-resistant bacteria are surfacing too, including Carbapenem-resistant Acinetobacter baumannii, which is considered an “urgent health threat” by the Centers for Disease Control and Prevention. In December, the C.D.C. reported a cluster of Acinetobacter baumannii during a surge of Covid-19 patients in an urban New Jersey hospital with about 500 beds. The hospital was not identified. And hospitals in Italy and Peru saw the spread of the bacteria Klebsiella pneumoniae.

In an acknowledgment of the issue, three major medical societies sent a letter on Dec. 28 to the Centers for Medicare and Medicaid Services asking for a temporary suspension of rules that tie reimbursement rates to hospital-acquired infections. The three groups — the Society of Healthcare Epidemiology of America, the Society of Infectious Diseases Pharmacists, and the Association for Infection Control and Epidemiology — feared that the infection rates may have risen because of Covid-19.

“Patient care staffing, supplies, care sites and standard practices have all changed during this extraordinary time,” the letter stated.

Not all types of drug-resistant infections have risen. For instance, some research shows no particular change during the pandemic in the rate of hospital patients acquiring the bacterium Clostridioides difficile — a finding that suggests the overall long-term impact of the pandemic on these infections is not yet clear.

Dr. Huang and other experts said they are not suggesting that the priority on fighting Covid-19 was misplaced. Rather, they say that renewed attention must be paid to drug-resistant germs. Earlier research has shown that as many as 65 percent of residents of nursing homes carry some form of drug-resistant infection.

Over the years, critics have charged that hospitals and, in particular, nursing homes, have been lax in their efforts to confront these infections because it is expensive to disinfect equipment, train staff, isolate infected patients and screen for the germs.

In response to these and other concerns, a greater effort was beginning to be made before the pandemic to monitor patients for these infections, particularly as they cycled in and out of nursing homes and intensive care units. This revolving door is known to spread germs that are carried by infected patients.

Go Nakamura/Getty Images

But after the pandemic began, there was much less monitoring and even, at times, a wholesale breakdown of communications about the transfer of such patients, experts said. Plus, the sickest Covid-19 patients were put on ventilators, where drug-resistant infections can cling and then spread.

Another possible contributor has been the heavy and regular use of steroids to treat Covid-19. These drugs help alleviate the virus’s most dangerous symptoms but can leave the immune system compromised in a way that allows other germs to more easily infiltrate the body.

The combination of these factors “is perfect” for the fungus to “take hold,” said Dr. Tom Chiller, the head of the fungal division of the C.D.C.

Earlier this month, the Florida Department of Health published a case report of four Candida auris cases at a hospital in Florida. (The hospital’s identity is masked by the C.D.C. and the state). In an effort to understand the spread, the Florida department of health visited the Covid unit there in August. Their inquiry found that 35 of 67 patients admitted to the unit from Aug. 4 to 18 were colonized with C. auris, meaning that the fungus was on their skin but they were not yet infected. Subsequently, six of the patients became infected.

Crucially, the study found that the spread of the fungus from one patient to the next may well have come from health care providers carrying the germ on protective gowns or gloves, as well as on mobile computers and other equipment that had been insufficiently cleaned. This was, the C.D.C. and other experts said, a breakdown in so-called infection control, a practice that had come under intense scrutiny in 2019 after C. auris took root in the East Coast and began to spread.

Nationally, the number of infections had increased to around 1,625 by November 2020, from 952 since the end of October 2019. The current number is likely far higher, Dr. Chiller said, because screening for the germ was largely halted early in the pandemic. When it picked up again, the numbers rose to 83 infections in August and 195 patients colonized — and, even then, testing was not as widespread as pre-pandemic.

The upshot is that the confirmed cases are “likely the tip of the iceberg,” Dr. Chiller said.

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