CDC’s findings are a setback for the national effort to encourage hospitals and their clinical laboratories to reduce the number of nosocomial infections and practice better antimicrobial stewardship
Nosocomial infections—also known as hospital-acquired infections—increased during the COVID-19 pandemic. That’s according to a Centers for Disease Control and Prevention (CDC) report that showed increases in several HAIs, including a 14% jump in Methicillin-resistant Staphylococcus aureus (MRSA) from 2020 to 2021.
Clinical laboratory testing is part of a concerted effort in the US to reduce HAIs in acute care hospitals. Additionally, diagnostic testing is vital to antimicrobial stewardship, which is designed to help physicians prescribe to patients only those antibiotics that are appropriate and reduce the chance for antimicrobial resistance (AMR).
So, it’s disturbing to see a setback in both HAIs and antimicrobial stewardship in the wake of the COVID-19 pandemic. Burda called the CDC’s findings a “regression” that “gives new meaning to the term long COVID.”
“I think, without any proof, doctors, nurses, medical technicians, and other clinicians who provide direct patient care regressed in terms of infection control best practices,” wrote healthcare journalist David Burda in his column for 4Sight Health. Clinical laboratories that processed COVID-19 tests during the pandemic can attest to the burnout. (Photo copyright: 4Sight Health.)
CDC Report Reveals Increase in Hospital Acquired Infections
The CDC used standardized infection ratios (SIRs) in its report to detail changes in nosocomial infections. CDC calculates SIRs by dividing the number of observed infections by the number of predicted infections.
“In 2021, the nation and the world continued to experience unprecedented challenges due to the COVID-19 pandemic, which impacted surveillance for and incidence of HAIs,” the CDC explained in its report.
“Compared to pre-pandemic years, hospitals across the nation experienced higher than usual hospitalizations and shortages in healthcare personnel and equipment, which may have resulted in deterioration in multiple patient safety metrics since the beginning of the pandemic,” the CDC added.
In his 4Sight Health article, Burda noted that physicians and other care providers may have “regressed” in their infection control practices due to severe pressures during the COVID-19 pandemic. “I also think the traveling nurse and temporary staff situation had something to do with it. Who has time to learn or follow the infection control policies and protocols at every hospital when you’re moving from one hospital to the next every few weeks?” he added.
The CDC explored HAIs in acute care hospitals, critical access hospitals, inpatient rehabilitation facilities, and long-term acute care hospitals. According to the federal agency’s report, at acute care hospitals, increases in nosocomial infections from 2020 to 2021 include the following:
27 states performed better on at least two types of infection.
30 states performed worse on at least two infection types.
In response to the CDC’s report, the American Hospital Association (AHA) wrote, “In acute care hospitals, the increases seen in some HAIs in 2021 contrast with the success in reducing these infections prior to the pandemic. Despite the challenges of the COVID-19 pandemic, acute care hospitals performed significantly better than the 2015 national baseline in preventing CLABSI, CAUTI, SSIs following colon surgeries, and C. difficile infections.”
The AHA recommended that hospitals “continue to reinforce prevention practices and review HAI surveillance data to identify areas for improvement.”
Dangers of Antimicrobial Resistance
According to CDC data, in the US there are 2.8 million antimicrobial infections each year, and more than 35,000 people die as a result. Dark Daily has reported extensively on the growing danger of antibiotic resistance and outlined the importance of clinical laboratory involvement in hospital antimicrobial stewardship programs.
In “During Pandemic, Clinical Laboratories Should Be Alert for Drug Resistant Infections That Pose High Risk to COVID-19 Patients,” we covered a study conducted at the University of Minnesota which highlighted the continuing need for microbiologists and clinical laboratories to stay alert for COVID-19 patients with drug-resistant infections following a CDC report on 941 confirmed and probable Candida auris cases that had been reported in 13 states, with an additional 1,830 patients that had been found to be colonized with the multidrug-resistant fungus.
The Joint Commission’s expansion of antibiotic stewardship standards, which went into effect on January 1, 2023, could help hospitals reduce nosocomial infections and fight antimicrobial resistance.
Pew conducted research related to the requirements and found “significant room for improvement in adoption and implementation of stewardship practices” in acute care hospitals, Hyun wrote.
Allocate financial resources for staffing and IT to support the antimicrobial stewardship program.
Implement evidence-based guidelines to improve antibiotic use for infections such as urinary tract c. diff. community-acquired pneumonia.
Evaluate the program using evidenced-based criteria.
“New antibiotic stewardship standards should help limit the emergence and spread of new drug-resistant superbugs,” Hyun noted.
Clinical Laboratories Need to Deepen Involvement
By testing patients and quickly reporting results to physicians, hospital-based and independent medical laboratories play an important role in appropriate antibiotic use and elimination of HAIs.
Heightened involvement by microbiologists and other medical laboratory professionals is key to success in light of recent setbacks in elimination of HAIs and antimicrobial resistance due to the SARS-CoV-2 outbreak.
Understanding why some people display no symptoms during a COVID-19 infection could lead to new precision medicine genetic tests medical labs could use to identify people with the mutated gene
New research from the University of California San Francisco (UCSF) may explain why some people could get COVID-19 but never test positive on a clinical laboratory test or develop symptoms despite exposure to the SARS-CoV-2 coronavirus.
According to the UCSF study, variations in a specific gene in a system of genes responsible for regulating the human immune system appears to be the factor in why about 10% of those who become infected with the virus are asymptomatic.
These scientific insights did not receive widespread news coverage but will be of interest to clinical laboratory managers and pathologists who oversee SARS-CoV-2 testing in their labs.
“Some people just don’t have symptoms at all,” Jill Hollenbach, PhD (above), Professor of Neurology atUCSF’s Weill Institute for Neurosciences and lead researcher in the study, told NBC News. “There’s something happening at a really fundamental level in the immune response that is helping those people to just completely wipe out this infection.” Identifying a genetic reason why some people are asymptomatic could lead to new precision medicine clinical laboratory diagnostics for COVID-19. (Photo copyright: Elena Zhukova /University of California San Francisco.)
Fortunate Gene Mutation
According to the Centers for Disease Control and Prevention’s (CDC) COVID Data Tracker, as of April 5, 2023, a total of 104,242,889 COVID-19 cases have been reported in the United States. However, according to a CDC Morbidity and Mortality Weekly Report (MMWR), “Traditional methods of disease surveillance do not capture all COVID-19 cases because some are asymptomatic, not diagnosed, or not reported; therefore, [knowing the true] proportion of the population with SARS-CoV-2 antibodies (i.e., seroprevalence) can improve understanding of population-level incidence of COVID-19.”
She also participates in the COVID-19 HLA and Immunogenetics Consortium, a group of academic researchers, clinical laboratory directors, journal editors, and others who examine the role of HLA variations in determining COVID-19 risk.
Hollenbach’s research identified an HLA variant—known as HLA-B*15:01—that causes the human immune system to react quickly to SARS-CoV-2 and “basically nuke the infection before you even start to have symptoms,” she told NPR.
“It’s definitely luck,” she added. “But, you know, this [gene] mutation is quite common. We estimate that maybe one in 10 people have it. And in people who are asymptomatic, that rises to one in five.”
“HLA variants are among the strongest reported associations with viral infections,” the UCSF study notes. So, the researchers theorized that HLA variations play a role in asymptomatic SARS-CoV-2 infections as well.
To conduct their study, shortly after the SARS-CoV-2 outbreak in 2020, the researchers recruited approximately 30,000 volunteer bone marrow donors from the National Marrow Donor Program to respond to periodic questions via a smartphone app or website. Because HLA variations can determine appropriate matches between donors and recipients, the database includes information about their HLA types.
Each week, respondents were asked to report if they had been tested for SARS-CoV-2. Each day, they were asked to report whether they had symptoms associated with COVID-19. “We were pretty stringent in our definition of asymptomatic,” Hollenbach told NBC News. “[The respondents couldn’t] even have a scratchy throat.”
The researchers eventually identified a cohort of 1,428 people who had tested positive for SARS-CoV-2 between February 2020 and April 30, 2021, before vaccines were widely available. Among these individuals, 136 reported no symptoms for two weeks before or two weeks after a positive test.
“Overall, one in five individuals (20%) who remained asymptomatic after infection carried HLA-B*15:01, compared to 9% among patients reporting symptoms,” the researchers wrote in their medRxiv preprint. Study participants with two copies of the gene were more than eight times more likely to be asymptomatic.
The UCSF researchers also looked at four other HLA variants and found none to be “significantly associated” with lack of symptoms. They confirmed their findings by reproducing the HLA-B association in two additional independent cohorts, one from an earlier study in the UK and the other consisting of San Francisco-area residents.
Individuals in the latter group had either tested positive for SARS-CoV-2 or reported COVID symptoms, and their DNA was analyzed to determine their HLA types.
Pre-existing T-Cell Immunity May Reduce Severity of COVID-19 Infection
The UCSF researchers also attempted to determine how HLA-B*15:01 plays a role in knocking out SARS-CoV-2 infections. They noted previous research that indicated previous exposure to seasonal coronaviruses, such as common cold viruses, could limit the severity of COVID-19. The scientists hypothesized that pre-existing T-cell immunity in HLA-B carriers may be the key.
The COVID-19 HLA and Immunogenetics Consortium website describes how HLA and T-cells work together to ward off disease. HLA “proteins are found on the surface of all cells except red-blood cells.” They’re “like windows into the inner workings of a cell,” and T-cells use the molecules to determine the presence of foreign proteins that are likely signs of infection. “Activated T-cells can kill infected cells, or activate B-cells, which produce antibodies in response to an infection,” the website explains.
Hollenbach’s research team analyzed T-cells from pre-pandemic individuals and observed that in more than half of HLA-B carriers, the T-cells were reactive to a SARS-CoV-2 peptide. The scientists corroborated the hypothesis by examining crystal structures of the HLA-B*15:01 molecule in the presence of coronavirus spike peptides from SARS-CoV-2 and two other human coronaviruses: OC43-CoV and HKU1-CoV.
“Altogether, our results strongly support the hypothesis that HLA-B*15:01 mediates asymptomatic COVID-19 disease via pre-existing T-cell immunity due to previous exposure to HKU1-CoV and OC43-CoV,” the researchers wrote.
Can Genes Prevent COVID-19 Infections?
Meanwhile, researchers at The Rockefeller University in New York City are attempting to go further and see if there are mutations that prevent people from getting infected in the first place. NPR reported that they were seeking participants for a study seeking to identify so-called “superdodger” genes.
Study participants identified as possibly having superdodger genes receive a kit designed to collect saliva samples, after which the researchers sequence the respondents’ genomes. “We hope that in a group of 2,000 to 4,000 people, some people will have genetic mutations that tell us why they’re resistant to infection,” Casanova told NPR.
All this genetic research is in very early stages. But results are promising and may lead to new precision medicine clinical laboratory tests for identifying people who are predisposed to having an asymptomatic response to COVID-19 infection. That in turn could help scientists learn how to moderate or even eliminate symptoms in those unfortunate people who suffer the typical symptoms of the disease.
Dogs’ acute sense of smell can even surpass effectiveness of some clinical laboratory testing in detecting certain diseases in humans When it comes to COVID-19 testing, a recent Italian study demonstrates that trained dogs can detect SARS-CoV-2 with accuracy comparable to rapid molecular tests used in clinical laboratories. The researchers wanted to determine if dogs could be more effective at screening people for COVID-19 at airports, schools, and other high-traffic environments as a way to...
Some healthcare experts point to an “immunity gap” tied to the COVID-19 pandemic, while others suggest alternative theories such as temporary immunodeficiency brought on by COVID-19. In most cases, RSV causes “mild, cold-like symptoms,” but the CDC states it also can cause serious illness, especially for infants, young children, and older adults, leading to emergency room visits, hospitalizations, and an increased demand for clinical laboratory testing.
Pulmonology Advisor reported that the disease typically peaks between December and February, but hospitalizations this season hit their peak in November with numbers far higher than in previous years. In addition to infants and older adults, children between five and 17 years of age were “being hospitalized far in excess of their numbers in previous seasons,” the publication reported.
“Age by itself is a risk factor for more severe disease, meaning that the younger babies are usually the ones that are sick-sick,” pediatrician Asuncion Mejias, MD, PhD (above), a principal investigator with the Center for Vaccines and Immunity at Nationwide Children’s Hospital in Columbus, Ohio, told MarketWatch. Now, she added, “we are also seeing older kids, probably because they were not exposed to RSV the previous season.” Clinical laboratories in hospitals caught the brunt of those RSV inpatient admissions. (Photo copyright: Nationwide Children’s Hospital.)
Did COVID-19 Cause Immunity Gap and Surge in Respiratory Diseases?
CDC data shows that hospitalization rates linked to RSV have steadily declined since hitting their peak of 5.2 per 100,000 people in mid-November. In contrast, hospitalizations linked to the flu peaked in late November and early December at 8.7 per 100,000. Hospitalizations linked to COVID 19—which still exceed those of the other respiratory diseases—reached a plateau of 9.7 per 100,000 in early December, then saw an uptick later that month before declining in the early part of January, 2023, according to the CDC’s Respiratory Virus Hospitalization Surveillance Network (RESP-NET) dashboard.
Surveillance by the CDC’s National Center for Immunization and Respiratory Diseases (NCIRD) revealed a similar pattern: An early peak in weekly numbers for emergency room visits for RSV, followed by a spike for influenza and steadier numbers for COVID-19.
So, why was the RSV outbreak so severe?
Respiratory diseases tend to hit hardest in winter months when people are more likely to gather indoors. Beyond that, some experts have cited social distancing and masking requirements imposed in 2020 and 2021 to limit the spread of COVID 19. These measures, along with school closures, had the side effect of reducing exposure to influenza and RSV.
“It’s what’s being referred to as this ‘immunity gap’ that people have experienced from not having been exposed to our typical respiratory viruses for the last couple of years, combined with reintroduction to indoor gatherings, indoor venues, indoor school, and day care without any of the mitigation measures that we had in place for the last couple of years,” infectious disease expert Kristin Moffitt, MD, of Boston Children’s Hospital told NPR.
Term ‘Immunity Debt’ Sparks Controversy
Other experts have pushed back against the notion that pandemic-related public health measures are largely to blame for the RSV upsurge. Many have objected to the term “immunity debt,” a term Forbes reported on in November.
“Immunity debt is a made-up term that did not exist until last year,” pediatrician Dave Stukus, MD, wrote on Twitter. Stukus is a Professor of Clinical Pediatrics in the Division of Allergy and Immunology at Nationwide Children’s Hospital in Columbus, Ohio.
An article published by Texas Public Radio (TPR) suggests further grounds for skepticism, stating that “the immunity debt theory doesn’t seem to hold up to scrutiny.”
“That was sort of the great unmasking, and everybody got viral illnesses,” she told TPR. “Now we’re past that. We’ve already been through that. We should have some immunity from that and we’re having it again.”
She added that “the hospital is filled with babies who are less than a year of age who have RSV infection. Those children weren’t locked down in 2020.”
The story also noted that not all Americans complied with social distancing or masking guidelines.
“We’re not seeing [less viral illness in] states in the United States that were less strict compared to states that were stricter during mask mandates and things like that. All the states are being impacted,” Barton told TPR.
Perfect Storm of Demand for Clinical Laboratory Testing
Barton suggested that COVID-19 might have compromised people’s immune systems in ways that made them more susceptible to other respiratory diseases. For example, a study published in Nature Immunology, titled, “Immunological Dysfunction Persists for Eight Months following Initial Mild-to-Moderate SARS-CoV-2 Infection,” found that some patients who survived COVID-19 infection developed post-acute long COVID (LC, aka, COVID syndrome) which lasted longer than 12 weeks. And that “patients with LC had highly activated innate immune cells, lacked naive T and naive B cells, and showed elevated expression of type I IFN (IFN-β) and type III IFN (IFN-λ1) that remained persistently high at eight months after infection.”
Experts speaking to The Boston Globe said that multiple factors are likely to blame for the severity and early arrival of the RSV outbreak. Pediatric hospitalist and infectious disease specialist Chadi El Saleeby, MD, of Massachusetts General Hospital, said the severity of some cases might be tied to simultaneous infection with multiple viruses.
Clinical laboratories experienced a perfect storm of infectious disease testing demands during this tripledemic. Hopefully, with the arrival of spring and summer, that demand for lab tests will wane and allow for a return to a normal rate of traditional laboratory testing.
