Though they are a mystery, once solved, Obelisks could lead to new biomarkers for clinical laboratory testing
Microbiologists and clinical laboratories know that human microbiota play many important roles in the body. Now, scientists from Stanford University have discovered an entirely new class of “viroid-like” lifeforms residing inside the human body. The researchers detected their presence in both the gut microbiome and saliva samples. Most interesting of all, the researchers are not sure what the lifeforms actually are.
The Stanford researchers, led by PhD student Ivan Zheludev, called the new discovery “Obelisks” due to their RNA structures, which are short and can fold into structures that resemble rods.
The scientists believe the Obelisks went undetected until now in the human microbiome due to their compact genetic elements, which are only around 1,000 characters or nucleotides in size. A typical human DNA structure consists of around three billion nucleotides.
In an article they published on the biology preprint server bioRxiv titled, “Viroid-like Colonists of Human Microbiomes,” the Stanford researchers wrote, “Here, we describe the ‘Obelisks,’ a previously unrecognized class of viroid-like elements that we first identified in human gut metatranscriptomic data. … Obelisks comprise a class of diverse RNAs that have colonized and gone unnoticed in human and global microbiomes.”
The researchers discovered that Obelisks “form their own distinct phylogenetic group with no detectable sequence or structural similarity to known biological agents.”
This is yet another example of how researchers are digging deeper into human biology and finding things never before identified or isolated.
“I am really impressed by the approach. The authors were really creative,” computational biologist Simon Roux, PhD (above) of the Department of Energy (DEO) Joint Genome Institute at Lawrence Berkeley National Laboratory told Science in response to the Stanford researcher’s published findings. “I think this [work] is one more clear indication that we are still exploring the frontiers of this viral universe. This is one of the most exciting parts of being in this field right now. We can see the picture of the long-term evolution of viruses on Earth start to slowly emerge.” How these findings might eventually spark new biomarkers for clinical laboratory testing remains to be seen. (Photo copyright: Berkeley Lab.)
Researchers Bewildered by Obelisks
In their study, “Zheludev and team searched 5.4 million datasets of published genetic sequences and identified almost 30,000 different Obelisks. They appeared in about 10% of the human microbiomes the team examined,” Science reported.
The Stanford researchers found that various types of Obelisks seem to inhabit different areas of the body. In one dataset, the Obelisks were found in half of the oral samples.
The function of Obelisks is unknown, but their discovery is bewildering experts.
Rod-like secondary structures encompassing the entire genome, and
Open reading frames coding for a novel protein superfamily, which the researchers dubbed “Oblins.”
At least half of the genetic material of the Obelisks was taken up by these Oblins. The researchers suspect those proteins may be involved in the replication process of the newly-discovered lifeforms.
The Oblins are also significantly larger than other genetic molecules that live inside cells and they do not have the genes to create protein shells that RNA viruses live within when they are outside of cells.
“Obelisks, therefore, need some kind of host. The researchers managed to identify one: A bacterium called Streptococcus sanguinis that lives mostly in dental plaque in our mouths. Exactly which other hosts obelisks inhabit is yet another mystery, as are what they do to their host and how they spread,” Vice reported.
“While we don’t know the ‘hosts’ of other Obelisks, it is reasonable to assume that at least a fraction may be present in bacteria,” the researchers noted in their bioRxiv paper.
Researchers are Stumped
The Stanford scientists were unable to identify any impact the Obelisks were having on their bacterial hosts—either negative or positive—or determine how they could spread between cells.
“These elements might not even be ‘viral’ in nature and might more closely resemble ‘RNA plasmids,’” they concluded in their paper.
The Stanford scientists are uncertain as to where or what the hosts of the Obelisks are, but they suspect that at least some of them are present in bacteria. However, Obelisks do not appear to be similar to any biological agents that could provide a link between genetic molecules and viruses.
And so, Obelisks are a true mystery—one the Stanford researchers may one day solve. If they do, new biomarkers for clinical laboratory testing may not be far behind.
As with clinical laboratories, worker shortage is affecting large retail pharmacy chains and independent pharmacies alike
Staffing shortages in clinical laboratories and anatomic pathology groups caused by the Great Resignation is having a similar impact on retail pharmacy chains. Consequently, pharmacy chains are reducing store hours and even closing sites, according to USA Today.
As Dark Daily covered in “Clinical Laboratories Suffer During the ‘Great Resignation,” the US Bureau of Labor Statistics reported that from August 2021 through December 2021, the healthcare and social assistance workforce saw nearly 2.8 million workers quit—an average of 551,000 people during each of those months. By comparison, in December 2020, 419,000 healthcare workers left their jobs.
Pharmacies now report similar shortages in qualified workers, partly due to the sharp decrease in revenue from COVID-19 vaccinations, but also due to worker burnout. Both developments have counterparts in clinical laboratories as well.
“I’m concerned that without the help from the COVID-19 vaccinations that everyone needed, these pharmacies that were able to tough it out for another year or two might not be able to continue,” B. Douglas Hoey, PharmD, CEO of the National Community Pharmacists Association (NCPA), told USA Today. Clinical laboratories that processed large numbers of SARS-CoV-2 diagnostics have experienced the same sudden drop in revenue causing similar difficulties maintaining staffing levels. (Photo copyright: Cardinal Health.)
Staffing Shortages Leading to Safety Concerns
According to the Washington Post’s coverage of a study conducted in 2021 of 6,400 pharmacists in various retail and hospital environments, a majority did not feel they could conduct their jobs efficiently or safely.
“75% of the pharmacists in [the] survey disagreed with the statement ‘Sufficient time is allocated for me to safely perform patient care/clinical duties.’”
“71% said there were not enough pharmacists working to ‘meet patient care/clinical duties.’”
“65% said ‘payment for pharmacy services’ did not support their ‘ability to meet clinical and non-clinical duties.’”
“Workplace conditions have pushed many pharmacists and pharmacy teams to the brink of despair,” said the board of trustees of the American Pharmacists Association (APhA) in a press release, the Washington Post reported. “Pharmacy burnout is a significant patient safety issue. It is impacting patients today with delayed prescription fulfillment, unacceptable waits for vaccines and testing, and potential errors due to high volume, long hours, and pressure to meet performance metrics.”
This is a sentiment that has been repeated across every facet of healthcare—including in clinical laboratories—where staff shortages are being felt.
Shortage of Pharmacists or Lack of Morale?
In “Drugstores Make Slow Headway on Staffing Problems,” the Associated Press outlined from where it believes the staffing problems originate. “There isn’t a shortage of pharmacists. There’s just a shortage of pharmacists who want to work in those high-stress environments that aren’t adequately resourced,” Richard Dang, PharmD, Assistant Professor of Clinical Pharmacy at the University of Southern California (USC), told the Associated Press.
“The pressure never let up. No matter how mind-numbing and repetitive the work could get, we had to work with constant vigilance, as there was absolutely no room for error,” Bator wrote.
“We techs were left unsupported and unmentored throughout the pandemic,” she continued. “No one cared if we were learning or growing in our job, and there was little encouragement for us to enter training or residency programs. We were just expendable foot soldiers: this is not a policy that leads to long-term job retention.”
Healthcare workers feeling burnt out and under-appreciated during the pandemic led to mass resignations that produced staffing shortages throughout the industry. It appears this trend has caught up to pharmacies as well.
Workforce Wasn’t Ready
Local and chain pharmacies played an important role in the COVID-19 pandemic. Pharmacists distributed COVID-19 tests and treatment to their communities. But for many it was a struggle to keep up.
Stefanie Ferreri, PharmD, Distinguished Professor in Pharmacy Practice and Chair of the Division of Practice Advancement and Clinical Education at University of North Carolina’s Eshelman School of Pharmacy, told the Associated Press that she felt the expanding role of pharmacies in public health was “awesome” but stated that “the workforce wasn’t quite ready” for what took place during the pandemic.
Much like Bator recounted in her essay, pharmacy workers suddenly had new responsibilities, longer working hours, and little room for error.
“There are multiple stories about pharmacists just getting overwhelmed. The stress level and burnout is high,” Dima M. Qato, PharmD, PhD, told USA Today. Qato is Hygeia Centennial Chair and Associate Professor (with tenure) in the Titus Family Department of Clinical Pharmacy at the University of Southern California. “So, pharmacists leave, and stores have to shorten” their hours, she added.
Scheduling and Patience Can Help
What can be done to soften some of the issues staff shortages are causing? Ferreri suggests that pharmacies set appointment times for regular customers so that a pharmacist’s workload can be more predictable. An appointment system can ease stress for both the pharmacist and patient. Ferreri advises customers to be patient when it comes to their prescriptions. She suggests patients give pharmacies more than a day’s notice for refills.
“I think on both sides of the counter, we need to all have grace and realize this is a very challenging and stressful time for everyone,” said Brigid Groves, PharmD, Vice President, Pharmacy Practice at the American Pharmacists Association.
With burnout, staff shortages, and stress affecting nearly every aspect of the healthcare industry, having patience with each other will go a long way to helping clinical laboratories, pharmacies, and patients navigate the road ahead.
Critical shortages in medical laboratory workers and supplies are yet to be offset by new applicants and improved supply chains. But there is cause for hope.
Medical laboratory scientists (aka, medical technologists) can be hard to find and retain under normal circumstances. During the current coronavirus pandemic, that’s becoming even more challenging. As demand for COVID-19 tests increases, clinical laboratories need more technologists and lab scientists with certifications, skills, and experience to perform these complex assays. But how can lab managers find, attract, and retain them?
The Johns Hopkins Coronavirus Resource Center reports that as of mid-October more than one million tests for SARS-CoV-2 were being performed daily in the US. And as flu season approaches, the pandemic appears to be intensifying. However, supply of lab technologists remains severely constrained, as it has been for a long time.
Still, qualified medical technologists (MT) and clinical laboratory scientists (CLS) are hard to find.
Demand for COVID Tests Exceeds Available Clinical Lab Applicants
“I can replace hardware and I can manage not having enough reagents, but I can’t easily replace a qualified [medical] technologist,” said David Grenache, PhD, Chief Scientific Officer at TriCore Reference Laboratories, Albuquerque, N.M., in the WSJ.
Another area where demand outstrips supply is California. Megan Crumpler, PhD, Laboratory Director, Orange County Public Health Laboratory, told the WSJ, “We are constantly scrambling for personnel, and right now we don’t have a good feel about being able to fill these vacancies, because we know there’s not a pool of applicants.”
Are Reductions in Academic Programs Responsible for Lack of Available Lab Workers?
Recent data from the US Bureau of Labor Statistics (BLS) show 337,800 clinical laboratory technologists and technicians employed by hospitals, public health, and commercial labs, with Job Outlook (projected percent change in employment) growing at 7% from 2019 to 2029. This, according to the BLS’ Occupational Outlook Handbook on Clinical Laboratory Technologists and Technicians, is “faster than average.”
“The average growth rate for all occupations is 4%,” the BLS notes.
Medical laboratories have the most staff vacancies in phlebotomy (13%) and the least openings in point-of-care (4%), according to an American Society for Clinical Pathology 2018 Vacancy Survey published in the American Journal of Clinical Pathology (AJCP).
Becker’s Hospital Review reported that “Labor shortages in [clinical] testing labs have existed for years due to factors including low recruitment, an aging workforce, and relatively low pay for [medical] lab technicians and technologists compared to that of other healthcare workers with similar education requirements.
“In 2019, the median annual salary for clinical laboratory technologists and technicians was $53,000, according to the US Bureau of Labor Statistics. The skills required for lab workers also are often specialized and not easily transferred from other fields.”
At the “root” of the problem, according to an article in Medical Technology Schools, is a decrease in available academic programs. Laboratory technologists require a Bachelor of Science (BS) degree and technicians need an associate degree or post-secondary certificate.
“(The programs) are expensive to offer, so when it comes to cuts and budgets, some of those cuts have been based on how much it costs to run them. That, and they may not have high enough enrollments,” said Lisa Cremeans, MMDS, CLS(NCA), MLS(ASCP), Clinical Assistant Professor at University of North Carolina at Chapel Hill, in the Medical Technology Schools article. (Photo copyright: University of North Carolina.)
AACC has called for federal funding of these programs, which now number 608, down from 720 programs for medical laboratory scientists in 1990.
“The pandemic has shone a spotlight on how crucial testing is to patient care. It also has revealed the weak points in our country’s [clinical laboratory] testing infrastructure, such as the fact that the US has allowed the number of laboratory training programs to diminish for years now,” said Grenache, who is also AACC President, in a news release.
Creative Staffing Strategies Clinical Labs Can Take Now
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How Some Clinical Labs are Coping with Staff and Recruitment Challenges
The Arizona Chamber Business News reported that Sonora Quest Laboratories in Tempe earlier this year launched “Operation Catapult” to help with a 60,000 COVID-19 test increase in daily test orders. The strategy involved hiring 215 employees and securing tests with the help of partners:
Meanwhile, students in the UMass Lowell (UML) medical laboratory science (MLS) program, see brighter skies ahead.
“The job outlook even before COVID-19 was so amazing,” said Dannalee Watson, a UML MLS student, in a news release. “It’s like you’re figuring out a puzzle with your patient. Then, we help the doctor make decisions.”
Such enthusiasm is refreshing and reassuring. In the end, the SARS-CoV-2 pandemic and the resultant demand for clinical laboratory testing may call more students’ attention to careers in medical laboratories and actually help to solve the lab technologist/technician shortage. We can hope.
By offering DTC preventative gene sequencing, hospital leaders
hope to help physicians better predict cancer risk and provide more accurate
diagnoses
Two Boston health systems, Brigham and Women’s Hospital and Massachusetts General Hospital (MGH), are the latest to open preventative gene sequencing clinics and compete with consumer gene sequencing companies, such as 23andMe and Ancestry, as well as with other hospital systems that already provide similar services.
This may provide opportunities for clinical laboratories. However, some experts are concerned that genetic sequencing may not be equally available to patients of all socioeconomic classes. Nor is it clear how health systems plan to pay for the equipment and services, since health insurance companies continue to deny coverage for “elective” gene sequencing, or when there is not a “clear medical reason for it, such as for people with a long family history of cancer,” notes STAT.
Therefore, not everyone is convinced of the value of gene sequencing to either patients or hospitals, even though advocates tout gene sequencing as a key element of precision medicine.
Is Preventative Genetic Sequencing Ready for the Masses?
Brigham’s Preventive Genomics Clinic offers comprehensive DNA sequencing, interpretation, and risk reporting to both adults and children. And MGH “plans to launch its own clinic for adults that will offer elective sequencing at a similar price range as the Brigham,” STAT reported.
The Brigham and MGH already offer similar gene sequencing services as other large health systems, such as Mayo Clinic and University of California San Francisco (UCSF), which are primarily used for research and cancer diagnoses and range in price depending on the depth of the scan, interpretation of the results, and storage options.
However, some experts question whether offering the
technology to consumers for preventative purposes will benefit anyone other
than a small percentage of patients.
“It’s clearly not been demonstrated to be cost-effective to promote this on a societal basis,” Robert Green, MD, MPH, medical geneticist at Brigham and Women’s Hospital, and professor of genetics at Harvard, told STAT. “The question that’s hard to answer is whether there are long-term benefits that justify those healthcare costs—whether the sequencing itself, the physician visit, and any downstream testing that’s stimulated will be justified by the situations where you can find and prevent disease.”
Additionally, large medical centers typically charge more
for genomic scans than consumer companies such as 23andMe and Ancestry. Hospital-based
sequencing may be out of the reach of many consumers, and this concerns some
experts.
“The idea that genomic sequencing is only going to be
accessible by wealthy, well-educated patrons who can pay out of pocket is
anathema to the goals of the publicly funded Human Genome Project,” Jonathan
Berg, MD, PhD, Genetics Professor, University of North Carolina at Chapel
Hill, told Scientific
American.
And, according to the American Journal of Managed Care, “It’s estimated that by 2021, 100 million people will have used a direct-to-consumer (DTC) genetic test. As these tests continue to gain popularity, there is a need for educating consumers on their DTC testing results and validating these results with confirmatory testing in a medical-grade laboratory.”
This is why it’s critical that clinical laboratories and
anatomic pathology groups have a genetic testing and gene sequencing strategy,
as Dark
Daily reported.
David Bick, MD, Chief Medical Officer at the HudsonAlpha Institute for Biotechnology and Medical Director of the Smith Family Clinic for Genomic Medicine, told Scientific American, “there’s just more and more interest from patients and families not only because of 23andMe and the like, but because there’s just this understanding that if you can find out information about your health before you become sick, then really our opportunity as physicians to do something to help you is much greater.”
In an article he penned for Medium, Robert Green, MD, MPH (shown above counseling a patient), medical geneticist at Brigham and Women’s Hospital and professor of genetics at Harvard, wrote, “The ultimate aim of our Genomes2People Research Program is to contribute to the transformation of medicine from reactive to proactive, from treatment-oriented to preventive. We are trying to help build the evidence base that will justify societal decision to make these technologies and services accessible to anyone who wants them, regardless of means, education or race and ethnicity.” (Photo copyright: Wall Street Journal.)
Is Preventative Genomics Elitist?
As large medical centers penetrate the consumer genetic
testing market some experts express concerns. In a paper he wrote for Medium,
titled, “Is Preventive Genomics Elitist?” Green asked, “Is a service like this
further widening the inequities in our healthcare system?”
Green reported that while building the Preventive Genomics Clinic at Brigham, “we … struggled with the reality that there is no health insurance coverage for preventive genomic testing, and our patients must therefore pay out of pocket. This is a troubling feature for a clinic at Brigham and Women’s Hospital, which is known for its ties to communities in Boston with diverse ethnic and socioeconomic backgrounds.”
Most of Brigham’s early genetics patients would likely be “well-off,
well-educated, and largely white,” Green wrote. “This represents the profile of
typical early adopters in genetic medicine, and in technology writ large. It
does not, however, represent the Clinic’s ultimate target audience.”
More Data for Clinical Laboratories
Nevertheless, preventive genomics programs offered by large
health systems will likely grow as primary care doctors and others see evidence
of value.
Therefore, medical laboratories that process genetic
sequencing data may soon be working with growing data sets as more people reach
out to healthcare systems for comprehensive DNA sequencing and reporting.
