DNA analysis of early plague victims pinpoints Black Death’s start on Silk Road trading communities in mountain region of what is now modern-day Kyrgyzstan in Central Asia
Microbiologists and clinical laboratory scientists will likely find it fascinating that an international team of scientists may have solved one of history’s greatest mysteries—the origin of the bubonic plague that ravaged Afro-Eurasia in the mid fourteenth century. Also known as the Black Death, the plague killed 60% of the population of Europe, Asia, and North Africa between 1346-1353 and, until now, the original source of this disease has largely gone unsolved.
In their study published in the journal Nature, titled, “The Source of the Black Death in Fourteenth-Century Central Eurasia,” the authors outlined their investigation of cemeteries in the Chüy Valley of modern-day Kyrgyzstan. The tombstone inscriptions showed a disproportionally high number of burials dating between 1338 and 1339 with inscriptions stating “pestilence” as the cause of death.
Big Bang of Plague
Using 30 skeletons that were excavated from these cemeteries in the late 1880s and moved to St. Petersburg, Russia, the scientists analyzed the DNA of ancient pathogens recovered from the remains of seven people. They discovered Yersinia pestis (Y. pestis) DNA in three burials from Kara-Djigach, which lies in the foothills of the Tian Shan mountains.
According to another article in Nature, the scientists showed that a pair of full Y. pestis genomes from their data were direct ancestors of strains linked to the Black Death, and that the Kara-Djigach strain was an ancestor of the vast majority of Y. pestis lineages circulating today.
“It was like a big bang of plague,” Krause stated at a press briefing, Nature reported.
The research team concluded that the Tian Shan region was the location where Y. pestis first spread from rodents to people, and that the local marmot colonies likely the prevalent rodent carriers of plague.
“We found that modern strains [of the plague] most closely related to the ancient strain are today found in plague reservoirs around the Tian Shan mountains, so very close to where the ancient strain was found. This points to an origin of Black Death’s ancestor in Central Asia,” Krause explained in a Max Planck Institute news release.
He told Nature that fleas likely passed the marmot-based infection on to humans, sparking a local Kyrgyzstan epidemic. The disease then spread along the Silk Road trade routes, eventually reaching Europe, where rats (and the fleas that they carried) spread the disease.
Understanding Context of Plague
Writing in The Conversation, Associate Professor of Medieval and Environmental History Philip Slavin, PhD, University of Stirling, who co-authored the study, explained that Kara-Djigach is unlikely to be “the specific source of the pandemic,” but rather that the “disaster started somewhere in the wider Tian Shan area, perhaps not too far from that site,” where marmot colonies were likely the source of the 1338-1339 outbreak.
Making a modern-day comparison, Krause told Nature, “It is like finding the place where all the strains come together, like with coronavirus where we have Alpha, Delta, Omicron all coming from this strain in Wuhan.”
Slavin maintains that understanding the “big evolutionary picture” is key when studying the phenomenon of emerging epidemic diseases.
“It is important to see how these diseases develop evolutionary and historically, and avoid treating different strains as isolated phenomena,” he wrote in The Conversation. “To understand how the diseases develop and get transmitted, it is also crucial to consider the environmental and socioeconomic contexts.”
Scientists have spent centuries debating the source of the Black Death that devastated the medieval world. The multidisciplinary process used by the Slavin/Krause-led team provides a lesson to clinical laboratory managers and pathologists on the important role they play when collaborating with colleagues from different fields on scientific investigations.
Employer group in Houston plans to use the numbers to pressure lawmakers for policy changes involving how hospitals and health plans price their services
Clinical laboratory leaders will probably not be surprised to learn that wide disparities exist between what Medicare pays hospitals and what is paid by private insurers and employers. That’s according to analysis by the Houston Business Coalition on Health (HBCH) which examined costs and billing practices at four of the region’s top hospitals, each a flagship for its respective health system.
This study—by a business group concerned about the spiraling cost of healthcare for their employees—is significant because it indicates that some large employers are willing to become more aggressive in driving down healthcare costs. In the Houston study, three of these hospitals—Houston Methodist, Memorial Hermann, and HCA Houston Medical Center—charged more than 250% over Medicare, noted a press release, which stated the group plans to use the numbers to lobby Texas lawmakers for policy changes.
“The prices employers paid to hospitals are unsustainable and negatively impact business growth, family quality of life, and resources needed for other critical community social needs,” said HBCH executive director Chris Skisak, PhD, in the press release. “Our intent in sharing and publicizing these resources is to facilitate direct discussions with health systems and employers to better understand the ramifications to Houston businesses and the greater community.”
The HBCH describes itself as a resource for local employers and healthcare providers seeking to promote cost-effective healthcare delivery and health benefits. It has 60 members that collectively provide healthcare coverage for 500,000 area residents.
Hospital Claims Medicare Reimbursement Flawed
A spokesperson for Memorial Hermann disputed the HBCH’s analysis, telling the Houston Chronicle that “Medicare reimbursement is a flawed and an inappropriate benchmark to use for commercial payments, as Medicare payments do not cover the cost of services provided.”
But the HBCH analysis also disclosed that each hospital was charging private insurers more than double the breakeven, defined as the amount needed “to make up for any shortfalls from public sector payers such as Medicare and Medicaid and uninsured patients.” And they “achieved a commercial profit margin of more than 45%” over the breakeven.
The fourth hospital, Baylor St. Luke’s, charged 216% over Medicare and had a commercial profit margin of close to 20%.
The Medicare claims data came from a RAND study, titled, “Prices Paid to Hospitals by Private Health Plans.” The 53-page report is accompanied by a downloadable spreadsheet with details on prices at more than 4,000 hospitals in 49 states plus the District of Columbia. Released in May, it covers data from 2018 through 2020.
The HBCH analysts combined data from this report with data from the NASHP Hospital Cost Tool (HCT), which was released in April. The HCT allows anyone with a web browser to look up cost metrics for 4,600 hospitals in the US. The numbers, available through 2019, include revenue, profitability, and breakeven points. It also incorporates an earlier set of the RAND Medicare claims data.
An NASHP press release notes that the breakeven calculation “accounts for a hospital’s operating costs, profit or loss from public coverage programs, charity care and uninsured patient hospital costs, Medicare disallowed costs, and a hospital’s other income and expense.”
The HBCH press release notes that hospitals need only 127% of Medicare to break even.
National Numbers
Nationally, the RAND study found wide variations in prices paid by private health plans from state to state. “In Texas, prices paid to hospitals for privately insured patients by employers averaged 252% of what Medicare would have paid,” the HBCH press release noted.
But that places Texas around the middle of the pack compared with other states. According to a Rand press release, prices charged to commercial payers were over 310% of Medicare in Florida, West Virginia, and South Carolina. But in Arkansas, Hawaii, and Washington, the numbers were below 175% of Medicare. The overall national average was 224%, the study found.
The RAND report’s downloadable spreadsheet breaks out the numbers by state and for individual health systems by name.
Numbers like these could have policy ramifications as employers seek to reduce the costs of providing health benefits. “The data is already being used to guide a new path forward,” states the HBCH press release. “As an example, HBCH and its members are working to demand transparency and change policies in the upcoming Texas 88th Legislative Session to eliminate anti-competitive language between hospitals and health plans.”
Clinical laboratory managers and pathologists working in hospitals and health systems will want to watch how employer groups respond to future studies of hospital pricing compared to the Medicare program. Employers increasingly are dissatisfied with the status quo in how hospitals and doctors price their services to health insurers.
It is reasonable to expect more studies to be published that compare what hospitals charge private health insurers versus what they are paid by the Medicare program.
Shultz and fellow whistleblower Erika Cheung spoke to clinical laboratory scientists and attendees at the AACC Annual Scientific Meeting in Chicago
Two whistleblowers who raised concerns about the accuracy of Theranos’ blood test results offered thought-provoking comments on how the maligned company operated within current requirements for clinical laboratory-developed tests (LDTs) during last week’s American Association of Clinical Chemistry (AACC) Annual Scientific Meeting.
“The laboratory-developed test loophole that Theranos exploited should be closed,” said Tyler Shultz, who complained about Theranos’ inaccurate testing to regulators and TheWall Street Journal. Both Shultz and fellow Theranos whistleblower Erika Cheung were former employees at the now-defunct company.
“There are a lot of good use cases for LDTs, so they shouldn’t all be shut down,” Shultz continued. “But in general, I do think that if FDA-cleared clinical laboratory tests are available, those tests should be used instead of a homebrew test that hasn’t been held to the same standard that an FDA-cleared product has.”
Both trials examined the dubious claims that Theranos’ technology worked properly during the company’s blazing ascent with both Silicon Valley investors and the media from 2003 to 2014. The company said it could take a few drops of blood from a patient and successfully analyze the specimen using a machine called Edison, although Shultz, Cheung, and others questioned the results.
By 2015, problems with Theranos’ testing began to go public. The company shut down in 2018 after Holmes and Balwani were indicted.
However, proposed legislation is before Congress that would transfer oversight of LDTs to the US Food and Drug Administration (FDA). The bill, known as the Verifying Accurate Leading-edge IVCT Development (VALID) Act, is now embedded in the larger Senate bill FDA Safety and Landmark Advancements Act of 2022 (S.4348).
Theranos’ saga did provide at least some inspiration for legislators filing the VALID Act. However, Cheung noted that trying to regulate all LDTs based the bad behavior of Theranos’ executives is a complex issue.
“Regulation is always tricky,” she said. “When you take an example of a very extraordinary case and a very specific circumstance [such as Theranos] and try to generalize that in terms of what is the behavior of all labs, you have to be careful.”
Proponents state FDA pre-market approval is needed for in vitro diagnostic tests because they are like medical devices. Opponents counter that the VALID Act would stifle innovation because of the costs involved with FDA review, particularly at academic medical laboratories.
Cheung questioned whether FDA review of Theranos’ technology would have averted patient and investor fraud by Holmes and Balwani.
“Would it have been the case that if it was necessary for the FDA to review Theranos’ LDTs, that it could have stopped it? Maybe,” Cheung told AACC attendees. “But you’re also dealing with a company that lied a lot. There were lots of things that Theranos had to submit to CLIA or to CMS in order to say that they were able to test certain types of patients.”
Shultz had similar feelings regarding a hypothetical FDA review of Theranos’ product, which will ring true with pathologists and clinical laboratory professionals who understand medical laboratory compliance and how the FDA regulate diagnostic instruments and kits.
“When you bring something to the FDA, they look at the data. They don’t go in and actually do third-party validation to see if your device works,” he said. “They just look at the data, and the [Theranos] data was largely manipulated. So, if you forced Theranos to go through the FDA process, I’m not sure if it would have prevented [the fraud].”
Genetic testing for the health and wellbeing of beloved pets is not unlike clinical laboratory testing to develop personalized treatments for humans
Clinical laboratory professionals know that the same patients who complain about a $10 copay for their own laboratory testing will happily pay veterinarians tons of cash to test and treat their beloved pets. And as genetic testing for humans becomes commonplace, more people are seemingly willing to pay for genetic analyses of their pets as well.
In June, animal health company Zoetis, Inc. announced it had completed the acquisition of pet care genetics company Basepaws. The financial terms of the deal were not disclosed.
California-based Basepaws is a privately-held company that provides pet owners with analytics, genetic tests, and early health risk assessments for their pets through oral microbiome analysis. Founded in 2017, Basepaws was responsible for the creation of the first at-home genetic testing platform for cats.
Basepaws sells easy-to-use genetic testing kits for cats that allow pet owners and veterinarians to better understand an individual pet’s predisposition to certain illnesses and increase the likelihood of early detection and treatment of those diseases.
It’s not unlike the drive toward personalized medicine and genetic testing that is at the core of human precision medicine.
Different Breeds, Different Needs
Basepaws has a slogan: “Different breeds, different needs.” This means, according to their website, each individual cat has a unique composition of genetic traits that can relate to its needs for optimal health and wellbeing. Obviously, this would apply to all pets.
“As a pioneer in pet care genetics, the California-based Basepaws offers easy-to-use genetic screening tools for the early detection of disease risk in pets, as well as individualized breed and health reports that can identify traits, biomarkers, and potential hereditary conditions for pets. Basepaws helps pet owners and veterinarians understand an individual pet’s risk for disease and can lead to more meaningful engagements and increased likelihood of early detection and treatment of disease,” states a Zoetis press release announcing the acquisition.
“The addition of Basepaws will enhance our portfolio in the precision animal health space and inform our future pipeline of pet care innovations,” said Kristin Peck, CEO of Zoetis, in the press release. “Working together, we can continue to provide veterinarians and pet owners with more comprehensive ways to proactively manage the health, wellness, and quality of care for their animals.”
Test Results for Hundreds of Genetic Disorders and Health Markers
Basepaws currently sells three DNA test kits for felines on their webpage. The current price for an oral health test kit that identifies active signs of dental diseases is $69. Their breed and cat health DNA test kit, which provides results for over 115 known feline genetic markers, is $129. Their most comprehensive testing kit is a whole genome sequencing (WGS) kit which is currently on sale for $399.
After receiving a test kit by mail, the purchaser registers the kit online, takes a single buccal swab from their kitty’s inner cheek, and then mails the sample to Basepaws. Lab personnel then extract the cat’s DNA from the sample and perform quality checks to ensure the sample is acceptable for genetic testing. It takes four to six weeks for consumers to receive test results.
According to the company’s website, Basepaws’ WGS test provides results related to 43 genetic disorders that are represented by 65 health markers. The listing of genetic disorders contained in the Health Marker section of the Basepaws report includes data on:
Metabolic disorders,
Musculoskeletal and connective tissue disorders,
Renal disorders,
Cardiovascular disorders,
Blood disorders,
Eye disorders,
Endocrine disorders,
Skin disorders, and
Autoimmune disorders.
“The Basepaws team has done an amazing job demonstrating how genetic testing and data can improve how we care for the pets in our lives,” Abhay Nayak, Executive Vice President at Zoetis, told ROI-NJ. “With the addition of Basepaws, Zoetis will continue to strengthen our portfolio of products for precision animal health, across genetics, diagnostics, and data analytics for pets and livestock. We are also excited by how Basepaws’ feline genomic and microbiome database will help enhance our [research and development] capabilities and inform the future of our pet care pipeline.”
Zoetis, based in Parsippany, N.J., manufactures vaccines, medicines, clinical laboratory diagnostics, and other technologies for the benefit of companion pets and livestock. The Fortune 500 company generated $7.8 billion in revenue in 2021, according to its website.
The article also stated that the global animal genetic testing market was valued at $990 million in 2020 and is only expected to rise.
Thus, spending money keeping our pets healthy is not only a typical element of Americans’ lives, but also a mega-billion-dollar industry. With at-home genetic testing for humans increasing in popularity, it’s likely testing for animals will follow that trend as well.
In the future, some clinical laboratory organizations may want to consider assessing the animal DNA testing market for its potential to be a useful source of new revenue, especially because potential customers will pay cash when they order genetic tests for their dogs and cats.
In fact, the UB study suggests traditional anatomical methods for determining the evolutionary relationships between species may not be as accurate as once thought, an article in SciTechDaily reported.
Nevertheless, the UB’s research into convergent evolution is unlocking new insights into how genes evolve over time and this new knowledge may help researchers develop genetic tests that more accurately identify different diseases and health conditions.
Additionally, studies that bring a better understanding of how beneficial genetic mutations work their way into a species’ genome might also aid researchers in developing personalized clinical laboratory testing and therapies based on manipulating a patient’s genetic sequences in ways that would be beneficial.
Gene Sequencing More Accurate at Determining Evolutionary Relationships
The UB study suggests that existing evolutionary (phylogenetic) trees may need to be reconsidered. To put a finer point on the findings, a UB news release on the study states, “determining evolutionary trees of organisms by comparing anatomy rather than gene sequences is misleading.”
The UB scientists used genetic sequencing to quickly—and more cost effectively—determine evolutionary relationships as compared to traditional morphology (anatomy and structure), according to the news release.
They found genetic data that revealed surprising relationships about where the sequenced species originated, and which differed with prior conclusions that were drawn based on the species’ appearance. The findings suggest there may be need to “overturn centuries of scientific work in classifying relation of species by physical traits,” the UB scientists said.
Molecular Data Leads to New Insights into Convergent Evolution
The UB study’s use of genetic sequencing led the researchers to a greater understanding of convergent evolution, defined by “a characteristic evolving separately in two genetically unrelated groups of organisms,” according to UB.
For example, wings are a widely developed characteristic. But they are not necessarily a sign of relatedness when it comes to birds, bats, and insects.
“Now with molecular data, we can see that convergent evolution happens all the time—things we thought were closely related often turn out to be far apart on the tree of life,” Wills said, adding, “Individuals within a family don’t always look similar; it’s the same with evolutionary trees, too.”
Family Trees: Morphology Versus Molecular
In their paper, the UB researchers acknowledged the importance of phylogenies (evolutionary history of species) in areas of biology, including medicine. They aimed to study a better way to produce accurate phylogenetic trees.
“Phylogenetic relationships are inferred principally from two classes of data: morphological and molecular,” they wrote, adding, “The superiority of molecular trees has rarely been assessed empirically.”
So, they set out to compare the two approaches to building evolutionary trees:
Traditional morphology analysis, and
Phylogenetic trees developed using molecular data.
Using 48 pairs of morphological and molecular trees, they mapped data geographically.
“We show that, on average, molecular trees provide a better fit to biogeographic data than their morphological counterparts, and that biogeographic congruence increases over research time,” the researchers wrote.
Biogeography a Better Gauge of Relatedness than Anatomy
The study also found animals on molecular trees lived geographically closer as compared to groups on morphological trees.
For example, molecular studies put aardvarks, elephants, golden moles, swimming manatees, and elephant shews in an Afrotheria group, named for Africa, which is where they came from. Therefore, the biogeography matches, however the appearances of these mammals clearly do not, the UB scientists point out.
“What’s most exciting is that we find strong statistical proof of molecular trees fitting better not just in groups like Afrotheria, but across the tree of life in birds, reptiles, insects, and plants,” said Jack Oyston PhD, UB Department of Biology and Biochemistry Research Associate and first author of the study, in the news release.
The researchers believe their findings support the accuracy of genetic-themed trees.
“It being such a widespread pattern makes it much more potentially useful as a general test of different evolutionary trees. But it also shows just how pervasive convergent evolution has been when it comes to misleading us,” Oyston added.
Advantages of Molecular Data
In their Nature Communications Biology paper, the UB scientists wrote that molecular data offer up these advantages over morphology:
Widely available in vast quantity.
Opportunity exists to “search, repurpose, and reanalyze sequenced data alongside novel sequences.”
Less subjectivity in researchers’ analysis.
Well-developed data at the ready and “still in their infancy.”
The University of Bath’s study of convergent evolution, phylogenetic trees, and comparison of molecular data versus morphology, has implications for medical laboratories. Should their research lead to new insights into how genes evolve over time, diagnostics professionals may have new information to identity diseases and work with others to precisely treat patients.
Nearly two years after passage of price transparency law, only a small number of the nation’s hospitals are fully compliant, according to two separate reports
Price transparency is a major trend in the US healthcare system. Yet, hospitals, physicians, clinical laboratories, and other providers have been reticent to design their websites so it is easy for patients to find prices in advance of clinical care. Now comes news that federal officials are ready to issue fines to hospitals that fail to comply with regulations mandating price transparency for patients.
Many of the largest healthcare networks claim that complying with federal hospital price transparency regulation is costly, time consuming, and provides no return on investment. Nevertheless, the federal Centers for Medicare and Medicaid Services is quite serious about enforcing price transparency laws, and to that end the agency has, for the first time, levied fines against two hospitals in Georgia that have not complied with the regulations.
As many pathologists and medical laboratory managers know, on January 1, 2021, a federal rule on price transparency for medical facilities went into effect. The rule requires hospitals—as well as clinical laboratories and other healthcare providers—to post a comprehensive list of their services and the pricing for those services on their websites, and to provide access to a patient-friendly tool to help consumers shop for 300 common services.
The CMS recently issued its first penalties to two hospitals located in Georgia for violating the law by not updating their websites or replying to the agency’s warning letters. The letters CMS sent to the two hospitals alleged there were several violations of the transparency rules, including the failure to post a listing of their charges on their websites and requested corrective action plans by the hospitals.
In November 2021, Northside Hospital Atlanta informed regulators that consumers should call or email the facility to obtain price estimates for services. Later in January 2022, during a “technical assistance call,” a hospital representative told CMS “the previous violations had not been corrected and, in fact, the hospital system had intentionally removed all previously posted pricing files,” according to a Notice of Imposition of a Civil Monetary Penalty letter CMS sent to Robert Quattrocchi, President and Chief Executive Officer, Northside Hospital Atlanta.
Under the rules of the Hospital Price Transparency law, each hospital operating in the US is required to provide clear, accessible pricing information online about the items and services they provide in two ways:
As a comprehensive machine-readable file listing all items and services.
In a display of shoppable services in a consumer-friendly format.
CMS fined Northside Hospital Atlanta $883,180 and Northside Cherokee Hospital $214,320 for noncompliance with the law. The penalties are calculated based on the size of the hospital and the length of time of the noncompliance—up to $300 per day. In addition, the facilities could endure further monetary penalties if they continue to fail to comply. The organizations will have 30 days to appeal the charges or have 60 days to remit payment for the fines.
Both hospitals are owned by Northside, a Georgia health system with five acute care hospitals, more than 250 outpatient facilities, over 4,100 providers, and 25,500 employees, according to the provider’s website.
Compliance with Price Transparency Laws Low
Analysis of the healthcare industry shows that many facilities are not in compliance with the transparency rules. In April, a report released by health IT firm KLAS Research, found that hospitals believe the transparency rule is too costly to implement and confusing to consumers, which helps explain the low compliance issues. KLAS surveyed 66 hospital revenue cycle leaders for their report.
“There are concerns about cost, data accuracy, and patient options of pricing tools; some respondents worry about patients’ ability to understand the displayed pricing data, and today, most patients are unaware online pricing information exists,” the report states. In addition, the report notes that “many organizations are not investing beyond the bare minimum requirements, and they don’t plan to do more until there is further clarity around the regulations and the expectations going forward.”
The KLAS report also noted that organizations are struggling to find the resources to comply with the price transparency rule and consider it a financial burden to continually add new employees and technology to become and remain in compliance. Many organizations see no merit in investing in a regulation that provides no return on that investment.
Another compliance report released in February by Patient Rights Advocate maintained that only 14.3% of the 1,000 hospitals they reviewed were in full compliance with the Hospital Price Transparency regulation. About 37.9% of the hospitals posted a sufficient detailing of service rates, but over half of those hospitals were noncompliant in other criteria of the rule, such as rates by insurer and insurance plans.
“We are now entering the second year since the Hospital Price Transparency rule became law, and compliance remains at very low levels,” according to the report. “The largest hospital systems are effectively ignoring the law, with no consequences.”
The Patient Rights Advocate analysis also found that a mere 0.5% of hospitals owned by the three largest hospital systems in the country—HCA Healthcare, CommonSpirit Health, and Ascension—were in full compliance of the law.
Notably, only two of the 361 hospitals owned by these three hospital systems were fully compliant. In addition, none of the 188 hospitals owned by HCA Healthcare, the largest for-profit hospital system in the country, were in compliance.
Hospitals Fail to Provide Consumers with Critical Information
The Patient Rights Advocate report found that the most significant reason for noncompliance was failure to post all payer-specific and plan-specific negotiated rates on their websites. They estimated that 85.7% of the 1,000 hospitals reviewed did not post a complete machine-readable file of standard charges, as required by the law.
“The lack of compliance by hospitals is about more than simply the failure to follow the legal requirements,” the report states. “It is also about the failure of hospitals to provide critically needed information to consumers so they can make better health decisions. Empowered with comparative price and quality information in advance of care, consumers, including employers and unions, can improve health outcomes while lowering costs by taking advantage of the benefits of competitive market efficiencies.”
With the CMS starting to issue fines for noncompliance, it is probable that more healthcare organizations will focus on adhering to the Hospital Price Transparency law. Since the transparency rules also apply to clinical laboratories, lab managers should be aware of the regulations and any further enforcement actions taken by the CMS.