Clinical laboratory data was key in identifying antibiotic-resistant bacteria responsible for surge in BSIs in hospitals and other healthcare facilities in 2020 and 2021
Clinical laboratory data compiled by the European Antimicrobial Resistance Surveillance Network (EARS-Net) shows that a massive increase in bloodstream infections (BSIs) occurred among EU nations during the first two years of the COVID-19 pandemic. The study found that BSIs caused by certain antimicrobial-resistant (AMR) pathogens, known as superbugs, more than doubled in EU hospitals and healthcare facilities in 2020 and 2021.
Microbiologists and clinical laboratory managers in the US may find it valuable to examine this peer-reviewed study into AMR involved in blood stream infections. It could contain useful insights for diagnosing patients suspected of BSIs in US hospitals where sepsis prevention and antibiotic stewardship programs are major priorities.
“Antimicrobial resistance undermines modern medicine and puts millions of lives at risk,” said Tedros Adhanom Ghebreyesus, PhD, Director-General, World Health Organization, in a WHO press release. “To truly understand the extent of the global threat and mount an effective public health response to [antimicrobial resistance], we must scale up microbiology testing and provide quality-assured data across all countries, not just wealthier ones.” Clinical laboratories in the US may be called upon to submit data on bloodstream infections in this country. (Photo copyright: WHO.)
Clinical Laboratories in EU Report Huge Increase in Carbapenem Resistance
To perform their study, researchers measured the increase in Acinetobacter BSIs between 2020 and 2021, the first two years of the COVID-19 pandemic. Their data originated from qualitative regular antimicrobial susceptibility testing (AST) from blood samples collected by local clinical laboratories in the European Union/European economic area (EU/EEA) nations.
The researchers limited their dataset to Acinetobacter BSI information from the European medical laboratories that documented results of carbapenem susceptibility testing for the bacterial species.
Carbapenems are a class of very powerful antibiotics that are typically used to treat severe bacterial infections. A total of 255 EU/EEA clinical laboratories reported their data for the study. The scientists found that the percentages of Acinetobacter resistance varied considerably between EU/EEA nations, so they separated the countries into three different groups:
Nations in Group One—The Netherlands, Belgium, Austria, Estonia, Denmark, Germany, Iceland, Finland, Luxembourg, Ireland, Norway, Sweden, and Malta—experienced less than 10% resistance to carbapenems.
Nations in Group Two—Slovenia, Czech Republic, and Portugal—had carbapenem resistance between 10% and 50%.
Nations in Group Three—Croatia, Bulgaria, Greece, Cyprus, Italy, Hungary, Lithuania, Latvia, Romania, Poland, Spain, and Slovakia—demonstrated carbapenem resistance equal or greater than 50%.
The study also found that Acinetobacter BSIs rose by 57% and case counts increased by 114% in 2020 and 2021 when compared to 2018 and 2019. The percentage of resistance to carbapenems rose to 66% in 2020 and 2021, up from 48% in 2018 and 2019.
Antimicrobial Resistance Especially High in Hospital Settings
The researchers further arranged the data into three hospital ward types: intensive care unit (ICU), non-ICU, and unknown. The increase in BSIs caused by Acinetobacter species resistant to carbapenems was greater in ICU-admitted individuals (144%) than non-ICU-admitted individuals (41%).
There are more than 50 species of Acinetobacter bacteria and various strains are often resistant to many types of commonly-used antibiotics. Symptoms of an Acinetobacter infection usually appear within 12 days after a person comes into contact with the bacteria. These symptoms may include:
Blood infections,
Urinary tract infections,
Pneumonia, and
Wound infections.
Healthy people have a low risk of contracting an Acinetobacter infection with the highest number of these infections occurring in hospitals and other healthcare settings. Acinetobacter bacteria can survive for a long time on surfaces and equipment, and those working in healthcare or receiving treatment are in the highest risk category.
The prevalence of this type of bacteria increases in relation to the use of medical equipment, such as ventilators and catheters, as well as antibiotic treatments.
WHO Report Validates EARS-Net Research
In December of 2022, the World Health Organization (WHO) issued a Global Antimicrobial Resistance and Use Surveillance System (GLASS) report that revealed the presence of an increasing resistance to antibiotics in some bacterial infections. That report showed high levels (above 50%) of resistance in bacteria that frequently caused bloodstream infections in hospitals, such as Klebsiella pneumonia and Acinetobacter.
The WHO report examined data collected during 2020 from 87 different countries and found that common bacterial infections are becoming increasingly resistant to treatments. Both Klebsiella pneumoniae and Acinetobacter can be life threatening and often require treatment with strong antibiotics, such as carbapenems.
More research is needed to determine the reasons behind increases in Acinetobacter infections as reported in European hospitals and other healthcare settings, and to ascertain the extent to which they are related to hospitalizations and the upsurge in antimicrobial resistance during the COVID-19 pandemic.
Microbiologists and clinical laboratory managers in the US may want to learn more about the fIndings of this European study involving AMR and use those insights to plan accordingly for any future increase in bloodstream infections in this country.
OIG warns that without adequate clinical laboratory testing healthcare organizations could see more deaths and increased spending
Clinical laboratory leaders and pathologists know that lab test volume decreased dramatically during the early months of the COVID-19 pandemic. That was primarily because community lockdowns stopped people from seeing their doctors for the standard range of chronic health conditions, many of which require clinical laboratory tests for diagnosis and chronic disease management.
• 24% reduction in Medicare Part B test volumes in March • 53% in April • 30% in May
The decline of Medicare patients visiting clinical laboratories continued through the balance of 2020. During the first 10 months of the pandemic—March through December 2020—Medicare beneficiaries who pursued lab testing decreased by about 9% compared to the same 10-month period in 2019, according to a news release.
This is a strong indicator that the government’s response to the pandemic had a measurable effect on clinical laboratory testing volume among all age groups, especially among the elderly.
“The cumulative decline in lab test volume across all client labs for [March 9 to April 12] was just over 40%. But in that time, some of our lab customers were hit with a decline of maybe 50% to 60% in test volume,” Kyle Fetter (above), COO, XIFIN, told The Dark Report in 2020. Clinical laboratory testing that originates from a routine patient visit to a doctor—such as blood testing—may have been affected the most, Fetter explained. (Photo copyright: XIFIN.)
Clinical Laboratory Tests Key to Well-being of Patients with Chronic Conditions
The OIG study was limited to Medicare beneficiaries and thus did not provide information about testing fall-off among people who have private health insurance. But in “From Mid-March, Labs Saw Big Drop in Revenue,” Dark Daily’s sister publication The Dark Report reported early in 2020 on a 40% decline in test volumes and the pandemic’s varying effects on clinical labs, anatomic pathology (AP) groups, and AP subspecialties.
The OIG’s Report in Brief on its study recognized that medical laboratory testing is critical to helping healthcare providers manage chronic conditions that affect patients’ well-being and increase their healthcare costs.
“Lab tests are important for beneficiaries with chronic medical conditions, which are associated with hospitalizations, billions of dollars in Medicare costs, and deaths,” the OIG said.
“The information may be useful to stakeholders involved in ensuring that beneficiaries avoid the potential bad outcomes that may result from missing or delaying appropriate care,” the report noted.
Overall, 23.7 million Medicare beneficiaries received medical laboratory tests during the first 10 months of the pandemic, down 2.4 million from 26.1 million in 2019, the OIG reported.
Overall Medicare lab test volume and spending also declined during the reported period:
Part B clinical laboratory tests for Medicare beneficiaries decreased 15% from 419.9 million tests in 2019 to 358.4 million tests in the first 10 months of the pandemic.
Medicare spending for these tests decreased 16% from $6.6 billion in 2019 to $5.5 billion during the first 10 months of the pandemic.
“OIG’s audit of Part B clinical laboratory tests, reimbursed under the Clinical Laboratory Fee Schedule (CLFS) is a useful benchmark for how Medicare beneficiaries received fewer lab tests during the pandemic, especially during the early months,” said Robert Michel, Editor-in-Chief of Dark Daily and The Dark Report.
Medical Laboratory Tests That Were Down Most During COVID-19
The following 10 clinical laboratory tests experienced a 10% or more decline in Medicare beneficiaries seeking them during the pandemic period as compared to pre-pandemic, according to the OIG report:
Comprehensive urine culture test fell 16% to three million Medicare patients.
Uric acid level blood down 13% to 1.9 million Medicare beneficiaries.
Evaluation of antimicrobial drug decreased 17% to 1.74 million Medicare patients.
Folic acid level down 12% to 1.73 million Medicare beneficiaries.
Urinalysis manual test plunged 28% to 1.4 million Medicare patients.
Beyond Medicare, Clinical Laboratory Test Volume Dropped 40%
OIG was not the only organization to analyze medical laboratory testing volume during the pandemic’s early phase.
The Dark Report correlated data tracked by XIFIN, a San Diego-based health information technology (HIT) company providing revenue cycle management services to clinical laboratories and pathology groups. XIFIN’s collected data showed a steep drop in routine test volume as COVID-19 testing ramped up.
“Starting in the third week of March, we saw medical laboratories suffer a sharp drop in routine testing. But at about the same time, many labs began to offset those revenue losses with testing for the novel coronavirus,” Kyle Fetter, XIFIN’s then Executive Vice President and General Manager of Diagnostic Services told The Dark Report in 2020. Fetter is now XIFIN’S Chief Operating Officer.
“Over four weeks beginning March 9, we saw a cumulative drop of over 40% in test volume from all of our lab clients,” he added.
According to XIFIN’s data, lab specialty organizations experienced the following drop in routine testing during the period March 9 to April 16, 2020:
58% at clinical laboratories.
61% at hospital outreach laboratories.
52% at molecular and genetic testing laboratories.
44% at anatomic pathology (AP) groups.
70% to 80% at AP dermatology and other AP subspecialties.
Many medical laboratories are still recovering from the COVID-19 pandemic’s effects on testing volume.
Notably, the OIG’s report acknowledges the importance of adequate clinical laboratory testing and declares that—without these essential lab tests to manage some healthcare conditions—the healthcare industry could see increased morbidity, deaths, and Medicare spending.
Experts advise clinical laboratories to prepare now for a marked increase in demand for RSV, COVID-19, and influenza testing
Are the COVID-19 lockdowns responsible for the increase in cases of respiratory syncytial virus (RSV)? Some physicians believe that may be the case and it has hospitals, clinical laboratories, and pathology groups scrambling to prepare for a possible “tripledemic,” according to UC Davis Health.
The addition of RSV as we move into what is predicted to be a bad influenza (flu) season has prompted the Centers for Disease Control and Prevention (CDC) to issue a Health Alert Network (HAN) advisory which states, “Co-circulation of respiratory syncytial virus (RSV), influenza viruses, SARS-CoV-2, and others could place stress on healthcare systems this fall and winter.” This is especially true of clinical laboratories that still struggle to keep pace with demand for COVID-19 testing.
“COVID cases are expected to rise during the winter. This will be occurring at the same time we expect to see influenza rates increase while we are already seeing an early start to RSV season,” said Dean Blumberg, MD (above), chief of pediatric infectious diseases at UC Davis Children’s Hospital. “With all three viruses on the rise, we are worried about an increase in the rates of viral infection that may lead to an increase in hospitalizations.” Clinical laboratories should prepare for a marked increase in demand for RSV testing, as well as COVID-19 and influenza. (Photo copyright: UC Davis Health.)
Masking, Lockdowns, and Social Distancing Could be Responsible
Every winter in the United States, outbreaks of the flu and RSV occur. However, this year the RSV outbreak appears to be more serious. The CDC warns that “surveillance has shown an increase in RSV detections and RSV-associated emergency department visits and hospitalizations in multiple US regions, with some regions nearing seasonal peak levels.”
The current spread of RSV infections taking place in the US varies from prior outbreaks in notable ways:
Incidents are happening in the fall, whereas RSV outbreaks usually peak starting in late December.
Older children as well as infants are being hospitalized.
Current cases appear to be more severe.
Episodes are rising at a time when pediatric hospitalizations are already higher than usual due to other illnesses like COVID-19, influenza, and biennial enteroviruses.
Some experts believe that masking and social distancing due to the COVID-19 pandemic resulted in a respite of RSV infections in 2020. However, cases intensified in 2021, most likely a result of fewer young children being exposed to RSV during the previous year.
Most children typically have had at least one RSV infection before the age of two and the illness becomes less troublesome as children get older.
“The theory is that everyone’s now back together and this is a rebound phenomenon,” Jeffrey Kline, MD, Associate Chair of Research, Wayne State University School of Medicine in Detroit, told MarketWatch. “If we think about the relative increase—ninefold increase—that’s not nothing, especially in the pediatric [emergency departments]. Holy mackerel.”
Most RSV Infected Children Require Hospitalization
Kline is in charge of a surveillance network that aggregates information regarding incidents of viral infections from 70 US hospitals. The data shows that more children are being hospitalized with COVID-19 than with RSV, but that 5% of children are testing positive for both illnesses. About 60% of children in that group require hospitalization.
According to the CDC, individuals with RSV will typically begin to experience symptoms within four to six days after getting infected. Symptoms of RSV, which tend to appear in stages, include:
Runny nose
Decrease in appetite
Coughing
Sneezing
Fever
Wheezing
“RSV causes a mild cold illness in most people. But it can be very dangerous for very young children and older adults. And young infants are usually the most at risk of hospitalizations in what physicians would call their first RSV season,” said Andrea Garcia, JD, Vice President, Medicine and Public Health, American Medical Association (AMA), in a November 2 AMA update on the current flu season.
“In a pre-pandemic year,” she added, “we would see 1% to 2% of babies younger than six months with an RSV infection maybe needing to be hospitalized. And virtually all children have gotten an RSV infection by the time they’re two-years-old.”
Infants are at a much higher risk of experiencing severe disease due to RSV because their immune systems are not fully developed, and those under six months old are unable to breathe through their mouths if they are congested.
Mejias is studying whether prior exposure to COVID-19 alters how a baby’s immune system reacts to RSV, and if it may lead to more severe illness in those babies.
“That is something to work on and understand,” she said.
Comorbidities and Compromised Immune Systems also a Factor
Older adults and adults with weakened immune systems are predisposed to RSV infections, but there are things people can do to mitigate their chances of becoming ill from RSV.
“[RSV] is spread through contact with droplets from the nose and throat of infected people when they cough or sneeze. It can also be spread through respiratory secretions on surfaces,” said Garcia in the AMA update. “So, it’s a really good idea to clean and disinfect surfaces, especially in areas where young children are constantly touching things. Handwashing is always important. And if you are sick, please stay home.”
She added, “Premature infants, children with certain medical conditions, are also eligible to take a monthly monoclonal antibody treatment during RSV season, and that can help them stay out of the hospital.”
Most RSV infections typically go away on their own within a week or two. But such infections can lead to more severe illnesses, such as bronchiolitis and pneumonia. The more serious cases may require hospitalization with additional oxygen, IV fluids, and even intubation with mechanical ventilation. In most cases, hospitalization only lasts a few days, according to the CDC.
Be Prepared for a Tripledemic
“Health officials are concerned that this could be a sign of what’s to come,” stated Garcia in the AMA update. “A difficult winter, with multiple respiratory viruses circulating.”
For clinical laboratory managers, the early arrival of RSV cases at the front end of this influenza season provides an opportunity to position their labs to better meet the demand for RSV testing. They should also advise their client physicians that there may be a surge of respiratory illnesses during this flu season.
Encouraging patients—even children—to be more directly involved in their own medical care may reduce the burden on healthcare workers and might even help those clinical laboratories struggling to hire enough phlebotomists to collect specimens
Researchers at Emory University School of Medicine have concluded a study which found that school-aged children can successfully use a nasal swab to obtain their own SARS-CoV-2 test specimens. This may come as a surprise to hospital and clinical laboratory personnel who have performed nasal swabbing for COVID-19 tests. Some people, adults included, find the procedure so uncomfortable it brings tears.
And yet, after being shown a 90-second how-to video and given a handout with written instructions and pictures, 197 Atlanta children who had COVID-19 symptoms between July and August of 2021 performed their own self-swabbing. A healthcare worker then collected a second swabbed sample. All samples were submitted to a clinical laboratory for PCR analysis.
The Emory study provides another example of how the healthcare system is engaging patients to be directly involved in their own medical care. Results of the study could positively impact clinical laboratories facing a shortage of personnel, as well as schools where children have to take repeated COVID-19 tests with the assistance of trained professionals.
In a study with 197 school-age children, researchers at Emory University School of Medicine found that children could self-swab themselves for COVID-19 testing after watching a 90-second instructional video. Clinical laboratory leaders who are short on personnel may find these results intriguing. (Photo copyright: Emory University.)
How Did the Children Do?
The self-collected swabs and those collected by a healthcare worker agreed 97.8% of the time for a positive result and 98.1% of the time for a negative result. The analysis showed that both collection methods identified the 44% of symptomatic kids who were positive for COVID-19.
“Seeing how closely the results line up between the children and trained healthcare workers is a strong indicator that these age groups are fully capable of swabbing themselves if given proper instruction,” said Jesse Waggoner, MD, an Assistant Professor of Infectious Diseases with the Emory University School of Medicine and one of the lead authors on the study, in an Emory University press release.
A higher percentage of children age eight and under needed assistance, such as more instruction before correctly completing self-collection—21.8% compared to 6.1% for children older—but SARS-CoV-2 detection among the two age groups did not differ.
Does FDA Approve of Self-Swabbing?
The US Food and Drug Administration (FDA) has not authorized COVID-19 tests that include self-swabbing by children under age 14. However, data from the Emory study, published in JAMA, is now available to test manufacturers seeking authorization for pediatric self-collection.
“Pediatric self-swabbing will support expanded testing access and should make it even easier to test school age populations with fewer resources,” said Tim Stenzel, MD, PhD, Director of the Office of In Vitro Diagnostics at the FDA, in the Emory statement. “This study furthers our knowledge of test accuracy with these types of samples and provides test manufacturers with data to support their EUA (Emergency Use Authorization) requests to the FDA.”
Self-swabbing versus Clinical Laboratory Worker
While it has been longstanding medical practice to have healthcare workers collect samples for respiratory tract infection testing, the Emory researchers suggest that allowing children to collect their own COVID-19 samples could be one way to reduce the burden of a shortage of healthcare workers.
The researchers also believe pediatric self-swabbing would expand access to diagnostic tests and make it easier to test school-age populations.
“Every minute of a healthcare worker’s time is at a premium,” said senior study author Wilbur Lam, MD, Professor of Pediatrics and Biomedical Engineering, Emory University and Georgia Tech, in a National Institutes of Health (NIH) press release. “Why not allow a kid to self-swab? It’s a win-win! They would rather do it themselves and it frees up the healthcare worker to do other things,” he added.
In 2020, a Stanford University School of Medicine study published in JAMA showed test samples collected by adults who swabbed their own nasal passages were as accurate as those collected by healthcare workers. This study involved 30 participants who had previously tested positive for COVID-19.
Though the Emory University and Stamford University studies were small, they agreed in their findings which is significant. Clinical laboratory executives and pathologists should expect this trend toward direct-to-consumer and other forms of self-testing to continue, even among young patients.
These findings may be useful to clinical laboratory professionals when physicians want guidance in effective treatments for COVID-19 patients, particularly when there are concerns about a rebound of the infection
Drug interactions are a major concern for physicians and clinical laboratories. That is especially true given the push for nearly universal COVID-19 vaccinations and boosters. Now, a study conducted in Denmark may show that the use of Paxlovid as an antiviral drug to treat early SARS-CoV-2 infection could trigger drug-drug interactions (DDI) in some patients.
For clinical laboratory managers, insights into the issues associated with Paxlovid may be useful in helping client physicians diagnose their patients and anticipate possible negative drug reactions where other anti-viral drugs are involved.
Also of interest to medical laboratory leaders is the fact that the federal Centers for Disease Control and Prevention (CDC) in May released a Health Alert Network (HAN) Health Advisory about the potential for COVID-19 rebound after Paxlovid treatment.
COVID-19 Rebound, according to the CDC, “has been reported to occur between two and eight days after initial recovery and is characterized by a recurrence of COVID-19 symptoms or a new positive viral test after having tested negative.”
In an article she penned for STAT, Joan Susan Bregstein, MD (above), a pediatric emergency medicine physician and professor of pediatrics at Columbia University Irving Medical Center in New York, wrote, “Is Paxlovid worth it? The CDC advisory states in black, bold, and no uncertain terms that, despite the risk of rebound COVID, ‘Paxlovid continues to be recommended for early-stage treatment of mild to moderate COVID-19 among persons at high risk for progression to severe disease.’ But the definition of ‘high risk’ in this situation has been a moving target since the first days of COVID-19.” Clinical laboratory leaders can attest to the accuracy of that statement. (Photo copyright: Columbia University.)
Do Anti-Viral Drugs Interact with Other Medications?
Paxlovid is the retail name for a combination of two anti-viral drugs: nirmatrelvir and ritonavir. The medication for COVID-19 was developed by American pharmaceutical company Pfizer (NYSE:PFE) and received Emergency Use Authorization from the US Food and Drug Administration in August of this year.
The drug is taken orally for five days by people who test positive for the SARS-CoV-2 coronavirus to head off disease progression as well as serious illness, according to the CDC advisory.
But a “sizeable proportion” of elderly people are on medications that could interact with Paxlovid, Reuters reported.
“Two oral antiviral drugs—nirmatrelvir/ritonavir (NMV/r) and molnupiravir—have been approved for early outpatient treatment of COVID-19 to prevent severe disease. Ritonavir, contained in NMV/r is known to have significant DDI with several drugs frequently used by the elderly. This communication puts the problem with DDI with oral antiviral COVID-19 treatment into perspective,” the study authors wrote.
Their analysis of prescription data from Denmark residents found “extensive use of drugs likely to interact with NMV/r” as follows:
Anticoagulants (blood thinners): used by 20% of people over age 65 and by 30% of people over 80.
Statins (cholesterol-lowering medications): taken by 15% to 18% of people over 65.
Analgesics (for pain), calcium channel blockers (used to decrease blood pressure in patients with hypertension), or digoxin (used to treat heart conditions): taken by 20% of those studied.
In their paper, the researchers offered guidance to physicians. “Before prescribing NMV/r, the patient’s full medical history, including herbals and over-the-counter and recreational drugs, must be known and co-treatment carefully managed by the treating physician or by a specialist to avoid detrimental effects.”
However, one infectious disease specialist told Scientific American it may just take the elderly who were taking Paxlovid more time to completely get over COVID-19.
“Being of an elderly age and then having other risk factors—like diabetes, heart disease, kidney disease, or some sort of cancer—does put you at higher risk of rebound,” Aditya Shah, MBBS, Mayo Clinic Infectious Disease Physician and Researcher, told Scientific American.
That study’s researchers retrospectively reviewed 92 million electronic health records (EHR) from US patients. They found most people (11,270) had been treated with Paxlovid. However, 2,374 patients took molnupiravir, which also was granted EUA status by the FDA and is marketed as Lagevrio.
That COVID-19-rebound study found:
After nirmatrelvir/ritonavir (Paxlovid) treatment: 3.53% had rebound infections, 2.3% with rebound symptoms, and .44% were hospitalized.
After molnupiravir (Lagevrio) treatment: 5.86% had rebound infections, 3.75% with rebound symptoms, and .84% were hospitalized.
“Patients who took molnupiravir were significantly older and had more comorbidities than those who took Paxlovid,” the researchers wrote. “Results further suggest that rebound was not unique to Paxlovid and may be associated with persistent viral infection in some patients treated with either of these two antivirals. There has been more attention to COVID-19 rebound following Paxlovid treatment than molnupiravir, which may be attributable to more people being treated with Paxlovid,” they concluded.
Clinical Laboratories Can Guide Doctors
In an article she penned for STAT, titled, “Paxlovid Rebound Happens, Though Why and to Whom Are Still a Mystery,” Joan Susan Bregstein, MD, a pediatric emergency medicine physician and professor of pediatrics at Columbia University Irving Medical Center in New York, wrote of COVID-19 rebound, “My emergency medicine physician colleagues are seeing tons of it. Although people tend to think of medical care as something that is certain, it is actually a real-time experiment. Paxlovid, like a lot of COVID-19 care, is a reminder of this.”
Similarly, Mayo Clinic’s Shah acknowledged difficulty in identifying a COVID-19 rebound case. “You need real documentation of three tests—a positive, a negative, a positive—and clear documentation of symptoms—all symptoms gone, symptoms come back,” Shah told Scientific American.
Thus, clinical laboratories play a vital role in diagnosing and treating COVID-19 rebound patients, because that is what clinical labs do: test, document, and report. And as the study of the Danish population pointed out, doctors need guidance as they prescribe oral antivirals to COVID-19 patients who are on other drugs and at possible risk of drug-drug interactions.
