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Number of Unfilled Medical Residencies Increases in Alberta and Other Areas of Canada

Family medicine academic departments in Canada are dealing with a shortage of applicants qualified for their residency programs, mirroring the shortage of pathologists

For the past decade, the number of medical residencies in Alberta Canada that went unfilled have increased each year. Now, just like in many parts of America, the province is experiencing severe medical staffing shortages that includes clinical laboratories and pathology groups.

According to data compiled by the Canadian Resident Matching Service (CaRMS), after the first round of matching for post-graduate training spots as many as 12% of all spots went unfilled, especially in family medicine, the Canadian Broadcasting Corporation (CBC) reported.

Though the trend seems to be worse in Alberta, the resident shortage is affecting the entire Canadian healthcare system. According to the Angus Reid Institute, approximately half of all Canadians cannot find a doctor or get a timely appointment with their current doctor.

That is fueling predictions of an increased physician shortage in coming years, particularly in Alberta.

The graphic above taken from the CBC report shows how the number of residencies in family medicine that go unfilled has been increasing for the past 10 years. This trend mirrors similar trends affecting clinical laboratories and pathology groups around the world. (Graphic copyright: Canadian Broadcasting Corporation.)

Internationally Trained versus Home-grown Doctors

Canada’s current doctor shortage appears to be rooted in red tape that determines which MDs qualify for residency matching. According to John Paul Tasker, a senior journalist at the CBC, “there’s no shortage of doctors in Canada. What we have is a shortage of licensed doctors.” In his article, “Canada Is Short of Doctors—and It’s Turning Away Hundreds of Its Own Physicians Each Year,” Tasker notes that there may be as many as 13,000 medical doctors in Canada who are not currently practicing.

What’s standing in the way of Canadian doctors becoming licensed to practice? Some claim the system of residency matching is discriminatory towards Canadian doctors who received their training outside of Canada. Rosemary Pawliuk, President of the Society for Canadians Studying Medicine Abroad, is one of those who believe the system of matching is broken.

“They have cute slogans like, ‘You’re wanted and welcome in Canada,’ but when you look at the barriers, it’s very clear that you should not come home. Their message is essentially, ‘Go away’ and so [doctors] do,” Pawliuk told the CBC.

According the Pawliuk, “the current residency selection system puts internationally trained Canadian doctors at a serious disadvantage,” the CBC reported. “The Canadian public should be entitled to the best qualified Canadian applicant. Whether they’ve graduated from a Canadian school or an international school, whether they’re a Canadian by birth or if they’re an immigrant, they should be competing on individual merit,” she added.

Canada’s Medical School Matching Bias

In Canada’s current matching system, medical schools decide who gets a residency. Critics say the schools are biased towards Canadian-educated doctors and overlook foreign-trained doctors. About 90% of all residencies in Canada are set aside for Canadian-trained doctors and the remaining spots are left for the physicians trained abroad, CBC noted.

It is important to note that these doctors who are trained abroad are either Canadian citizens or permanent residents. Thus, it’s not a question of citizens from other countries competing with Canadian citizens.

So, if a surplus of doctors are being shut out of residency training opportunities, why are there open slots in Alberta? Some believe this indicates individuals are not interested in practicing medicine in Alberta.

“People aren’t interested in staying or coming to Alberta,” family physician and Alberta Medical Association (AMA) President, Fredrykka Rinaldi, MD, told CBC.

But, Nathan Rider, MD, President of the Professional Association of the Resident Physicians of Alberta (PARA), claims he has not heard of residents turning down Alberta. He notes that the factors of where a resident may want to go geographically often depend on factors such as proximity to loved ones, cost of living, and program culture.

Second Round Residency Matching Fairs Better

Not all are concerned about the vacancies in the first round of matching, however. University of Calgary Dean of Medicine, Todd Anderson, MD, and the University of Alberta Dean of Medicine and Dentistry Brenda Hemmelgarn, MD, PhD, both see the second round as more important.

But Rinaldi still has concerns, “We may fill them with 42 disinterested people who have no interest in family medicine,” she says.

Anderson admits that “Across the country, over the last five or more years, family medicine has become less popular with medical students graduating from medical schools than it was in the years before.”

Therefore, both Anderson’s and Hemmelgarn’s schools have changed curriculum to put more of an emphasis on family medicine. Perhaps with these changes, and possibly an opening for internationally-trained Canadian doctors to achieve residency positions, Alberta’s—indeed all of Canada’s—residency match days will be better attended.

In the United States, there is little news coverage about serious problems with the health systems in other nations. The experience of residency programs in Canada, as explained above, demonstrates how a different national health system has unique issues that are not identical to issues in the US healthcare system. What is true is that Canada is dealing with a similar shortage of skilled medical technologists (MTs) and clinical laboratory scientists (CLSs), just like here in the United States.

Ashley Croce

Related Information:

Alberta Doctors Sound Alarm Over Low Number of Grads Seeking Residency in Province

Doc Deficits: Half of Canadians Either Can’t Find a Doctor or Can’t Get a Timely Appointment with the One They Have

Canada is Short of Doctors—and It’s Turning Away Hundreds of Its Own Physicians Each Year

B.C. Fights to Maintain the Barriers That Keep Foreign-Trained Doctors from Working

Can’t Find a Family Doctor in Alberta? Training More Medical Students Is Not the Silver Bullet

Forbes Senior Contributor Covers Reasons for Growing Staff Shortages at Medical Laboratories and Possible Solutions

US Hospitals Continue to Be Squeezed by Shortage of Nurses, Rising Salaries

US Hospitals Continue to Be Squeezed by Shortage of Nurses, Rising Salaries

It is more than a shortage of nurses, as most clinical laboratories report the same shortages of medical technologists and increased labor costs

Just as hospital-based clinical laboratories are unable to hire and retain adequate numbers of medical technologists (MTs) and clinical laboratory scientists (CLSs), the nursing shortage is also acute. Compounding the challenge of staffing nurses is the rapid rise in the salaries of nurses because hospitals need nurses to keep their emergency departments, operating rooms, and other services open and treating patients while also generating revenue.

The nursing shortage has been blamed on burnout due to the COVID-19 pandemic, but nurses also report consistently deteriorating conditions and say they feel undervalued and under-appreciated, according to Michigan Advance, which recently covered an averted strike by nurses at 118-bed acute care McLaren Central Hospital in Mt. Pleasant and 97-bed teaching hospital MyMichigan Medical Center Alma, both in Central Michigan.

“Nurses are leaving the bedside because the conditions that hospital corporations are creating are unbearable. The more nurses leave, the worse it becomes. This was a problem before the pandemic, and the situation has only deteriorated over the last three years,” said Jamie Brown, RN, President of the Michigan Nurses Association (MNA) and a critical care nurse at Ascension Borgess Hospital in Kalamazoo, Michigan Advance reported.

Jamie Brown, RN

“The staffing crisis will never be adequately addressed until working conditions at hospitals are improved,” said Jamie Brown, RN (above), President of the Michigan Nurses Association in a press release. Brown’s statement correlates with claims by laboratory technicians about working conditions in clinical laboratories all over the country that are experiencing similar shortages of critical staff. (Photo copyright: Michigan Nurses Association.)

Nurse Understaffing Dangerous to Patients

In the lead up to the Michigan nurses’ strike, NPR reported on a poll conducted by market research firm Emma White Research LLC on behalf of the MNA that found 42% of nurses surveyed claimed “they know of a patient death due to nurses being assigned too many patients.” The same poll in 2016 found only 22% of nurses making the same claim.

And yet, according to an MNA news release, “There is no law that sets safe RN-to-patient ratios in hospitals, leading to RNs having too many patients at one time too often. This puts patients in danger and drives nurses out of the profession.”

Other survey findings noted in the Emma White Research memo to NPR include:

  • Seven in 10 RNs working in direct care say they are assigned an unsafe patient load in half or more of their shifts.
  • Over nine in 10 RNs say requiring nurses to care for too many patients at once is affecting the quality of patient care.
  • Requiring set nurse-to-patient ratios could also make a difference in retention and in returning qualified nurses to the field.

According to NPR, “Nurses across the state say dangerous levels of understaffing are becoming the norm, even though hospitals are no longer overwhelmed by COVID-19 patients.”

Thus, nursing organizations in Michigan, and the legislators who support change, have proposed the Safe Patient Care Act which sets out to “to increase patient safety in Michigan hospitals by establishing minimum nurse staffing levels, limiting mandatory overtime for RNs, and adding transparency,” according to an MNA news release.

Huge Increase in Nursing Costs

Another pressure on hospitals is the rise in the cost of replacing nurses with temporary or travel nurses to maintain adequate staffing levels.

In “Hospital Temporary Labor Costs: a Staggering $1.52 Billion in FY2022,” the Massachusetts Health and Hospital Association noted that “To fill gaps in staffing, hospitals hire registered nurses and other staff through ‘traveler’ agencies. Traveler workers, especially RNs in high demand, command higher hourly wages—at least two or three times more than what an on-staff clinician would earn. Many often receive signing bonuses. In Fiscal Year 2019, [Massachusetts] hospitals spent $204 million on temporary staff. In FY2022, they spent $1.52 billion—a 610% increase. According to the MHA survey, approximately 77% of the $1.52 billion went to hiring temporary RNs.”

It’s likely this same scenario is playing out in hospitals all across America.

Are Nursing Strikes a Symptom of a Larger Healthcare Problem?

In “Nurses on Strike Are Just the Tip of the Iceberg. The Care Worker Shortage Is About to Touch Every Corner of the US Economy,” Fortune reported that nationally the US is facing a shortage of more than 200,000 nurses.

“But the problem is much bigger,” Fortune wrote. “Care workers—physicians, home health aides, early childhood care workers, physician assistants, and more—face critical challenges as a result of America’s immense care gap that may soon touch every corner of the American economy.”

Clinical laboratories are experiencing the same shortages of critical staff due in large part to the same workplace issues affecting nurses. Dark Daily covered this growing crisis in several ebriefings.

In “Forbes Senior Contributor Covers Reasons for Growing Staff Shortages at Medical Laboratories and Possible Solutions,” we covered an article written by infectious disease expert Judy Stone, MD, in which she noted that factors contributing to the shortage of medical technologists and other clinical laboratory scientists include limited training programs in clinical laboratory science, pay disparity, and staff retention.

We also covered in that ebrief how the so-called “Great Resignation” caused by the COVID-19 pandemic has had a severe impact on clinical laboratory staffs, creating shortages of pathologists as well as of medical technologists, medical laboratory technicians, and other lab scientists who are vital to the nation’s network of clinical laboratories.

And in “Clinical Laboratory Technician Shares Personal Journey and Experience with Burnout During the COVID-19 Pandemic,” we reported on the personal story of Suzanna Bator, a former laboratory technician with the Cleveland Clinic and with MetroHealth System in Cleveland, Ohio. Bator shared her experiences in an essay for Daily Nurse that took a personalized, human look at the strain clinical laboratory technicians were put under during the SARS-CoV-2 pandemic. Her story presents the quandary of how to keep these critical frontline healthcare workers from experiencing burnout and leaving the field.

Did Experts See the Shortages Coming?

Hospitals across the United States—and in the UK, according to Reuters—are facing worker strikes, staff shortages, rising costs, and uncertainty about the future. Just like clinical laboratories and other segments of the healthcare industry, worker burnout and exhaustion in the wake of the COVID-19 pandemic are being cited as culprits for these woes.

But was it predictable and could it have been avoided?

“One of the big things to clear up for the public is that … we saw the writing on the wall that vacancies were going to be a problem for us, before the pandemic hit our shores,” Christopher Friese, PhD, professor of Nursing and Health Management Policy at the University of Michigan (UM), told NPR. Friese is also Director of the Center for Improving Patient and Population Health at UM.

Effects of the COVID-19 pandemic, and staffing shortages exasperated by it, will be felt by clinical laboratories, pathology groups, and the healthcare industry in general for years to come. Creative solutions must be employed to avoid more staff shortages and increase employee retention and recruitment.

Ashley Croce

Related Information:

Amid Burnout and Exhaustion, Nurses at Two Mid-Michigan Hospitals OK New Contracts

‘Everyone Is Exhausted and Burned Out’: McLaren Central Nurses Authorize Potential Strike

New Poll Shows a Nurse-to-Patient Ratio Law Could Be Key to Addressing Staffing Crisis

42% of Michigan Nurses Say High Patient Load Led to Deaths

Michigan Nurses Report More Patients Dying Due to Understaffing, Poll Finds

COVID-19’s Impact on Nursing Shortages, the Rise of Travel Nurses, and Price Gouging

Survey of Registered Nurses Living or Working in Michigan

This Nursing Shortage Requires Innovative Solutions

Nurses on Strike Are Just the Tip of the iceberg. The Care Worker Shortage Is About to Touch Every Corner of the US Economy

Workers Stage Largest Strike in History of Britain’s Health Service

Nursing Shortage by State: Which US States Need Nurses the Most and Which Ones Will Have Too Many?

England’s National Health Service to Offer Widespread Rapid Whole Genome Sequencing for Children and Babies

Research in the UK and US into how rapid WGS can prevent deaths and improve outcomes for kids with rare genetic diseases may lead to more genetic testing based in local clinical laboratories

Genetic scientists with the National Health Service (NHS) in England have embarked on an ambitious plan to offer rapid whole genome sequencing (rWGS) for children and babies with serious illnesses, as part of a larger initiative to embrace genomic medicine in the United Kingdom (UK).

The NHS estimates that the plan will benefit more than 1,000 children and babies each year, including newborns with rare diseases such as cancer, as well as kids placed in intensive care after being admitted to hospitals. Instead of waiting weeks for results from conventional tests, clinicians will be able to administer a simple blood test and get results within days, the NHS said in a press release.

The press release notes that about 75% of rare genetic diseases appear during childhood “and are responsible for almost a third of neonatal intensive care deaths.”

Here in the United States, pathologists and clinical laboratory managers should see this development as a progressive step toward expanding access to genetic tests and whole genome sequencing services. The UK is looking at this service as a nationwide service. By contrast, given the size of the population and geography of the United States, as this line of medical laboratory testing expands in the US, it will probably be centered in select regional centers of excellence.

The NHS laid out its implementation plan in a strategy paper published on NHS England’s website titled, “Accelerating Genomic Medicine in the NHS.”

“This strategy sets out how more people will be empowered to take preventative action following risk-based predictions, receive life-changing diagnoses, and get the support needed to live with genomically-informed diagnoses alongside improved access to cutting-edge precision [medicine] treatments. It also outlines how the NHS will accelerate future high-quality genomic innovation that can be adopted and spread across the country, leading to positive impacts for current and future generations,” the NHS wrote.

Amanda Pritchard

“This global first is an incredible moment for the NHS and will be revolutionary in helping us to rapidly diagnose the illnesses of thousands of seriously ill children and babies—saving countless lives in the years to come,” said NHS chief executive Amanda Pritchard (above) in a press release announcing the program. (Photo copyright: Hospital Times.)

New Rapid Whole Genome Sequencing Service

The NHS announced the plan following a series of trials last year. In one trial, a five-day old infant was admitted to a hospital in Cheltenham, Gloucester, with potentially deadly levels of ammonia in his blood. Whole genome sequencing revealed that changes in the CPS1 gene were preventing his body from breaking down nitrogen, which led to the spike in ammonia. He was given life-saving medication in advance of a liver transplant that doctors believed would cure the condition. Without the rapid genetic test, doctors likely would have performed an invasive liver biopsy.

Following sample collection at NHS locations, the genetic tests will be performed at the new National Rapid Whole Genome Sequencing Service, part of the South West NHS Genomic Laboratory Hub run by the Royal Devon University Healthcare NHS Foundation Trust in Exeter, UK.

Using a simple blood test, the new newborn genetic screening service in England is expected to benefit more than 1,000 critically ill infants each year, potentially saving their lives. “The rapid whole genome testing service will transform how rare genetic conditions are diagnosed,” explained Emma Baple, PhD, Professor of Genomic Medicine at University of Exeter Medical School and leader of the National Rapid Whole Genome Sequencing Service in the press release. “We know that with prompt and accurate diagnosis, conditions could be cured or better managed with the right clinical care, which would be life-altering—and potentially life-saving—for so many seriously unwell babies and children,” Precision Medicine Institute reported.

According to The Guardian, test results will be available in two to seven days.

Along with the new rWGS testing service, the NHS announced a five-year plan to implement genomic medicine more broadly. The provisions include establishment of an ethics advisory board, more training for NHS personnel, and an expansion of genomic testing within the existing NHS diagnostic infrastructure. The latter could include using NHS Community Diagnostics centers to collect blood samples from family members to test for inherited diseases.

UK’s Longtime Interest in Whole Genome Sequencing

The UK government has long been interested in the potential role of WGS for delivering better outcomes for patients with genetic diseases, The Guardian reported.

In 2013, the government launched the 100,000 Genomes Project to examine the usefulness of the technology. In November 2021, investigators with the project reported the results of a large pilot study in which they analyzed the genomes of 4,660 individuals with rare diseases. The study, published in the New England Journal of Medicine (NEJM) titled, “100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care—Preliminary Report,” found “a substantial increase in yield of genomic diagnoses made in patients with the use of genome sequencing across a broad spectrum of rare disease.”

The study’s findings suggest that use of WGS “could save the NHS millions of pounds,” The Guardian reported.

Whole Genome Sequencing System for Newborns in the US

Researchers in the United States are also looking at the potential for WGS to improve health outcomes in children with genetic conditions. Last August, a research team led by Stephen F. Kingsmore, MD, DSc, President/CEO of Rady Children’s Institute for Genomic Medicine in San Diego, authored a study published in the American Journal of Human Genetics (AJHG) titled, “A Genome Sequencing System for Universal Newborn Screening, Diagnosis, and Precision Medicine for Severe Genetic Diseases,” that described a scalable prototype for a newborn screening system.

“This NBS-rWGS [newborn screening by rapid whole genome sequencing] system is designed to complement the existing newborn screening process and has the potential to eliminate the diagnostic and therapeutic odyssey that many children and parents face,” Kingsmore said in a press release. “Currently, only 35 core genetic disorders are recommended for newborn screening in the United States, but there are more than 7,200 known genetic diseases. Outcomes remain poor for newborns with a genetic disease because of the limited number of recommended screenings. With NBS-rWGS, we can more quickly expand that number and therefore potentially improve outcomes through precision medicine.”

A more recent 2023 study which examined 112 infant deaths at Rady Children’s Hospital found that 40% of the babies had genetic diseases. In seven infants, genetic diseases were identified post-mortem, and in five of them “death might have been avoided had rapid, diagnostic WGS been performed at time of symptom onset or regional intensive care unit admission,” the authors wrote.

“Prior etiologic studies of infant mortality are generally retrospective, based on electronic health record and death certificate review, and without genome information, leading to underdiagnosis of genetic diseases,” said Christina Chambers, PhD, co-author of the study, in a press release. “In fact, prior studies show at least 30% of death certificates have inaccuracies. By implementing broad use of genome sequencing in newborns we might substantially reduce infant mortality.” 

Pioneering work with whole genome sequencing for newborns, such as that being conducted by the clinical laboratory and genetic teams at Rady Children’s Hospital and the UK’s NHS, could allow doctors to make timely interventions for our most vulnerable patients.

—Stephen Beale

Related Information:

Study Suggests DNA Sequencing Could Reduce Infant Deaths, Often Caused by Genetic Disease

Novel Newborn Screening System Uses Rapid Whole Genome Sequencing and Acute Management Guidance to Screen and Diagnosis Genetic Diseases

Study Finds Association of Genetic Disease and Infant Mortality Higher than Previously Recognized: 41% of Infant Deaths Associated with Genetic Diseases

Genome Sequencing Could Prevent Infant Deaths

A Genome Sequencing System for Universal Newborn Screening, Diagnosis, and Precision Medicine for Severe Genetic Diseases

Genetic Testing in the PICU Prompts Meaningful Changes in Care

Major Policy Event in United Kingdom Aligns National Genetic Screening Program Using Rapid Whole Genome Sequencing

World-First National Genetic Testing Service to Deliver Rapid Life-Saving Checks for Babies and Kids

Genome Sequencing Trial to Test Benefits of Identifying Genetic Diseases at Birth

New NHS Genetic Testing Service ‘Could Save Thousands of Children’ in England

NHS England Completes Move Towards Rapid Whole Genome Sequencing of All Critically Ill Infants

Whole Genome Sequencing for Children: An Information Guide for Parents, Carers, and Families

Genomic Scientists Are Working to Make Human Reference Genome More Inclusive by Expanding the Pangenome

Project aims to create a new pangenome for genetic testing that will ensure better clinical laboratory testing and healthcare outcomes

Recent advances in genetics are motivating some scientists to proclaim the need to update the existing “master human genome”—currently based on a single individual’s genetic sequence—to make it more inclusive. This international research effort will have implications for personalized clinical laboratory testing and precision medicine.

Genetic scientists at the Human Pangenome Reference Consortium (HPRC), a project funded by the National Human Genome Research Institute (NHGRI), are working “to sequence and assemble genomes from individuals from diverse populations in order to better represent [the] genomic landscape of diverse human populations,” according to the organization’s website.

The project plans to evaluate a wide variety of reference genomes and develop a more diverse human pangenome (a multi-genome reference sequence) that will contain a larger cross-section of the human population. The HPRC scientists will be looking at genomes from specific countries, including Denmark, Japan, South Korea, Sweden, and the United Arab Emirates, The Guardian reported.

The increased diversity of reference genetic data will enable genomic researchers to increase the accuracy of precision medicine diagnostics and clinical laboratory testing.

Pui-Yan Kwok, MD, PhD

“One person is not representative of the world,” Pui-Yan Kwok, MD, PhD (above), Henry Bachrach Distinguished Professor, Cardiovascular Research Institute at the University of California, San Francisco, told The Guardian. “As a result, most genome sequencing is fundamentally biased.” And that bias, the researchers claim, affects the accuracy of clinical laboratory treatments and diagnostics. (Photo copyright: UCSF.)

Reference Genome for Genetic Sequencing is Based on One Person

Launched in 1990, The Human Genome Project studied all DNA in a select set of organisms. The project completed its first sequence of the human genome in 2003, which became the reference genome for thousands of genomic discoveries since then.

But there’s a problem.

Although a revolutionary breakthrough in genetic sequencing, that reference genome came from just one person. This means a significant portion of the human population is not represented in genetic research, and that bias, according to some scientists, “limits the kind of genetic variation that can be detected, leaving some patients without diagnoses and potentially without proper treatment,” according to The Guardian.

“Getting the right medicine to the right patient at the right time is the tagline,” Neil Hanchard, MD, DPhil, physician scientist and senior investigator for precision health research at the NHGRI in Bethesda, Maryland, told The Guardian.

The HPRC’s goal is to help mitigate reference biases that could hamper disease diagnoses and ensure all populations receive the best treatments for illness. 

According to its website, the organization’s main purpose includes:

  • Gene sequencing from a diverse set of samples with the newest technologies.
  • Fostering an ecosystem of assembly and pangenome tools.
  • Creating and releasing high-quality assemblies and pangenomes.
  • Embedding a team of scholars to address ethical, legal, and social implications of their work.
  • Forming international partnerships for the research.

HPRC Scientists Find Never-Sequenced Genetic Variants in Africa

Standard gene sequencing works by dividing DNA into tiny portions known as short reads, then sequencing and organizing the reads into a genome using an existing reference as a guide. However, this process renders larger blocks of variants, called structural variants (SVs), more difficult to read or even remain undetected, which can translate to a sequence that does not completely represent personal variations.

In 2019, the HPRC team of scientists analyzed genetic samples from 154 people from various parts of the world and discovered SV content that was missing from their reference sequence. A further study of genetic samples from 338 individuals that examined only extra inserted DNA detected the presence of almost 130,000 new sequences.

More recently, the HPRC researchers sampled 426 individuals from 50 ethnolinguistic groups from Africa and discovered a few million new single nucleotide variants (SNVs). Most of these distinct SNVs derived from populations that had not been previously sampled.

“We haven’t even touched SVs,” Hanchard told The Guardian. “But our preliminary data suggests it’s going to be more of the same.”

If an individual “is from a population quite different from the person from which the genome referenced is derived, there will be more misalignment when their short reads are mapped to the reference,” Pui-Yan Kwok, MD, PhD, Henry Bachrach Distinguished Professor, Cardiovascular Research Institute at the University of California, San Francisco, told The Guardian

“We may miss risk variants in those regions not represented in the reference,” he added.

HPRC Receives Clearance from NHGRI to Continue Research

Hanchard recognizes the benefits of regional references in genomic sequencing and is optimistic about the future of genomics and the ability to sequence more diverse populations.

“I would love to get to a point where everyone feels represented and that this is for them, as much as it is for any particular group,” he told The Guardian. “We are from one humanity, that’s the important part.”

On February 13, the HPRC received concept clearance for renewal of the program from the NHGRI, which plans to commit up to $10 million in total costs per year for the program over the next five years.

Genetic sequencing continues to emerge as a vital tool in the diagnoses and treatment of diseases. Ensuring that as many diverse populations as possible are included in genomic research is an important element for precision medicine and optimal healthcare.

Clinical laboratory managers and pathologists will want to stay updated on these developments, because much of this new knowledge about the pangenome will need to be incorporated when interpreting genetic sequences and developing diagnoses in support of personalized medicine.   

JP Schlingman

Related Information:

The Human Genome Needs Updating. But How Do We Make It Fair?

The Human Pangenome Project: A Global Resource to Map Genomic Diversity

Human Genome Project Fact Sheet

National Advisory Council for Human Genome Research (NACHGR)

Two New York City Hospitals Join New Genetic Study to Perform Whole Genome Sequencing on 100,000 Newborn Babies to Search for 250 Rare Diseases

Global Consortium of Scientists Develop New Whole Genome Sequencing Method That Brings Costs Down to $10 per Genome

Australian Researchers Discover New Form of Antimicrobial Resistance in Findings That Have Implications for Microbiology Laboratories

Study findings could lead to new biomarker targets for clinical laboratories working to identify AMR bacteria

Reducing and managing antimicrobial resistance (AMR) is a major goal of researchers and health systems across the globe. And it is the job of microbiologists and clinical laboratories to identify microbes that are AMR and those which are not to guide physicians as to the most appropriate therapies for patients with bacterial infections.

Thus, a recent discovery by researchers at the Wesfarmers Centre of Vaccines and Infectious Diseases, a division of the Telethon Kids Institute at Perth Children’s Hospital in Australia, will be of interest to medical laboratory leaders. The researchers may have learned how some bacteria dodge antibiotics in the human body. Their findings could lead to new diagnostics and better patient outcomes. 

The scientists published their findings in the journal Nature Communications titled, “Host-Dependent Resistance of Group A Streptococcus to Sulfamethoxazole Mediated by a Horizontally-Acquired Reduced Folate Transporter.”

Timothy Barnett, PhD

“AMR is a silent pandemic of much greater risk to society than COVID-19. In addition to 10 million deaths per year by 2050, the WHO estimates AMR will cost the global economy $100 trillion if we can’t find a way to combat antibiotic failure,” Timothy Barnett, PhD (above), Deputy Director and head of the Strep A Pathogenesis and Diagnostics team at Wesfarmers Centre of Vaccines and Infectious Diseases, told News Medical. Additional research may provide new targets for clinical laboratories tasked with identifying antimicrobial resistant bacteria. (Photo copyright: University of Western Australia.)

Rendering an Antibiotic Ineffective

According to the University of Oxford, about 1.2 million people died worldwide in 2019 due to AMR, and antimicrobial-resistant infections played a role in as many as 4.95 million deaths that same year. The World Health Organization (WHO) declared AMR one of the top ten global public health threats facing humanity.

While investigating antibiotic sensitivity of Group A Streptococcus—a potentially deadly bacteria often detected on the skin and in the throat—the Australian researchers uncovered a mechanism that enabled bacteria to absorb nutrients from their human host and evade the antibiotic sulfamethoxazole, a commonly-prescribed treatment for Group A Strep.

“Bacteria need to make their own folates to grow and, in turn, cause disease. Some antibiotics work by blocking this folate production to stop bacteria growing and treat the infection,” Timothy Barnett, PhD, Deputy Director of the Wesfarmers Centre of Vaccines and Infectious Diseases and head of the Strep A Pathogenesis and Diagnostics team, told News Medical.

“When looking at an antibiotic commonly prescribed to treat Group A Strep skin infections, we found a mechanism of resistance where, for the first time ever, the bacteria demonstrated the ability to take folates directly from its human host when blocked from producing their own. This makes the antibiotic ineffective and the infection would likely worsen when the patient should be getting better,” he added.

According to their study, the researchers identified an energy-coupling (ECF) factor transporter S component gene that allows Group A Strep to acquire extracellular reduced folate compounds that likely “expands the substrate specificity of an endogenous ECF transporter to acquire reduced folate compounds directly from the host, thereby bypassing the inhibition of folate biosynthesis by sulfamethoxazole.”

The study indicates that this new form of antibiotic resistance is indistinguishable under traditional testing used in microbiology and clinical laboratories, which in turn makes it difficult for clinicians to prescribe effective antibiotics to fight an infection. 

Understanding AMR before It Is Too Late

The research suggests that understanding AMR is more complicated and intricate than previously thought. Barnett and his team believe their discovery is just the “tip of the iceberg” and that it will prove to be a far-reaching issue across other bacterial pathogens in addition to Group A Strep.

In “CDC Ranks Two More Drug-Resistant Microbes as ‘Urgent Threat’ to Americans; Clinical Laboratories Are Advised to Increase Awareness of Antimicrobial Resistance,” Dark Daily covered a report by the federal Centers for Disease Control and Prevention (CDC) that calls attention the emergence of new antibiotic-resistant bacteria and fungi. In its report, the CDC lists 18 bacteria and fungi that pose either urgent, serious, or concerning threats to humans. It also placed one fungus and two bacteria on a “watch” list.

“Without antibiotics, we face a world where there will be no way to stop deadly infections, cancer patients won’t be able to have chemotherapy and people won’t have access to have life-saving surgeries,” Barnett told News Medical. “In order to preserve the long-term efficacy of antibiotics, we need to further identify and understand new mechanisms of antibiotic resistance, which will aid in the discovery of new antibiotics and allow us to monitor AMR as it arises.”

More research and clinical studies are needed before this discovery can become technology that clinical laboratories can use to test if microbes are AMR. The scientists at Wesfarmers Centre of Vaccines and Infectious Diseases are now developing testing methods to detect the presence of the antibiotic resistant mechanism and determine the best treatment options.

“It is vital we stay one step ahead of the challenges of AMR and, as researchers, we should continue to explore how resistance develops in pathogens and design rapid accurate diagnostic methods and therapeutics,” Kalindu Rodrigo, a PhD student in the Barnett lab and one of the authors of the study told News Medical. “On the other hand, equal efforts should be taken at all levels of the society including patients, health professionals, and policymakers to help reduce the impacts of AMR.”

JP Schlingman

Related Information:

Australian Researchers Unearth a New Form of Antimicrobial Resistance

New Antimicrobial Resistance Mechanism Discovered in Streptococci

Host-dependent Resistance of Group A Streptococcus to Sulfamethoxazole Mediated by a Horizontally-acquired Reduced Folate Transporter

WHO: Antimicrobial Resistance

An Estimated 1.2 Million People Died in 2019 from Antibiotic-resistant Bacterial Infections

CDC Ranks Two More Drug-Resistant Microbes as ‘Urgent Threat’ to Americans; Clinical Laboratories Are Advised to Increase Awareness of Antimicrobial Resistance

Study Shows Huge Increase in Bloodstream Infections in Europe During First Two Years of COVID-19 Pandemic

Clinical laboratory data was key in identifying antibiotic-resistant bacteria responsible for surge in BSIs in hospitals and other healthcare facilities in 2020 and 2021

Clinical laboratory data compiled by the European Antimicrobial Resistance Surveillance Network (EARS-Net) shows that a massive increase in bloodstream infections (BSIs) occurred among EU nations during the first two years of the COVID-19 pandemic. The study found that BSIs caused by certain antimicrobial-resistant (AMR) pathogens, known as superbugs, more than doubled in EU hospitals and healthcare facilities in 2020 and 2021. 

Microbiologists and clinical laboratory managers in the US may find it valuable to examine this peer-reviewed study into AMR involved in blood stream infections. It could contain useful insights for diagnosing patients suspected of BSIs in US hospitals where sepsis prevention and antibiotic stewardship programs are major priorities.

The EU researchers published their findings in the journal Eurosurveillance, titled, “Large Increase in Bloodstream Infections with Carbapenem-resistant Acinetobacter Species During the First Two years of the COVID-19 Pandemic, EU/EEA, 2020 and 2021.” The paper outlines what the author’s characterize as the alarming rise in BSIs caused by the Acinetobacter species of bacteria.

Tedros Adhanom Ghebreyesus, PhD

“Antimicrobial resistance undermines modern medicine and puts millions of lives at risk,” said Tedros Adhanom Ghebreyesus, PhD, Director-General, World Health Organization, in a WHO press release. “To truly understand the extent of the global threat and mount an effective public health response to [antimicrobial resistance], we must scale up microbiology testing and provide quality-assured data across all countries, not just wealthier ones.” Clinical laboratories in the US may be called upon to submit data on bloodstream infections in this country. (Photo copyright: WHO.)

Clinical Laboratories in EU Report Huge Increase in Carbapenem Resistance

To perform their study, researchers measured the increase in Acinetobacter BSIs between 2020 and 2021, the first two years of the COVID-19 pandemic. Their data originated from qualitative regular antimicrobial susceptibility testing (AST) from blood samples collected by local clinical laboratories in the European Union/European economic area (EU/EEA) nations.

The researchers limited their dataset to Acinetobacter BSI information from the European medical laboratories that documented results of carbapenem susceptibility testing for the bacterial species.

Carbapenems are a class of very powerful antibiotics that are typically used to treat severe bacterial infections. A total of 255 EU/EEA clinical laboratories reported their data for the study. The scientists found that the percentages of Acinetobacter resistance varied considerably between EU/EEA nations, so they separated the countries into three different groups: 

  • Nations in Group One—The Netherlands, Belgium, Austria, Estonia, Denmark, Germany, Iceland, Finland, Luxembourg, Ireland, Norway, Sweden, and Malta—experienced less than 10% resistance to carbapenems.
  • Nations in Group Two—Slovenia, Czech Republic, and Portugal—had carbapenem resistance between 10% and 50%.
  • Nations in Group Three—Croatia, Bulgaria, Greece, Cyprus, Italy, Hungary, Lithuania, Latvia, Romania, Poland, Spain, and Slovakia—demonstrated carbapenem resistance equal or greater than 50%.

The study also found that Acinetobacter BSIs rose by 57% and case counts increased by 114% in 2020 and 2021 when compared to 2018 and 2019. The percentage of resistance to carbapenems rose to 66% in 2020 and 2021, up from 48% in 2018 and 2019. 

Antimicrobial Resistance Especially High in Hospital Settings

The researchers further arranged the data into three hospital ward types: intensive care unit (ICU), non-ICU, and unknown. The increase in BSIs caused by Acinetobacter species resistant to carbapenems was greater in ICU-admitted individuals (144%) than non-ICU-admitted individuals (41%).

There are more than 50 species of Acinetobacter bacteria and various strains are often resistant to many types of commonly-used antibiotics. Symptoms of an Acinetobacter infection usually appear within 12 days after a person comes into contact with the bacteria. These symptoms may include:

  • Blood infections,
  • Urinary tract infections,
  • Pneumonia, and
  • Wound infections.

Healthy people have a low risk of contracting an Acinetobacter infection with the highest number of these infections occurring in hospitals and other healthcare settings. Acinetobacter bacteria can survive for a long time on surfaces and equipment, and those working in healthcare or receiving treatment are in the highest risk category.

The prevalence of this type of bacteria increases in relation to the use of medical equipment, such as ventilators and catheters, as well as antibiotic treatments.

WHO Report Validates EARS-Net Research

In December of 2022, the World Health Organization (WHO) issued a Global Antimicrobial Resistance and Use Surveillance System (GLASS) report that revealed the presence of an increasing resistance to antibiotics in some bacterial infections. That report showed high levels (above 50%) of resistance in bacteria that frequently caused bloodstream infections in hospitals, such as Klebsiella pneumonia and Acinetobacter.

The WHO report examined data collected during 2020 from 87 different countries and found that common bacterial infections are becoming increasingly resistant to treatments. Both Klebsiella pneumoniae and Acinetobacter can be life threatening and often require treatment with strong antibiotics, such as carbapenems.

More research is needed to determine the reasons behind increases in Acinetobacter infections as reported in European hospitals and other healthcare settings, and to ascertain the extent to which they are related to hospitalizations and the upsurge in antimicrobial resistance during the COVID-19 pandemic.

Microbiologists and clinical laboratory managers in the US may want to learn more about the fIndings of this European study involving AMR and use those insights to plan accordingly for any future increase in bloodstream infections in this country. 

JP Schlingman

Related Information:

Enormous Rise in Acinetobacter Bloodstream Infection Cases in Initial Two Years of COVID-19

COVID Pandemic Led to Surge in Superbug Infections, EU Agency Says

Large Increase in Bloodstream Infections with Carbapenem-resistant Acinetobacter Species During the First 2 years of the COVID-19 Pandemic, EU/EEA, 2020 and 2021

Antimicrobial Resistance in the EU/EEA (EARS-Net)–Annual Epidemiological Report for 2021

Acinetobacter: What to know

Some Bloodstream Infection Bacteria Grew Resistant to Last-resort Drugs in 2020 – WHO

Report Signals Increasing Resistance to Antibiotics in Bacterial Infections in Humans and Need for Better Data

Carbapenem-resistant Acinetobacter

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