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Clinical Laboratories and Pathology Groups

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Keio University and Broad Institute Researchers Identify 18 Bacterial Strains That Could Help Patients with Gastrointestinal Illnesses

Findings could lead to new therapies and clinical laboratory biomarkers for detecting and defeating antibiotic-resistant bacteria

Once again, new research shows that human gut bacteria (microbiota) may be useful in fighting antibiotic-resistant bacterial infections. The study findings could provide new therapeutics and clinical laboratory biomarkers for diagnosing and treating severe gastrointestinal disorders.

Researchers at Keio University School of Medicine in Tokyo and the Broad Institute of MIT and Harvard have identified a unique combination of 18 bacterial strains that could aid in combatting a particularly nasty bacteria called Enterobacteriaceae, the cause of several intestinal conditions such as inflammatory bowel disease (IBD), according to a news release.

Antibiotic-resistant bacterial infections often appear in patients with chronic intestinal conditions and in those with long-term antibiotic use. Enterobacteriaceae is a large family of gram-negative bacteria that includes more than 30 genera and over 100 species.

“Despite two decades of microbiome research, we are just beginning to understand how to define health-promoting features of the gut microbiome,” said Marie-Madlen Pust, PhD, a computational postdoctoral researcher at the Broad Institute and co-first author of the paper, in the news release.

“Part of the challenge is that each person’s microbiome is unique. This collaborative effort allowed us to functionally characterize the different mechanisms of action these bacteria use to reduce pathogen load and gut inflammation,” she added.

The researchers identified a way to treat patients infected by antibiotic-resistant strains of bacteria that does not involve antibiotics. Should further research validate these early findings, this could be a viable approach to treating patients with this condition.

They published their findings titled, “Commensal Consortia Decolonize Enterobacteriaceae via Ecological Control” in the peer-reviewed, scientific journal Nature.

“Microbiome studies can often consist of analyzing collections of genetic sequences, without understanding what each gene does or why certain microbes are beneficial,” said Ramnik Xavier, MD (above), director of Broad Institute’s immunology program, co-director of the infectious disease and microbiome program, and co-senior author on the study, in a news release. “Trying to uncover that function is the next frontier, and this is a nice first step towards figuring out how microbial metabolites influence health and inflammation.” Clinical laboratories that test for intestinal conditions caused by antibiotic resistance will want to follow the Broad Institute’s research. (Photo copyright: Broad Institute.)

Suppressing Growth of Antibiotic-resistant Bacteria

To perform their research, the scientists isolated about 40 strains of bacteria from the stools of five healthy fecal donors. They then used those stool samples in fecal microbiota transplants to treat mice that had been infected with either Escherichia coli (E. coli) or Klebsiella, both forms of Enterobacteriaceae. The scientists tested different combinations of the 40 strains and identified 18 that suppressed the growth of Enterobacteriaceae.

“Antibiotic-resistant Enterobacteriaceae such as E. coli and Klebsiella bacteria are common in hospitals, where they can proliferate in the gut of patients and cause dangerous systemic infections that are difficult to treat. Some research suggests that Enterobacteriaceae also perpetuates inflammation in the intestine and infection by other microbes,” the Broad Institute news release notes.

The researchers discovered that Klebsiella changed the gene expression in carbohydrate uptake and metabolism in the Klebsiella-infected mice that were treated with the 18 beneficial strains. The gene expression included the downregulating of gluconate kinase and transporter genes, which revealed there is increased competition among gut bacteria for nutrients. 

When combined, these 18 strains alleviated inflammation in the guts of the treated mice by depriving the harmful gut bacteria of carbohydrates. This non-antibiotic approach also prevented harmful bacteria from colonizing in the gut. 

“In partnership with the Broad’s Metabolomics Platform, led by senior director and study co-author Clary Clish, PhD, they analyzed samples from pediatric patients with ulcerative colitis, looking for the presence of alternate gluconate pathway genes of gut microbes and fecal gluconate levels. They found higher levels of gluconate linked to more gluconate-consuming Enterobacteriaceae in samples from pediatric patients with ongoing inflammation, indicated by high levels of the protein calprotectin,” the study authors wrote in Nature.

“Together, the findings suggest that Enterobacteriaceae processes gluconate as a key nutrient and contributes to inflammation in patients. But when a gut microbiome includes the 18 helpful strains, they likely compete with Enterobacteriaceae for gluconate and other nutrient sources, limiting the proliferation of the harmful bacteria,” the scientists concluded.

Promising New Bacterial Therapies

This research could ultimately lead to the development of fecal microbiota transplants for individuals to eradicate antibiotic-resistant bacteria in a more objective and specific manner, with fewer side effects than current treatments. 

“Harnessing these activities in the form of live bacterial therapies may represent a promising solution to combat the growing threat of proinflammatory, antimicrobial-resistant Enterobacteriaceae infection,” the scientists wrote in Nature.

According to the news release, they plan to continue research to “uncover the identity and function of unknown metabolites that contribute to gut health and inflammation.” The team hopes to discover how different bacteria compete with each other, and to develop microbial therapeutics that improve gut microbiome and curb bacterial infections.

More studies are needed to prove the efficacy of this type of fecal bacterial treatment. However, this research demonstrates how using nano processes enabled by new technologies to identify the actual work of proteins, RNA, and DNA in the body cheaply, faster, and with greater precision, will open doors to both therapeutic and diagnostic clinical laboratory biomarkers.  

—JP Schlingman

Related Information:

Scientists Identify a Unique Combination of Bacterial Strains That Could Treat Antibiotic-resistant Gut Infections

Commensal Consortia Decolonize Enterobacteriaceae via Ecological Control

Combination of Bacterial Strains Could Potentially Treat Antibiotic-Resistant Gut Infections

Stanford University Scientists Discover New Lifeform Residing in Human Microbiome

Researchers Use Ingestible Device to Non-Invasively Sample Human Gut Bacteria in a Development That Could Enable More Clinical Laboratory Testing of Microbiomes

Linköping University/University of Florida Study Finds Gut Bacteria May Affect Developing Neurodevelopmental Disorders in Infants

Further research could eventually lead to clinical laboratory biomarkers and screening tests to identify infants whose gut bacteria may predispose them to neurodevelopment disorders later in life

Microbiologists and clinical laboratory scientists working with gut bacteria will be intrigued to learn that a study conducted by scientists from Linköping University in Sweden and the Department of Microbiology and Cell Science at the University of Florida (UFL) recently found that gut microbiota (aka, gut flora) in infancy can be correlated with developing a neurodevelopmental disorder (ND) later in life.

The researchers analyzed patient records from the 20-year All Babies in Southeast Sweden (ABIS) prospective cohort study into the etiology of obesity, diabetes, and other diseases. They found that “disturbances” in the microbiomes of children during the first years of life could be linked to later ND diagnoses, according to Neuroscience News.

Such ND diagnoses include autism spectrum disorder (autism), Attention Deficit Hyperactivity Disorder (ADHD), communication disorders, and intellectual disability.

“We’ve found associations with some factors that affect gut bacteria, such as antibiotic treatment during the child’s first year, which is linked to an increased risk of these diseases,” stated pediatrician Johnny Ludvigsson, MD, PhD, Senior Professor, Department of Biomedical and Clinical Sciences at Linköping University, who co-led the study, in a Linköping University news release.

“Analyzing over 16,000 children from the ABIS study, researchers identified significant biomarkers in cord blood and stool samples that correlate with future diagnoses of these disorders,” Neuroscience News reported.

This study adds evidence to the growing theory that every individual’s microbiome has much to do with his/her state of health and specific health conditions.

The scientists published their findings in the journal Cell titled, “Infant Microbes and Metabolites Point to Childhood Neurodevelopmental Disorders.”

“We can see in the study that there are clear differences in the intestinal flora already during the first year of life between those who develop autism or ADHD and those who don’t,” said pediatrician and study co-author Johnny Ludvigsson, MD, PhD (above), Senior Professor, Department of Biomedical and Clinical Sciences at Linköping University, in a news release. Clinical laboratory scientists and microbiologists who work with gut microbiota will find these observations intriguing. (Photo copyright: Linköping University.)

Analysis of the ABIS Study

To conduct their study, the researchers analyzed the health records of 16,440 children born between 1997 and 1999 who participated in the ABIS study. The subjects were a close representation of the general Swedish population and were followed from birth into their twenties. 

Research showed that 1,197 of the 16,440 children (7.28%) had been diagnosed with either autism, ADHD, communication disorders, or an intellectual disability. 

The researchers also surveyed the ABIS study participants concerning their lifestyles and environmental factors during childhood. They analyzed substances found in the umbilical cord blood and stool bacteria collected at age one in some of the study participants. Cord blood remains in the placenta and umbilical cord after birth and is rich in stem cells

“The remarkable aspect of the work is that these biomarkers are found at birth in cord blood or in the child’s stool at one year of age over a decade prior to the diagnosis,” said Eric Triplett, PhD, Professor and Chair of the Department of Microbiology and Cell Science at UFL and a co-leader of the study, in the Linköping University news release.

The investigation found that children who had numerous ear infections during the first year of life were more prone to receiving a diagnosis of a neurodevelopmental disorder later in life. The scientists surmised that it was not the infections that caused the issues. Rather, it was that repeated antibiotic treatments had disturbed the balance of healthy gut bacteria.

“We’re not trying to say that antibiotics are necessarily a bad thing,” stated Angelica Ahrens, PhD, Assistant Research Scientist in the Triplett Research Group at the University of Florida and first author of the study, in a UFL blog. “But perhaps overuse can be detrimental to the microbiome, and for some children, for whatever reason, their microbiome might not recover as readily.”

Deficits in Important Bacteria

The researchers discovered that the presence of Citrobacter bacteria increased the risk of a future ND diagnosis. According to ScienceDirect, “organisms of the genus Citrobacter are gram-negative bacilli that are occasional inhabitants of the gastrointestinal tract and are responsible for disease in neonates [newborns that are four weeks or younger] and debilitated or immunocompromised patients.”

They also discovered that the absence of Coprococcus bacteria increased the risk of getting an ND as well. One of the main producers of butyrate, Coprococcus is known to support gut barrier function, suppress harmful bacteria, and contain anti-inflammatory properties.

Coprococcus and Akkermansia muciniphila have potential protective effects,” said Ahrens in the Linköping University news release. “These bacteria were correlated with important substances in the stool, such as vitamin B and precursors to neurotransmitters which play vital roles orchestrating signaling in the brain. Overall, we saw deficits in these bacteria in children who later received a developmental neurological diagnosis.”

Environmental/Behavioral Findings of the ABIS Study

Through the analysis of toxins present in study participants’ cord blood, the researchers confirmed that risk of developing an ND increases when babies are exposed to parents who smoke. The scientists also found that breastfeeding offers a protective effect against NDs.

More research is needed to determine whether gut flora in infants can have an effect on developing NDs later in life, and it is not yet known if similar findings will be detected in other populations. Nevertheless, the findings that many biomarkers for NDs can be observed in infancy may enable scientists to create clinical laboratory screening protocols, preventative measures, and innovative treatments for neurodevelopmental disorders. 

Further research and studies linking certain microbiome factors to specific health conditions will create opportunities for microbiologists and clinical laboratories as well, to perform diagnostic testing that identifies if a patient—in this case a newborn or infant—has a microbiome that will lead to immediate or later neurological health conditions.   

—JP Schlingman

Related Information:

Autism and ADHD Are Linked to Disturbed Gut Flora Very Early in Life

Early Gut Flora Imbalance May Predict Autism and ADHD

Disturbed Gut Flora in Early Years Linked to Autism

Infant Microbes and Metabolites Point to Childhood Neurodevelopmental Disorders

All Babies in Southeast Sweden (ABIS) – ABIS-II. A Prospective Cohort Study of the Aetiology of Obesity, Diabetes and Other Diseases.

UF and Swedish Researchers Connect Childhood Microbiome with Development of Autism, ADHD

Multiple Medical Teams Use Apple Vision Pro XR Headset During Surgical Procedures, Signaling Emergence of Extended Reality Applications in Healthcare

Technology like Apple’s VR/AR headsets may prove useful to clinical laboratories in accessioning and in pathology labs during biopsy grossing

In what has been billed as a first, medical teams in the US and UK used Apple’s Extended Reality (XR) Vision Pro headset system to assist in surgical procedures. The surgeons themselves did not wear the $3,500 headset. Instead, surgical nurses used the device for touch-free access to a software application that assisted them in setting up, organizing, and performing the operations. For pathologists and clinical laboratories, in the histology laboratory, such an arrangement involving XR headsets could be used when a biopsy is at the grossing station as well.

The headset software the team used during surgery was developed by eXpanded eXistence, Inc. (eXeX), a Florida-based company whose primary product is an iOS (Apple mobile operating system) application that provides similar functions for mobile devices. eXeX adapted the iOS app to work on Apple’s Extended Reality headset.

Extended Reality is an umbrella term for augmented reality (AR) and virtual reality (VR). Apple refers to the technology as “spatial” computing.

Within the clinical laboratory, XR headsets could be used in the accessioning process as the accessioner works through the steps to confirm all required information accompanies the test requisition and that the patient’s specimen is processed/aliquoted appropriately.

“The eXeX platform, enhanced by artificial intelligence, is designed not as a medical device but as an organizational and logistics tool. It aims to streamline the management of tens of thousands of items, including equipment, tools, technologies, consumables, implants, and surgical products,” said neurosurgeon Robert Masson, MD, eXeX’s founder and CEO, in a February news release.

Masson first deployed the software in his own surgical practice. Then in March, eXeX announced that a surgical team at Cromwell Hospital in London used the system in two microsurgical spine procedures, according to a March new release.

That news garnered media coverage in the UK as well as in US-based publications that follow Apple.

Another early user, eXeX announced, was G. Russell Huffman, MD, MPH, of Rothman Orthopaedic Institute. Huffman’s team used the software to perform a reverse total shoulder arthroplasty procedure at the AdventHealth Surgery Center Innovation Tower in Orlando, according to an April news release.

“We are in a new era of surgery, and for the first time, our surgical teams have the brilliance of visual holographic guidance and maps, improving visuospatial and temporal orientation for each surgical team and for each surgery in all specialties,” said neurosurgeon Robert Masson, MD (above), eXeX’s founder and CEO, in a press release. Clinical laboratories may one day use XR headsets in the histology lab at the grossing station. (Photo copyright: Masson Spine Institute.)

Surgical Process Not Glamorous, But Important

Despite being on a cutting-edge XR platform, the eXeX software addresses “the least glamorous part” of the surgical process, Masson told Gizmodo.

“People assume that surgical healthcare has got to be sophisticated and modern,” he said. “The reality is the way we organize it is probably the most archaic of all the major industries on the planet. It’s all memorization and guesswork with scribbles on pieces of paper.”

The advantage of an XR headset is that it allows use of the eXeX software in a sterile environment, he added. “The ability to interact with digital screens and holograms and lists and maps and products unlocks all kinds of possibilities. Suddenly, you’ve got an interactive digital tool that you can use without violating the sanctity of sterility.”

Does he foresee a future when the surgeons themselves use XR headsets in the operating room? Not necessarily, Masson told Gizmodo.

“There’s always a tendency to say, ‘look at this amazing tech, let’s put a screw in with it,’” he said. “Well, we’re already putting screws in without the headset, so it doesn’t really solve a problem. People tend to think of floating spines, floating heights, you know, an overlay that tells you where to put a catheter in the liver. Honestly, it’s all unnecessary because we already do that pretty well. What we don’t do really well is stay organized.”

Other XR Apps for Healthcare

In a news release, Apple showcased other healthcare apps for its Vision Pro platform.

Epic Systems, an electronic health record (EHR) system developer, has an app called Epic Spatial Computing Concept that allows clinicians “to easily complete charting, review labs, communicate using secure chat, and complete in-basket workflows through intuitive gestures, like simply tapping their fingers to select, flicking their wrist to scroll, or using a virtual keyboard or dictation to type,” Apple stated in the news release.

Stryker, manufacturer of Mako surgical robotic arms for joint-replacement procedures, has an Apple iOS app called myMako that “allows surgeons to visualize and review patients’ Mako surgical plans at any time in a brilliant, immersive visual experience,” Apple said.

Boston Children’s Hospital developed an Apple iOS app called CyranoHealth designed to train nurses and other healthcare professionals in how to use new medical technologies, such as infusion pumps.

Cinematic Reality, from Siemens Healthineers, is an Apple iOS app that “allows surgeons, medical students, and patients to view immersive, interactive holograms of the human body captured through medical scans in their real-world environment,” Apple said.

New Era in Technology

For the past 20 years, manufacturing companies have installed systems at workstations with audio and video that show each step in a work process and with written checklists on the computer screen. This allows workers to check off each required step as proof that each required work element was performed.

This is similar to professional pilots who use checklists at every step in a flight process. One pilot will read the checklist items, the other will perform the step and confirm it was complete.

These procedures are generally completed on computer displays, but with the advent of XR headset technology, these types of procedures are evolving toward mobility.

To prepare for the emergence of XR-based healthcare apps, the US Food and Drug Administration (FDA) has organized a research team to devise best practices for testing these headset devices, CNBC reported.

It will be some time before XR headset technology finds its way into histology laboratories, clinical laboratories, and pathology practices, but since the rate of technology adoption accelerates exponentially, it might not take very long.

—Stephen Beale

Related Information:

eXeX and Neurosurgeon Dr. Robert Masson Achieve World First Using Apple Vision Pro

eXeX and Cromwell Hospital Pioneer the First Use of Apple Vision Pro in UK Surgery

eXeX and AdventHealth Surgery Center Innovation Tower Pioneer Use of Apple Vision Pro in Joint Replacement Surgery

Vision Pro Used in Surgery “To Eliminate Human Error”

This Startup Wants to Use the Apple Vision Pro for the Most Boring Part of Surgery

Doctors Are Using the Apple Vision Pro During Surgery

Apple’s Vision Pro Was Used in Surgery to Help Perform Spinal Operations

Apple Vision Pro Unlocks New Opportunities for Health App Developers

WHO/IARC Study Projects Increase of 77% in Global Cancer Cases by 2050, Reports 20 Million Global Cancer Cases in 2022

Predicted steady increase in the number of new cancer cases globally will stress pathologist and clinical laboratories to process specimens and issue timely cancer diagnoses to referring physicians and patients

In many nations today, it is recognized that the demand for cancer testing services outstrips the capacity of anatomic pathology laboratories to perform cancer testing in a timely manner. Now a new report published in CA, a journal of the American Cancer Society, estimates that the number of new cancers globally will increase substantially during the next few decades.

With today’s cancer diagnostic technologies and standards of practice, it is anatomic pathologists who will typically receive biopsies or patient specimens, perform the tests, and confirm/report whether a patient has cancer. Thus, this new report projecting that the disease will grow 77% to 35 million cases by the year 2050 should be of interest to pathology groups and clinical laboratories worldwide.

According to the published study, titled, “Global Cancer Statistics 2022: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries,” there were 20 million new cancer cases and 9.7 million cancer-related deaths in 2022.

The report is a collaboration between the World Health Organization’s International Agency for Research on Cancer (WHO/IARC) and the American Cancer Society (ACS). The report called for “global escalation of cancer control measures” and paying close attention to risk factors such as smoking, obesity, and infections, according to an IARC statement

Unfortunately, the news about increasing cancer cases comes at a time when worldwide demand for pathologists already far exceeds available supply.

“The impact of this increase will not be felt evenly across countries of different HDI [human development index] levels. Those who have the fewest resources to manage their cancer burdens will bear the brunt of the global cancer burden,” said epidemiology of cancer researcher Freddie Bray, PhD (above), Head of the Cancer Surveillance Branch at the IARC in Lyon, France, in a press release. Bray “specializes in estimating the global cancer burden and predicting future trends,” according to the organization’s website. He also “leads the Global Initiative for Cancer Registry Development (GICR), which is aimed at expanding the coverage and quality of population-based cancer registries in low- and middle-income countries.” Clinical laboratories and anatomic pathologists in the United States and abroad would be wise to keep an eye on the coming cancer burden. (Photo copyright: IARC.)

Top Diagnosed Cancers

To complete their study, the WHO/IARC researchers tapped GLOBOCAN [Global Cancer Observatory] estimates of cancer incidence and mortality, the disease’s geographical variability, and predictions based on global demographic projections.

The 10 most frequently diagnosed cancers for men and women (combined) by percent of cancer sites and number of new cases in 2022 include:            

  • Lung:                                12.4% (2.5 million cases).
  • Female breast:                  11.6% (2.3 million cases).
  • Colorectum:                       9.6% (1.9 million cases).
  • Prostate:                             7.3% (1.5 million cases).
  • Stomach:                            4.9% (968,350 cases).
  • Liver:                                 4.3% (865,269 cases).
  • Thyroid:                             4.1% (861,173 cases).
  • Cervix:                               3.3% (661,021 cases).
  • Bladder:                             3.1% (613,791 cases).
  • Non-Hodgkin lymphoma: 2.8% (553,010 cases).

For women, the cancer most often diagnosed was at the breast site. It was also the leading cause of death from cancer, the CA study noted, adding that lung and colorectal cancer cases and deaths in women followed breast cancer.

For men, lung cancer was the top cancer diagnosed in terms of cases and deaths, ahead of prostate and colorectal cancer for new cases.

Geographic HDI Affects Cancer of Citizens

The geographic areas with the highest distribution of new cancer cases and mortality rates in 2022, according to the CA paper, are:

  • Asia:          49.2% of cases, 56.1% of deaths.
  • Africa:         5.9% of cases,    7.8% of deaths.
  • Oceania:      1.4% of cases,    0.8% of deaths.
  • Euro:          22.4% of cases, 20.4% of deaths.
  • Americas:  21.2% of cases, 14.9% of deaths.

The WHO/IARC report also associated a country’s human development index (HDI)—a measure of health, longevity, and standard of living—with the likelihood of its residents developing cancer, USA Today reported.

“From a global perspective, the risk of developing cancer tends to increase with increasing HDI level. For example, the cumulative risk of men developing cancer before age of 75 years in 2022 ranged from approximately 10% in low HDI settings to over 30% in very high HDI settings,” the researchers wrote in their CA paper.

This suggests that a lack of resources to diagnose and treat cancer can hinder response and treatment.

In a news release, the WHO pointed out examples of what it termed “striking cancer inequity by HDI.”

“Women in lower HDI countries are 50% less likely to be diagnosed with breast cancer than women in high HDI countries, yet they are at much higher risk of dying of the disease due to late diagnosis and inadequate access to quality treatment,” said medical epidemiologist Isabelle Soerjomataram, MD, PhD, Deputy Head of the Cancer Surveillance Branch, WHO/IARC, in the news release.

Additionally, lung cancer-related resources were four to seven times more likely to be offered in a high-income country than a lower-income country, the WHO noted.

“WHO’s new global survey sheds light on major inequalities and lack of financial protection for cancer around the world, with populations—especially in lower income countries—unable to access the basics of cancer care,” said Bente Mikkelsen, MD, Director of the WHO’s Department of Noncommunicable Diseases, in the news release.

Current State of Pathology Demand

Is the pathology industry prepared for a global cancer burden? Hardly.

In “Examining the Worldwide Pathologist Shortage,” Dark Daily’s sister publication The Dark Report found that demand for pathology services is growing faster than the number of pathologists available to meet that demand. This is true for the United States and most other nations. Consequently, efforts are underway to more accurately measure the number of pathologists practicing in each country. Early data support the claim of an inadequate number of pathologists.

Thus, aligning clinical laboratory and anatomic pathology resources with cancer projections is especially important in light of the WHO/IARC’s recent report which suggests the number of cancer diagnoses and different types of cancer will increase dramatically in coming years. 

The data could be helpful to diagnostic leaders seeking evidence to support training of more anatomic pathologists and expansion of AP laboratories, where cancer is most often confirmed and reported.  

—Donna Marie Pocius

Related Information:

Global Cancer Statistics 2022: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries

New Report on Global Cancer Burden in 2022 by World Region and Human Development Index

Global Cancer Burden Growing Amidst Mounting Need for Services

Cancer Cases Could Increase 77% as Global Population Balloons. These Types Are Most Common

Examining the Worldwide Pathologist Shortage; How Many Pathologists Are Needed in Different Countries?

Dutch Patient with Longest COVID-19 Case of 612 Days Had More than 50 SARS-CoV-2 Mutations Before He Died

Study of the 50 Omicron variants could lead to new approaches to clinical laboratory testing and medical treatments for long COVID

Patients infected with SARS-CoV-2 can usually expect the COVID-19 illness to subside within a couple of weeks. However, one Dutch patient remained infected with the coronavirus for 612 days and fought more than 50 mutations (aka, variants) before dying late last year of complications due to pre-existing conditions. This extreme case has given doctors, virologists, microbiologists, and clinical laboratories new insights into how the SARS-CoV-2 virus mutates and may lead to new treatments for long COVID.

According to Scientific American, when the 72-year-old male patient was admitted to the Amsterdam University Medical Center (Amsterdam UMC) in 2022 with the Omicron variant of SARS-CoV-2, he was also found to have myelodysplastic syndrome (MDS) and myeloproliferative neoplasm (MPN) overlap syndromes. Thus, the patient was determined to be immunocompromised.

“This was complicated by the development of a post-transplant lymphoma for which he received rituximab [a monoclonal antibody medication used to treat certain autoimmune diseases and cancers] that depletes all available B-cells, including those that normally produce the SARS-CoV-2 directed antibodies,” according to a press release.

The medication the patient was taking for his pre-existing conditions may have contributed to his body being unable to produce antibodies in response to three shots of the Moderna mRNA COVID vaccine he received.

Magda Vergouwe, MD, PhD candidate at the Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC, who lead a study into the patient, theorized that some of the medications the patient was on for his pre-existing conditions could have destroyed healthy cells alongside the abnormal cancer-causing B cells the drugs were meant to target.

“This case underscores the risk of persistent SARS-CoV-2 infections in immunocompromised individuals,” the researchers said prior to presenting their report about the case at a meeting of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) in Barcelona, Spain, Time reported. “We emphasize the importance of continuing genomic surveillance of SARS-CoV-2 evolution in immunocompromised individuals with persistent infections.”

“Chronic infections and viral evolution [are] commonly described in [the] literature, and there are other cases of immunocompromised patients who have had [COVID] infections for hundreds of days,” Magda Vergouwe, MD, PhD candidate (above), Center for Experimental and Molecular Medicine at Amsterdam UMC, told Scientific American. “But this is unique due to the extreme length of the infection … and with the virus staying in his body for so long, it was possible for mutations to just develop and develop and develop.” Microbiologists, virologists, and clinical laboratories involved in testing patients with long COVID may want to follow this story. (Photo copyright: LinkedIn.)

Risks to Immunocompromised Patients

Pre-existing conditions increase the risk factor for COVID-19 infections. A 2021 study published in the Journal of the American Board of Family Medicine (JABFM) titled, “Prevalence of Pre-existing Conditions among Community Health Center Patients with COVID-19,” found that about 61% of that study’s test group had a pre-existing condition prior to the outbreak of the COVID-19 pandemic.

When the Dutch man was admitted to Amsterdam UMC with common and serious COVID-19 symptoms, such as shortness of breath, a cough, and low blood oxygen levels, he was prescribed sotrovimab (a monoclonal antibody) along with other COVID treatments.

About a month after being admitted his COVID-19 symptoms decreased, so he was first discharged to a rehab facility and then finally to his home. However, he continued to test positive for the coronavirus and developed other infections that may have been complicated by the persistent case of COVID-19.

The Amsterdam UMC doctors emphasized that the man ultimately succumbed to his pre-existing conditions and not necessarily COVID-19.

“It’s important to note that in the end he did not die from his COVID-19,” Vergouwe told Scientific American. “But he did keep it with him for a very long period of time until then, and this is why we made sure to sample [the virus in his body] as much as we could.”

One in Five Adults Develop Long COVID

Long COVID does not necessarily indicate an active infection. However, in as many as one in five US adults COVID symptoms persist after the acute phase of the infection is over, according to a study published recently in JAMA Network Open titled, “Epidemiologic Features of Recovery from SARS-CoV-2 Infection.”

“In this cohort study, more than one in five adults did not recover within three months of SARS-CoV-2 infection. Recovery within three months was less likely in women and those with pre-existing cardiovascular disease and more likely in those with COVID-19 vaccination or infection during the Omicron variant wave,” the JAMA authors wrote.

The origins of long COVID are not entirely clear, but according to the National Institutes of Health (NIH) it can develop when a patient is unable to sufficiently rest while battling off the initial virus. According to Vergouwe, the SARS-CoV-2 genome will always grow quicker when found in a patient with a compromised immune system.

Unique COVID-19 Mutations

More than 50 new mutations of the original Omicron variant were identified in the Dutch patient. According to Vergouwe, “while that number can sound shocking, mutations to the SARS-CoV-2 genome are expected to evolve more quickly in those who are immunocompromised (the average mutation rate of the virus is estimated to be two mutations per person per month),” Scientific American reported. “What does make these mutations unusual, she noted, is how their features differed vastly from mutations observed in other people with COVID. [Vergouwe] hypothesizes that the exceptional length of the individual’s infection, and his pre-existing conditions, allowed the virus to evolve extensively and uniquely.”

COVID-19 appears to be here to stay, and most clinical laboratory managers and pathologists understand why. As physicians continue to learn about the SARS-CoV-2 coronavirus, this is another example of how the knowledge about SARS-CoV-2 is growing as different individuals are infected with different variants of the virus.

—Ashley Croce

Related Information:

Longest-Ever COVID Infection Lasted More than 600 Days

COVID Patient’s Infection Lasts Record 613 Days—and Accumulated Over 50 Mutations

72-Year-Old Patient Had COVID for Record 613 Days, Accumulated over 50 Mutations from Virus Before It Killed Him

Prevalence of Preexisting Conditions among Community Health Center Patients with COVID-19: Implications for the Patient Protection and Affordable Care Act

The Risk Factors for Long COVID Have Finally Been Revealed

Prevalence of Pre-existing Conditions among Community Health Center Patients with COVID-19

Epidemiologic Features of Recovery from SARS-CoV-2 Infection

Genetic Testing of Wastewater Now Common in Detecting New Strains of COVID-19 and Other Infectious Diseases

University College London Study Shows Direct-to-Consumer DNA Tests Not Reliable in Assessing Disease Risk

Regulatory agencies in UK and US have yet to address dangers inherent in customer misunderstanding of DTC medical laboratory genetic test results

Direct-to-consumer (DTC) medical laboratory genetic tests are gaining popularity across the globe. But recent research out of the United Kingdom questions the reliability of these tests. The study, according to The Guardian, found that “Over the counter genetic tests in the UK that assess the risk of cancer or heart problems fail to identify 89% of those in danger of getting killer diseases.”

Researchers at University College London (UCL) examined 926 polygenic scores for risk of 310 different diseases from details retrieved from the Polygenic Score (PGS) Catalog. This catalog is an open-access database of published polygenic scores.

According the PGS website, “each PGS in the catalog is consistently annotated with relevant metadata; including scoring files (variants, effect alleles/weights), annotations of how the PGS was developed and applied, and evaluations of their predictive performance.”

However, the researchers told The Guardian, “Polygenic risk scores performed poorly in population screening, individual risk prediction, and population risk stratification. Strong claims about the effect of polygenic risk scores on healthcare seem to be disproportionate to their performance.”

The UCL researchers published their findings in the journal BMJ Medicine titled, “Performance of Polygenic Risk Scores in Screening, Prediction, and Risk Stratification: Secondary Analysis of Data in the Polygenic Source Catalog.”

“Strong claims have been made about the potential of polygenic risk scores in medicine, but our study shows that this is not justified,” Aroon Hingorani, PhD (above), Professor of Genetic Epidemiology at UCL and lead author of the study, told The Guardian. “We found that, when held to the same standards as employed for other tests in medicine, polygenic risk scores performed poorly for prediction and screening across a range of common diseases.” Consumer misunderstanding of DTC medical laboratory genetic tests is a real danger. (Photo copyright: University College London.)

Polygenic Scores Not Beneficial to Cancer Screening

To complete their study, the UCL researchers compared PGS genetic risk data to conventional clinical laboratory testing methods and discovered some troubling results. They include:

  • On average, only 11% of individuals who developed a disease had been identified by the tests.
  • A 5% false positive rate where people were informed that they would get a disease within 10 years but did not.
  • PGS only identified 10% of people who later developed breast cancer.
  • PGS only identified 12% of individuals who later developed coronary artery disease.

The researchers state in their BMJ Medicine paper that polygenic risk scores are not the same as testing for certain gene mutations, which could be critical in screening for some cancers. They also wrote that discovering genetic variants associated with the risk for disease is still crucial for drug development.

“It has been suggested that polygenic risk scores could be introduced early on to help prevent breast cancer and heart disease but, in the examples we looked at, we found that the scores contributed little, if any, health benefit while adding cost and complexity,” research physician and epidemiologist Sir Nicholas Wald, FRS, FRCP, FMedSci, Professor of Preventive Medicine at UCL Institute of Health Informatics and co-author of the study, told the Jersey Evening Post

“Our results build on evidence that indicates that polygenic risk scores do not have a role in public health screening programs,” Wald added.

“This research study rightly highlights that for many health conditions genetic risk scores alone may have limited usefulness, because other factors such as deprivation, lifestyles, and environment are also important,” clinical epidemiologist Raghib Ali, MD, CEO, Chief Investigator and Chief Medical Officer, Our Future Health UK, told The Guardian

Our Future Health is a collaboration between public, non-profit, and private sectors to create the UK’s largest health research program. The researchers in this endeavor intend to recruit over five million volunteers and use polygenic risk scores to develop innovative ways to prevent, detect, and treat disease. This program is funded by the UK’s National Health System (NHS).

“[Our] research program will be developing integrated risk scores that will take in all the important risk factors,” Ali explained. “We hope these integrated risk scores can identify people more likely to develop diseases, but this is a relatively new area of science and there are still unanswered questions around it.”

Danger of Misunderstanding DTC Genetic Tests

Here in the US, there have been news stories in recent years about the unreliability of certain genetic tests. Dark Daily covered these stories in previous ebriefs. News stories about the unreliability of genetic tests, particularly those marketed directly to consumers, reveal the problems that existing regulatory schemes have yet to address.

In “Consumer Reports Identifies ‘Potential Pitfalls’ of Direct-to-Consumer Genetic Tests,” we covered CR’s findings that though clinical laboratory and pathology professionals understand the difference between a doctor-ordered genetic health risk (GHR) test and a direct-to-consumer (DTC) genetic test, the typical genetic test customer may not. And that, misunderstanding the results of a DTC at-home genetic test can lead to confusion, loss of privacy, and potential harm.

Scientific American also covered the dangers of DTC testing in “The Problem with Direct-to-Consumer Genetic Tests,” in which the author notes that “despite caveats in ads and on packages, users can fail to understand their limitations,” and that “consumer-grade products are easily misconstrued as appropriate medical tests and create false reassurances in patients who could be at legitimate risk.”

Most clinical laboratory managers and pathologists are probably not surprised that the research performed at UCL shows that there are still issues surrounding genetic tests, particularly those marketed directly to consumers. While direct-to-consumer DNA tests can have some benefits, at this time, they are not always the best option for individuals seeking information about their personal risk for hereditary diseases.

—JP Schlingman

Related Information:

Over the Counter Genetic Tests in UK ‘Fail to Identify 89%’ of Those at Serious Risk

Performance of Polygenic Risk Scores in Screening, Prediction, and Risk Stratification: Secondary Analysis of Data in the Polygenic Score Catalog

3 Things to Know about At-home DNA Testing Kits

What Can At-home Genetic Tests Tell Me about My Health?

What are the Benefits and Risks of Direct-to-consumer Genetic Testing?

Genetic Risk Scores ‘Do Not Have a Place in Public Health Screening’

Consumer Reports Identifies ‘Potential Pitfalls’ of Direct-to-Consumer Genetic Tests

The Problem with Direct-to-Consumer Genetic Tests

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