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Researchers Use Whole Genome Sequencing to Make Surprising Discovery about Hospital-Acquired C. Diff Infections

By analyzing strains of the bacterium from a hospital ICU, the scientists learned that most infections were triggered within patients, not from cross-transmission

Tracking the source of Hospital-acquired infections (HAI) has long been centered around the assumption that most HAIs originate from cross-transmission within the hospital or healthcare setting. And prevention measures are costly for hospitals and medical laboratories. However, new research puts a surprising new angle on a different source for some proportion of these infections.

The study suggests that most infections caused by Clostridioides difficile (C. Diff), the bacterium most responsible for HAIs, arise not from cross-transmission in the hospital, but within patients who already carry the bacterium.

The research team, led by immunologist Evan Snitkin, PhD, and microbiologist Vincent Young, MD, PhD, both from the University of Michigan (UM), and epidemiologist Mary Hayden, MD, of Rush University Medical Center in Chicago, analyzed fecal samples from more than 1,100 patients in Rush Medical Center’s intensive care unit over a nine-month period.

A researcher performed whole genome sequencing on 425 strains of the bacterium isolated from the samples and found “very little evidence that the strains of C. diff from one patient to the next were the same, which would imply in-hospital acquisition,” according to a UM news story.

“In fact, there were only six genomically supported transmissions over the study period. Instead, people who were already colonized were at greater risk of transitioning to infection,” UM stated.

Arianna Miles-Jay, PhD, a postdoctoral fellow in The Snitkin Lab at the University of Michigan and Manager of the Genomic Analysis Unit at the Michigan Department of Health and Human Services, performed the genomic sequencing. “By systematically culturing every patient, we thought we could understand how transmission was happening. The surprise was that, based on the genomics, there was very little transmission,” she said in the UM news story.

The researchers published their findings in the journal Nature Medicine titled, “Longitudinal Genomic Surveillance of Carriage and Transmission of Clostridioides Difficile in an Intensive Care Unit.”

Evan Snitkin, PhD

“Something happened to these patients that we still don’t understand to trigger the transition from C. diff hanging out in the gut to the organism causing diarrhea and the other complications resulting from infection,” said Evan Snitkin, PhD (above), Associate Professor of Microbiology and Immunology, and Associate Professor of Internal Medicine, Division of Infectious Diseases at University of Michigan, in a UM news story. Medical laboratories involved in hospital-acquired infection prevention understand the importance of this research and its effect on patient safety. (Photo copyright: University of Michigan.)

Only a Fraction of HAIs Are Through Cross-Transmission

In the study abstract, the researchers wrote that “despite enhanced infection prevention efforts, Clostridioides difficile remains the leading cause of healthcare-associated infections in the United States.”

Citing data from the US Centers for Disease Control and Prevention (CDC), HealthDay reported that “nearly half a million C. diff infections occur in the United States each year. Between 13,000 and 16,000 people die from the bacterium, which causes watery diarrhea and inflammation of the colon. Many of these infections and deaths have been blamed on transmission between hospitalized patients.”

The new study, however, notes that 9.3% of the patients admitted to the ICU carried toxigenic (produces toxins) C. diff, but only 1% acquired it via cross-transmission. The carriers, the study authors wrote, “posed minimal risk to others,” but were 24 times more likely to develop a C. diff infection than non-carriers.

“Our findings suggest that measures in place in the ICU at the time of the study—high rates of compliance with hand hygiene among healthcare personnel, routine environmental disinfection with an agent active against C. diff, and single patient rooms —were effective in preventing C. diff transmission,” Snitkin told HealthDay. “This indicates that to make further progress in protecting patients from developing C. diff infections will require improving our understanding of the triggers that lead patients asymptomatically carrying C. diff to transition to having infections.”

Recognizing Risk Factors

Despite the finding that infections were largely triggered within the patients, the researchers still emphasized the importance of taking measures to prevent hospital-acquired infections.

“In fact, the measures in place in the Rush ICU at the time of the study—high rates of compliance with hand hygiene among healthcare personnel, routine environmental disinfection with an agent active against C. diff, and single patient rooms—were likely responsible for the low transmission rate,” the UM news story noted.

One expert not involved with the study suggested that hospitals’ use of antibiotics may be a factor in causing C. diff carriers to develop infections.

“These findings suggest that while we should continue our current infection prevention strategies, attention should also be given to identifying the individuals who are asymptomatic carriers and finding ways to reduce their risk of developing an infection, like carefully optimizing antibiotic usage and recognizing other risk factors,” Hannah Newman, Senior Director of Infection Prevention at Lenox Hill Hospital in New York City, told HealthDay.

Snitkin, however, told HealthDay that other factors are likely at play. “There is support for antibiotic disruption of the microbiota being one type of trigger event, but there is certainly more to it than that, as not every patient who carries C. diff and receives antibiotics will develop an infection.”

Another expert not involved with the study told HealthDay that “many patients are already colonized,” especially older ones or those who have been previously hospitalized.

“A lot of their normal flora in their GI tract can be altered either through surgery or antibiotics or some other mechanism, and then symptoms occur, and that’s when they are treated with antibiotics,” said Donna Armellino, RN, Senior VP of Infection Prevention at Northwell Health in Manhasset, New York.

Whatever is taking place, hospital-acquired infections kill thousands of people every years. It’s on the federal Centers for Medicare and Medicaid Services’ (CMS) “never event” list of hospital-acquired conditions (HOC) that should never happen to hospital patients. This affects reimbursement to hospitals for treatment of infections under Medicare’s Hospital-Acquired Condition Reduction Program

This research also demonstrates the value of faster, cheaper, more accurate gene sequencing for researching life-threatening conditions. Microbiologists, Clinical laboratory scientists, and pathologists will want monitor further developments involving these findings as researchers from University of Michigan and Rush University Medical Center continue to learn more about the source of C. diff infections.

—Stephen Beale

Related Information:

The Surprising Origin of a Deadly Hospital Infection

Patient-to-Patient Transmission Not to Blame for Most C. Difficile Infections in Hospitals

Longitudinal Genomic Surveillance of Carriage and Transmission of Clostridioides difficile in an Intensive Care Unit

Millions of COVID-19 At-Home Tests Set to Flood Market as HHS Asks 12 Test Manufacturers to Produce 200 Million Tests

Free at home clinical-laboratory testing for COVID-19 has been provided in the past, but this time the federal government wants to manufacture as many tests as possible in the US

Pathologists and clinical laboratory managers may be interested to learn that the US market is about to be flooded with millions of at-home COVID-19 rapid tests. The federal government has contracted with 12 US-based test manufacturers to produce 200 million at-home self-tests aimed at detecting “currently circulating COVID-19 variants” through the end of this year, according to a US Department of Health and Human Services (HHS) news release.

Through the Administration for Strategic Preparedness and Response (ASPR), HHS is investing $600 million to fund the self-tests, which are available for delivery through a reopening of the COVID.Gov/Test website.

Federal officials want to head off “supply chain issues” that developed in the past with reliance on tests made overseas, and to address a possible COVID-19 surge during the fall and winter, the Associated Press (AP) reported.

In fact, 500 million tests have already been distributed through US government channels to long-term care facilities, schools, and low-income senior housing.

Dawn O’Connell, JD

“Manufacturing COVID-19 tests in the United States strengthens our preparedness for the upcoming fall and winter seasons, reduces our reliance on other countries, and provides good jobs to hardworking Americans,” said Assistant Secretary for Preparedness and Response Dawn O’Connell, JD (above), in an HHS news release. “ASPR’s investments in these domestic manufacturers will increase availability of tests in the future.” With the federal government preparing for what it expects to be a surge in demand for COVID-19 testing, clinical laboratories may want to track the CDC’s weekly reports on the number of positive COVID-19 cases as this year’s influenza season progresses. (Photo copyright: Administration for Strategic Preparedness and Response.)

In Vitro Diagnostics Test Makers Get Government Gigs

This is not the first time federal officials sent out free COVID-19 tests to consumers. According to the AP, more than 755 million tests went out to US households in previous efforts to fight the spread of infections. But unlike those tests, these tests will be manufactured entirely within the US.

The government’s latest wave of free tests is meant to “complement ASPR’s ongoing distribution of free COVID-19 tests to long-term care facilities, low-income senior housing, uninsured individuals, and underserved communities, with 500 million tests provided to date through these channels,” the HHS news release noted.  

Both large and lesser-known in vitro diagnostics (IVD) manufacturers were selected by the federal government to receive funding. They include:

HHS advises people to take the test at the first sign of symptoms (fever, sore throat, runny nose, others), after coming into contact someone who has COVID-19, or prior to gathering with a group, as a preventative to spread of the coronavirus.

Tracking New BA.2.86 COVID Variant

Currently, the federal Centers for Disease Control and Prevention (CDC) is tracking BA.2.86 (aka, Pirola), a new SARS-CoV-2 variant.

According to CDC’s latest Respiratory Viruses Update:

  • Reporting laboratories say existing antibodies work against the BA.2.86 variant.
  • The variant does not appear to be linked in the US with increasing infections or hospitalizations.
  • It is “unclear how easily BA.2.86 spreads” relative to other variants.
  • BA.2.86 has been detected in nine states: Colorado, Delaware, Michigan, Ohio, Pennsylvania, Virginia, Washington, and in wastewater in New York and Ohio, as well as in other countries. 

For week ending Sept. 23, the CDC reported the following statistics compared to the prior week:

  • 19,079 COVID-19 hospitalizations, down 3.1%.
  • Total hospitalizations: 6.3 million.
  • 2.7% of total deaths were due to COVID-19, up 8%.
  • COVID-19 test positivity rate was 11.6%, down 1.1%.
  • 1.8% of emergency department visits were diagnosed with COVID-19, down 11.7%.

According to Verywell Health, BA.2.86 carries more than 30 mutations.  

“Even with a lot of mutations, there are a lot of spots in the virus that can be recognized by our immune system, and there are many shared mutations as well. There will be some protection from new vaccine booster as well as prior infections,” Rajendram Rajnarayanan, PhD, Assistant Dean of Research and Associate Professor, Basic Sciences, Arkansas State University, told Verywell Health.

During an online media briefing conducted by the World Health Organization (WHO), Maria Van Kerkhove, PhD, COVID-19 Technical Lead at WHO, said that the variant could be classified by WHO as a “variant of concern” in the event of widespread circulation. 

COVID-19, an Endemic Disease?

It’s worth noting that the common cold, influenza, SARS, and SARS-CoV-2 are all in the coronavirus family, and thus closely related with similar symptoms. It would not be a surprise that SARS-CoV-2 joins those other viruses as an endemic virus with a similar yearly cycle of infection rates.

If that happens, and no surge in infections appears that would motivate orders for the new COVID-19 at-home tests, the government may find itself with a lot of unused tests at the end of the year. The US Food and Drug Administration (FDA) is aware of this possibility and provides a website where people can check to see if their test has an extended expiration date.

Plus, folks who are tired of the pandemic may not respond at all to the government’s insistence to prepare for possible surges in infection rates.

“Whether or not people are done with it, we know the virus is there, we know that it’s circulating. We know, if past is prologue, it’ll circulate to a higher degree and spread, and cases will go up in the fall and winter seasons,” said Assistant Secretary for Preparedness and Response Dawn O’Connell, JD, in the HHS new release. “Anticipating that that would be true again, or something similar, we want to make sure the American people have these tools.”

Clinical laboratories may want to prepare as well. Many people are not comfortable with at-home self-testing and prefer to have their local medical labs perform the tests.

—Donna Marie Pocius

Related Information:

Biden-Harris Administration Awards $600 Million to Bolster US Manufacturing of COVID-19 Tests and Announces the Re-Opening of COVIDTests.gov

Biden Administration Announces $600 Million to Produce COVID-19 Tests and Will Reopen Website to Order Them

Free COVID Testing Will Fade with US Health Emergency in May

CDC’s COVID-19 Variant Update

CDC’s COVID-19 Data Tracker

Why B.2.86 Stands Out from Other COVID-19 Variants

Healthcare Experts Say Consumers Are Ready for Self-Test Flu Kits, But Are Physicians and Clinical Laboratories Ready to Let That Cat Out of the Bag?     

Clinical laboratories could play a key role in helping users collect their samples correctly, interpret results, and transfer flu test data to their health records

Clinical laboratories may have another opportunity to provide service to their clients and the physicians who treat them. With the success of at-home COVID-19 testing, consumer demand for self-tests is changing and advances in diagnostic technology now make it feasible to make more influenza (flu) tests available for consumers to buy and use at home.

At-home tests for SARS-CoV-2 can be found at pharmacies all across America. But that’s not the case with tests for influenza.

Should self-test flu kits eventually become available and common, clinical laboratories could offer the service of helping consumers understand:

  • that the test was conducted correctly (specimen collection and analysis),
  • that the result is accurate and reproducible, and
  • how to understand the results.

Clinical laboratories also could collect and input the results into their laboratory information system (LIS), then send those results to the patients’ electronic health record (EHR) at their physician’s clinic.

Christina Yen, MD

“Home flu testing would ensure that those who do need and receive antiviral medication for influenza are the ones who need it the most,” and that “we are making our treatment decisions based on data,” infectious disease specialist Christina Yen, MD (above), University of Texas Southwestern Medical Center, told STAT News. At-home flu self-tests could also bring opportunities for clinical laboratories to provide service to healthcare consumers and the physicians who treat them. (Photo copyright: UT Southwestern Medical Center.)

Pros and Cons of Consumers Doing At-home Influenza Testing

According to the federal Centers for Disease Control and Prevention (CDC), COVID-19 and influenza are both upper respiratory illnesses with similar symptoms. So, why don’t we have more at-home flu tests available? Partly because at-home testing is a relatively new phenomenon in modern healthcare.

“It’s really rare, and it’s really new that people are allowed to know about what’s happening inside their body without a physician in the middle,” Harvard epidemiologist Michael Mina, MD, PhD, told STAT News. The article uses the example of at-home pregnancy tests. Despite a prototype for an at-home pregnancy test being created in 1967, it took another decade before an over-the-counter pregnancy test became available to the public.

“The general thinking was, ‘How could a woman possibly know what to do if she found out she was pregnant on her own without a doctor in the room?’ That is a ridiculous concern because women have been doing that for millions of years,” Mina added.

So, why be cautious when it comes to giving patients the option of at-home flu testing?

There are some cons to at-home influenza tests. Average citizens are not clinical laboratory professionals. They might obtain too little sample for an accurate reading or read the results incorrectly. Then, there is the possibility for false-negatives or false-positives.

An at-home test user is not likely to consider the possibility of a false result, however clinicians look at the situation with more nuance. If the patient was still symptomatic or in a high-risk community, the provider could administer a more sensitive medical laboratory test to confirm the previous test results.

There are other concerns about at-home testing as well. Another STAT News article titled, “Growing Use of Home COVID-19 Tests Leaves Health Agencies in the Dark about Unreported Cases,” reported on a superspreading event that health officials did not know about: a Phish concert on Halloween.

“In a Facebook post from mid-November with hundreds of responses, concertgoers compared symptoms and positive test results, many of those from tests taken at home. But those data weren’t added to state public health tallies of COVID’s spread,” STAT News noted.

The larger concern is that samples obtained by at-home self-test users are not submitted for genomic sequencing. This could lead to incomplete data and delay identifying new variants of the coronavirus in communities.

“If nobody’s reporting the tests, are we really getting the information we need?” Atul Grover, MD, PhD, Executive Director of the Association of American Medical Colleges Research and Action Institute, told STAT News. “We have no idea what the true positivity rate is.”

Another barrier to at-home flu testing is that rapid influenza diagnostic testing can be unreliable. In 2009, the rapid influenza tests could only detect the H1N1 influenza virus in a mere 11% of samples, STAT News reported. Because of this, the FDA now requires manufacturers to test their rapid tests against eight different strains that change every year depending upon which strains are prevalent. This could present a problem if individuals use leftover tests from the previous flu season.

Do Pros of At-home Testing Outweigh the Cons?

At-home testing is convenient and makes testing more accessible to patients who may not be able to get to a clinic. Being able to test at home also encourages individuals to take precautions necessary to stop the spread of whichever illness they may have. Given the similarities in symptoms between influenza and COVID-19, people could benefit from having tools at home that correctly identify their illness.

At-home COVID-19 tests are here to stay, and at-home influenza tests may be on the way soon. Clinical laboratories could play an important role in educating the public on the correct handling of these tests.

Ashley Croce

Related Information:

Why Doesn’t the U.S. Have At-Home Flu Tests?

What Is the Difference between Influenza (Flu) and COVID-19?

We Still Don’t Have At-Home Testing for the Flu—But COVID-19 Has Changed the Stakes

Growing Use of Home COVID-19 Tests Leaves Health Agencies in the Dark about Unreported Cases

Healthcare Experts See Links Between COVID-19 and RSV as Tripledemic Pressures Ease on Hospitals and Clinical Laboratories

Some medical experts suggest an ‘immunity gap’ related to COVID-19 mitigation measures, while others point to alternative theories

Surge in fall/winter SARS-CoV-2, influenza (flu), and respiratory syncytial virus (RSV) hospitalizations and ensuing clinical laboratory test referrals—dubbed by some public health experts as a “tripledemic”—appear to have eased in the US, according to stats from the US Centers for Disease Control and Prevention (CDC), Becker’s Hospital Review reported. However, scientists are still left with questions about why the RSV outbreak was so pronounced.

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.

Asuncion Meijas MD, PhD

“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.”

Pediatrician and infectious disease expert Theresa Barton, MD, of UT Health San Antonio noted that there was also a big RSV surge in summer of 2021.

“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.

Stephen Beale

Related Information:

This Year’s RSV Surge: Bigger, Earlier, and Affecting Older Patients than Previous Seasonal Outbreaks

Experts Explain the ‘Perfect Storm’ of Rampant RSV and Flu

Flu, COVID-19 and RSV are All Trending Down for the First Time in Months

COVID, Flu, RSV Declining in Hospitals As ‘Tripledemic’ Threat Fades

COVID-19 May Be to Blame for the Surge in RSV Illness Among Children. Here’s Why.

Is Immunity Debt or Immunity Theft to Blame for Children’s Respiratory Virus Spike?

Don’t Blame ‘Immunity Debt’ If You Get Sick This Winter

Claims of an Immunity Debt in Children Owe Us Evidence

Some are Blaming ‘Immunity Debt’ for the ‘Tripledemic’—But Experts Disagree

Rapid Tests for COVID, RSV and the Flu are Available in Europe. Why Not in the US?

Australia’s Severe Flu Season Could be a Harbinger of Increased Influenza Cases in US and Canada Straining Already Burdened Clinical Laboratories

End of social distancing, masking, and other COVID-19 pandemic mitigations may lead to more severe flu-like infections in northern hemisphere, experts say

Clinical laboratory professionals in the United States and Canada should prepare now for a severe flu season. That is according to infectious disease experts at Johns Hopkin’s Center for Health Security who predict the rise in influenza (flu) cases in Australia signals what will likely be higher than normal numbers of flu-like infections starting this fall in the Northern Hemisphere.

As a Southern Hemisphere nation, Australia experiences winter from June through August. The land down under just concluded its worst flu season in five years. The flu arrived earlier than usual and was severe. Surveillance reports from the Aussie government’s Department of Health and Aged Care noted that influenza-like illness (ILI) peaked in May and June, but that starting in mid-April 2022 the weekly number of flu cases exceeded the five-year average.

If the same increase in flu cases happens here, healthcare systems and clinical laboratories already burdened with continuing COVID-19 testing and increasing demand for monkeypox testing could find the strain unbearable.

Amesh Adalja, MD

Amesh Adalja, MD (above), Infectious Disease Expert and Senior Scholar at the Johns Hopkin’s Center for Health Security, told Prevention that Australia’s flu season is typically a harbinger of what will follow in the US, Canada, and other Northern Hemisphere countries. “The planet has two hemispheres which have opposite respiratory viral seasons,” he said. “Therefore, Australia’s flu season—which is just ending—is often predictive of what will happen in the Northern Hemisphere.” Clinical laboratories in the United States should review their preparations as North America enters its influenza season. (Photo copyright: Johns Hopkins Bloomberg School of Public Health.)

Consequences of Decline in Flu Vaccinations and Social Distancing, Masks

The New York Times noted that in 2017, when Australia suffered through its worst flu season since modern surveillance techniques were adopted, the US experienced a deadly 2017-2018 flu season a half-year later that took an estimated 79,000 lives.

While the number of flu cases in this country is currently low, according to the weekly US Centers for Disease Control and Prevention’s (CDC) “Flu View,” that is expected to change as temperatures cool.

During the height of the COVID-19 pandemic in the US, influenza was nearly nonexistent. Pandemic-mitigation efforts such as masking, social distancing, and quarantining slowed the spread of the annual respiratory illness. But pandemic mitigation efforts are no longer the norm.

“Many have stopped masking,” said Abinash Virk MD, an Infectious Diseases Specialist at Mayo Clinic College of Medicine and Science, in a Mayo Clinic news blog that urged patients to get vaccinated for flu. “For the large part, we will see the re-emergence of influenza in the winter. In comparison, in 2020 winter … there was literally no influenza. But now that has all changed.”

Diminished Immunity Will Lead to More Severe Flu Cases

A CDC report published in July also noted that last winter’s flu season broke from the traditional pattern of arrival of the flu in the fall followed by a peak in cases in February.

During the 2021-22 season, influenza activity began to increase in November and remained elevated until mid-June. It featured two distinct waves, with A(H3N2) viruses predominating for the entire season. But the overall case counts were the lowest in at least 25 years preceding the COVID-19 pandemic.

Thomas Russo, MD, Professor and Chief of Infectious Disease at the University at Buffalo in New York, said the past two mild flu seasons could set the stage for a difficult year in 2022-23.

“Immunity to respiratory viruses, including the flu, wanes over time,” Russo told Prevention. “People have not seen the virus naturally for a couple of years and many individuals don’t get the flu vaccine.” That, he says, raises the risk that people who are unvaccinated against the flu will develop more severe cases if they do happen to get infected.

“People are interacting closely again and there are very few mandates,” he added. “That’s a set-up for increased transmission of influenza and other respiratory viruses.”

Anthony Fauci, MD, Director of the National Institute of Allergy and Infectious Diseases (NIAID), warns the US could see higher than normal rates of influenza while COVID-19 is still circulating widely.

“The Southern Hemisphere has had a pretty bad flu season, and it came on early,” Fauci, told Bloomberg in late August. “Influenza, as we all have experienced over many years, can be a serious disease, particularly when you have a bad season.”

CNN reported that US government modeling predicts flu will peak this year in early December.

CDC Advises Public to Get Flu Vaccine

Because COVID-19 and Influenza have many symptoms in common, such as fever, cough, shortness of breath, fatigue, sore throat, runny nose, headache, and muscle aches, the Mayo Clinic points out on its blog that testing is the only way to discern between the two when symptoms overlap.

According to the CDC, the best way to reduce risk from seasonal flu and its potentially serious complications is to get vaccinated every year. The best time to get vaccinated for the flu is in September and October before the flu starts spreading in communities, the CDC states. However, vaccination after October can still provide protection during the peak of flu season.

Yet, many people fail to get the flu vaccine even though it is recommended for everyone over the age of six months. CNN reported that just 45% of Americans got their flu shots last season. Flu vaccination rates fell for several at-risk groups, including pregnant women and children.

Though flu seasons are often unpredictable, clinical laboratories should prepare now for an influx of influenza test specimens and higher case rates than the past two pandemic-lightened flu seasons. Coupled with COVID-19 and monkeypox testing, already strained supply lines may be disrupted.

—Andrea Downing Peck

Related Information:

Frequently Asked Influenza (Flu) Questions: 2022-2023 Season

Weekly US Influenza Surveillance Report

Australia Just Had a Bad Flu Season. That May Be a Warning for the US

Experts Are Predicting a Bad 2022-2023 Flu Season: How to Prepare Now

Australian Influenza Surveillance Report No 07-Fortnight Ending 03 July 2022

Fauci Warns of a Bad Flu Season Brewing as He Nears Office Exit

Australia’s Tough Flu Season Could Spell Trouble for the US This Winter, Especially with COVID-19 in the Mix

Expect a Different Flu Season: Why You’ll Want to Be Vaccinated for Flu

Influenza Activity and Composition of the 2022–23 Influenza Vaccine—United States, 2021–22 Season

Prevent Seasonal Flu

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