Years of steady, incremental reductions in key healthcare-associated infections (HAIs) were lost in 2020 in the tsunami of the COVID-19 pandemic, with thinly staffed infection prevention departments being one of the critical issues as hospitals were overrun.

“Infection preventionists (IPs) — who are a finite number of people — have really been devoting their efforts to preventing the spread of COVID within the hospital to protect both healthcare workers and patients,” says Mary Hayden, MD, chief of infectious diseases at Rush University Medical Center in Chicago.

IPs did their best but could see the disaster unfolding as one surge of COVID-19 patients, who represented both higher census and higher acuity to besieged caregivers, followed another, says Ann Marie Pettis, RN, BSN, CIC, president of the Association for Professionals in Infection Control and Epidemiology (APIC) .

“We just couldn’t keep all of those plates spinning,” she says. “I hope those at the state and federal levels are really taking this to heart and realizing the importance of having a sustainable program with built-in reliance. Even with local [nonpandemic] outbreaks in a facility or in a community, you need resilience [in infection prevention programs]. And we just don’t have it. Our programs are operated on a shoestring in terms of resources.”

It also is a field that cannot be expanded easily with inexperienced personnel. “To be able to just pluck somebody out of the air and plop them into an IP program is difficult at best,” Pettis says. To address this, APIC is working on a program to get infection control training in college curriculums.

“We are very focused on the IP academic pathway because we recognize that we really need to beef up our pipeline,” Pettis says.

APIC also is expected to partner with the Centers for Disease Control and Prevention (CDC) in its ambitious infection control training program for healthcare workers of all stripes.

“This is really the first-ever national program from the CDC geared at training every healthcare provider in America — over 6 million of them — on the basics of infection control,” says Arjun Srinivasan, MD, the CDC’s associate director of HAI Prevention Programs.

Project Firstline, the CDC’s National Training Collaborative for Healthcare Infection Control, is online training that will connect specific expertise to a broad variety of medical roles.1

“So, when we are talking to nurses’ aides [who] work in nursing homes, that training is informed by nurses’ aides in nursing homes,” says Srinivasan, who also was one of the key researchers for the CDC report that documented the unprecedented increase in HAIs.

Data from the CDC’s National Healthcare Safety Network revealed that four important HAIs — including central line-associated bloodstream infections (CLABSIs) — were much higher in 2020 than in 2019.2 The rate of CLABSIs was 47% higher than 2019 in the third and fourth quarters of 2020. The CDC found also that catheter-associated urinary tract infections, ventilator-associated events, and methicillin-resistant Staphylococcus aureus (MRSA) infections rose sharply in 2020. In national preliminary data, MRSA infections increased 34% from 2019. With surging use of ventilators for COVID-19 patients, ventilator-associated infections increased 45% in 2020 compared to 2019, the CDC reported.

“These were ventilator-associated events, which include both infectious complications — that could be a bacterial pneumonia on top of COVID pneumonia, or it could be damage to the lungs that makes it much more difficult for the patient who recovers,” Srinivasan says.

In a typical, non-pandemic situation, such serious infections would prompt a hospital investigation by an IP to determine the root cause, Pettis says.

“In normal times you would have IPs working with the frontline staff using infection control bundles and all the protocols that we put in place,” she says. “We weren’t able to do that during the pandemic. The focus was just so strong in terms of what was happening with COVID that you just didn’t have the bandwidth.”

A ‘System Failure’

Characterizing the HAI increase as a “system failure,” Srinivasan emphasizes “this does not represent a failure of individual healthcare providers — they have done beyond extraordinary work throughout the pandemic. They have worked unbelievably long hours under very challenging circumstances at risk to themselves and their families. They have delivered incredible care. They learned how to take care of a disease that didn’t exist two years ago.”

Among the grim realizations is that while HAI prevention systems work well at baseline, they “don’t work at all when the system is stretched to the breaking point,” he says. “We need to build better systems for the future. So that when the next pandemic comes — we know it is ‘when,’ not ‘if’ — we have systems in place that are able to prevent these infections even when things are very challenging.”

Staffing for better resiliency in infection prevention and nursing in general seems a particularly hard lesson learned, but the longstanding argument that it is more cost-effective to prevent HAIs than to treat them has gone unheeded too often in healthcare delivery. Looking at the devastation caused by an ongoing pandemic, one wonders, if change does not come now, when will it? Must recovery be incremental, or could HAIs revert to typical rates fairly quickly at the end of the pandemic?

“That is the $64,000 question,” Srinivasan says. “There is certainly every indication that what happened here was an enormous and utterly unprecedented stress on the system. When the system is able to return to close-to-normal operations, we will see these infection rates back to where they were before the system was stressed. It is our definitive hope that will happen.”

The best way to make that happen is to increase the number of people vaccinated for COVID-19, he says. “We know that the vaccine is incredibly effective at reducing your risk of being hospitalized,” he says. “If you don’t go into a hospital, you are not at risk for adding an HAI.”

But if COVID-19 variants like Delta continue to emerge and large populations remain unvaccinated, it seems clear that a higher level of HAIs will be the byproduct of a perpetual pandemic.

“I think so,” Pettis says. “I tend to be a real optimist, but we have to put some realism into the equation. Based on everything that we are seeing right now, I would be very surprised if we gained back much ground yet. But that’s in our wheelhouse, and we will eventually get back to reclaim the ground lost, but it is going to take a recommitment to resources at the local, state, and federal level.”

Underscoring the connection, Pettis says as COVID-19 dropped at her facility so did HAI rates. “Then with Delta, we went back into crisis, so it was short-lived,” she says.

That means the conditions under which HAIs increased in 2020 are continuing at some hospitals even as staffing woes multiply.

“The staffing crisis has gotten even worse,” she says. “A lot of people have left healthcare because of burnout and the mandatory vaccination requirements. We still have many people in healthcare saying when that time comes [for mandated vaccines] they are going to leave.”

The American Nurses Association (ANA) recently sent a letter to the Department of Health and Human Services (HHS) calling for “robust and immediate action to address the unsustainable nurse staffing shortage facing our country,” adding, “ANA urges the [Biden] Administration to declare a national nurse staffing crisis and take immediate steps to develop and implement both short- and long-term solutions.”3 (See “ANA Sounds Alarm on National Nursing Shortage.”)

“This is getting serious,” Pettis says. “In my own organization, it’s frightening. We are having to shut down beds. We don’t have some ICU (intensive care unit) beds staffed. So, in the short term, this is only going to get more challenging. Who knows about the long term? I don’t know.”

The CDC report cited staffing challenges as a contributing factor but did not subject the issue to a detailed analysis.

“We know from other studies that short staffing is associated with higher incidence of HAIs,” Hayden says. “You have to have enough staff, so they have enough time to practice hand hygiene at every point they are supposed to, change dressings, and monitor devices.”

Progress Lost

Nationally, the increase in CLABSIs, which traditionally have an estimated 20% mortality rate, “wiped out” some five years of progress, Srinivasan says. “We had about a 50% reduction of CLABSIs over the past five years between 2015 and the start of 2020,” he says. “Now the standardized infection ratio is back about where it was in 2015. We don’t have numbers on [CLABSI] mortality. We know that a lot of these infections had a very high rate of mortality, but [we can’t] quantify it.”

In terms of overall mortality, the CDC estimated in 2015 that at least 72,000 U.S. patients die of HAIs in a nonpandemic year, which represents an improvement over the 99,000 deaths figure that has been cited frequently since it was reported in 2007.4,5 Both of those estimates were likely exceeded in 2020, when 375,000 Americans died of COVID-19.6 We know from the new CDC report that some incalculable share of them had an HAI that worsened their chances of survival or killed them outright. Attributable mortality is a gray area in cases of coinfection. In addition, it is not clear how many of the infections occurred among COVID-19 patients directly or to what degree the conditions of the pandemic generally contributed to the substantial increase in HAIs and excess mortality.

“We don’t have the data to correlate that one-to-one,” Srinivasan says. “So, we don’t know how many of these HAIs occurred in patients who had COVID. We do know that, certainly, these increases correspond to parts of the country at times when they were particularly hard-hit by COVID. There are some state-level metrics in the report that I think certainly suggests there is no question that COVID was a major driver of these HAIs.”

CLABSIs began to fall sharply several years ago when a checklist for careful aseptic insertion of central lines was widely adopted. It’s not hard to imagine that this highly successful protocol — under which anyone could stop the line if they saw an error — was an early casualty in the chaos of a pandemic.

“Another contributing factor was some of the things we had to do in the crisis, when there was no PPE (personal protective equipment) basically,” says Pettis, director of infection prevention at University of Rochester (NY) Medicine. “People got very creative, and one example was putting patient lines in outside the room. So, there are pictures of lines dragging along the floor. Because we didn’t have the necessary PPE, staff were probably not going in the patient’s room as often as they would normally do to check on the lines. Another thing is because these patients were so sick, lines were left in longer and that probably contributed to [infections].”

Another example of compromised practice, described by Hayden, was breaking a cardinal principle of contact isolation by wearing the same gowns from room to room out of necessity.

“We are trained to take off the gloves and remove the gown before you leave the room. You discard them, clean your hands and then move to next room,” Hayden says. “We were wearing the same gowns from room to room on the COVID unit unless a patient had a multidrug-resistant organism. But we had to wear those same gowns because we had shortages. If we were changing gowns the way we were pre-pandemic, we would have run out. That remained a challenge.”

When the hospital was able to reestablish proper infection control practices, HAIs started going down, she adds. Rush saw HAI increases early as some of the first COVID-19 cases hit Chicago, she says, but rates began falling early in the summer and currently, the hospital is not swamped with the Delta variant like some facilities.

“We are definitely seeing an uptick in our positive COVID PCR (polymerase chain reaction) tests, from 3% very early in the summer to almost 10% now,” Hayden said. “But the number of COVID patients we have in the hospital is still in the 20s, which is a pretty low number for us. During our first surge we had some 200 COVID patients in the hospital.”

Recipe for Disaster

With no vaccine nor definitive treatment as the first pandemic waves hit, healthcare settings were overwhelmed by incoming patients. Complicating the PPE shortages were confusing, seemingly constantly changing infection control guidelines as public health officials grappled with the rapid spread of SARS-CoV-2. The U.S. response also was delayed initially by inaccurate COVID-19 test kits created by the CDC. But the patients came on in droves.

“We had an unbelievable surge in census, and a lot of it was COVID-related,” Pettis says. “At my facility, at the highest point during our second surge, more than a third of our patients were COVID patients. That was some 140 patients [who] had COVID [in addition] to the census in general. We are licensed at 280 beds — and this happened all over the county — at the height [of the pandemic], we were up around 340 to 350 patients.”

As a result, the hospital had to turn an auditorium into a patient care area, “which took weeks to get all the necessary oxygen requirements and so on,” she adds.

“The increased census was amazing — you had the ‘worried well’ coming into your emergency department as well as the COVID patients,” Pettis says. “So, you are at increased census, decreased space, and we had a lack of supplies like PPE, gowns, disinfectants, testing materials. We had decreased staffing with a lot of staff members out with COVID and on quarantine. It was just a recipe for disaster.”

The study found that two other types of HAIs remained steady or declined during COVID-19. These included surgical-site infections, which dropped in national figures as fewer elective surgeries were performed. More surprisingly, rates of Clostridioides difficile went down or stayed about even, “possibly due to the greater attention on hand hygiene, environmental cleaning, patient isolation, and use of PPE during the pandemic,” the CDC reported.

“I honestly can’t support that, because our hand hygiene was worse,” Pettis says, noting that C. diff increased at her facility. “There were so many things going on, it’s hard to pinpoint. You can only do so many things well at one time.”

The national steady state for C. diff may be attributed in part to the decline in antibiotic use in the community in 2020, Srinivasan says.

“There were roughly 10 million fewer prescriptions for outpatient antibiotics,” he says. “As we speculate in the paper, it is possible that they could have played a role in reducing C. diff, even in hospitals. It’s possible that more people came to the hospital with a healthier microbiome and perhaps that protected them from C. diff while there.”


  1. Centers for Disease Control and Prevention. About Project Firstline. Updated July 20, 2021.
  2. Weiner-Lastinger LM, Pattabiraman V, Konnor RY, et al. The impact of coronavirus disease 2019 (COVID-19) on healthcare-associated infections in 2020: A summary of data reported to the National Healthcare Safety Network. Infect Control Hosp Epidemiol 2021; Sep 3:1-14.
  3. American Nurses Association. ANA urges US Department of Health and Human Services to declare nurse staffing shortage a national crisis. Published Sept. 1, 2021.
  4. Centers for Disease Control and Prevention. Healthcare-associated infections. Data portal. Updated Aug. 26, 2021.
  5. Klevens RM, Edwards JR, Richards CL Jr, et al. Estimating health care-associated infections and deaths in U.S. hospitals, 2002. Public Health Rep 2007;122:160-166.
  6. Ahmad FB, Cisewski JA, Minino A, Anderson RN. Provisional mortality data — United States, 2020. MMWR Morb Mortal Wkly Rep 2021;70:519-522.