Since the early 1980s, UBC’s CMPT program, led by medical microbiologist Michael Noble, MD, has provided external quality assessment (EQA) for clinical microbiology and water testing laboratories. This includes providing biological samples related to:
“Typical of every jurisdiction in North America and probably around the world, BCCDC got swamped beyond swamped,” said Noble, the Clinical Microbiology Proficiency Testing (CMPT) program’s first and current Chair, in an exclusive interview with Dark Daily. “The increase was 10-fold, and they were unable to provide all the services they wanted to do. And since I was already running a proficiency testing program across the province, they asked if I would provide that service for COVID-19 for laboratories that were doing the testing.”
Michael Noble, MD (above), is Professor Emeritus (active) in UBC’s Department of Pathology and Laboratory Medicine and Chair of the Program Office for Laboratory Quality Management (POLQM). He began his career as a medical microbiologist but soon focused on laboratory quality management. Within the Department of Pathology and Laboratory Medicine, Noble co-developed the Clinical Microbiology Proficiency Testing (CMPT) program in 1983, a program he still chairs but will soon pass on to a new leader. (Photo copyright: University of British Columbia.)
CMPT’s Proficiency Testing Serves Labs Worldwide
UBC’s CMPT external quality assessment (EQA) program serves all medical laboratories in British Columbia, as well as other labs in Canada, Europe, South America, and the Caribbean. Just over 200 laboratories currently participate in the program. More labs participated in past years, before lab consolidation affected CMPT and other programs as well, Noble said.
CMPT’s proficiency testing ensures that participant laboratories that have been provided with simulated samples can perform tests at the “level of quality and competence required,” notes UBC’s CMPT website.
“Samples are complex, highly realistic, and clinically relevant. CMPT samples contain host elements as well as targeted pathogens,” Noble explained on his blog, “Making Medical Laboratory Quality Relevant.”
COVID-19 Brings Non-Traditional ‘Laboratories’ to CMPT’s Proficiency Testing Program
UBC’s proficiency testing for SARS-CoV-2, the coronavirus that causes the COVID-19 infection, differs from other CMPT programs. That’s due to new participants that entered the laboratory testing program during the COVID-19 pandemic that are performing COVID-19 testing in non-traditional locations, Noble stated.
“In our proficiency programs, we had mainly been dealing with traditional clinical laboratories,” Noble explained. “But now, we find people doing COVID-19 testing—even though defined as medical laboratories—who are working in airports, or in tourism, or the movie industry, or forestry. They may never have worked in an actual clinical laboratory. So, it’s a very different style of proficiency testing. There has been a lot of handholding, teleconferences, discussions, and one-on-ones with that group,” Noble said.
Participant laboratories receive viral material that “simulates typical samples.” They need to demonstrate proficiency by performing the test and reporting it as positive, negative, or inconclusive.
“Our product is derived from a pure culture of a single strain of SARS-CoV-2, and it appears to be effective for all targets,” Noble stated.
Detecting COVID-19 by Gargling and Rinsing
UBC’s program typically offers simulated sampling for detection of SARS-CoV-2 in nasopharyngeal swabs. However, the BC Center for Disease Control’s (BCCDC) mouth rinse and gargle sample collection for diagnosis of COVID-19 also is available and widely used in Canada, Noble said.
In his career, Noble transitioned from medical microbiology to qualitology, which he describes as “the study of quality in the medical laboratory.”
In stressing the importance of laboratory quality testing, Noble describes the possibility of laboratory testing going awry and leading to a microbiological public health emergency.
“What happens if there’s a stool sample, and someone misses the presence of Campylobacteriosis in the stool? What happens if that’s part of a foodborne disease and there’s an outbreak in the city and samples are being missed? How many people will be impacted as a result of that error?” he asked.
University of British Columbia Endows a Chair for Laboratory Quality Management
Noble says UBC’s Program Office for Laboratory Quality Management (POLQM) has involved organizations worldwide and certified more than 500 people.
“The impact they have over their laboratories has been huge. Maybe that would have happened without us. But we were a part of that. And our impact is not one laboratory or one city or one province but widespread, and that’s a real and enriching experience to have,” he said.
But now it is time for him to move on. Noble secured (through UBC), a benefactor to establish the endowed Chair for Laboratory Quality Management. The family of the late Donald B. Rix, MD, a Canadian pathologist and philanthropist, gave $1.5 million (matched by the university) to create the Associate Professor (Grant Tenure) Donald B. Rix Professorship in Laboratory Quality at UBC, Department of Pathology and Laboratory Medicine.
Long-serving pathologists and medical laboratory professionals may remember that Rix was the founder and chair of MDS Metro Laboratory Services (now known as LifeLabs Medical Laboratory Services). It grew into the largest private medical laboratory in Western Canada.
Referring to this endowed new Chair for Laboratory Quality Management, Noble said, “I think this is the first named position of laboratory quality in North America.” UBC has commenced reviewing applications for the position, which is expected to be effective in January 2022. Pathologists and clinical laboratory scientists with appropriate qualifications and interest in this position should contact Dr. Noble’s office at the University of British Columbia Faculty of Medicine.
Bioeasy stands behind the accuracy of its coronavirus test kits and, in a statement, questioned whether they were being used correctly
How accurate are the SARS-CoV-2 test kits being offered by different in vitro diagnostics companies, as well as the internally-developed COVID-19 tests developed by individual medical laboratories, both here in the United States and in other countries? It’s a question that has not been addressed by the news media nor by healthcare regulators.
That
is why a recent news story reported complaints by authorities in several
European countries that COVID-19 tests they had purchased were “unreliable.”
The source of the COVID-19 test kits was a Chinese company.
On Wednesday, government officials in China announced that manufacturers of test kits for SARS-CoV-2, the novel coronavirus that causes the COVID-19 illness, can no longer export their tests unless China’s National Medical Products Administration (NMPA) has licensed and registered those tests, the South China Morning Post (SCMP) reported.
China issued the new rules after receiving complaints from buyers in Europe about the quality and accuracy of tests kits and other products, including personal protective equipment (PPE), ventilators, and infrared thermometers, SCMP wrote. Previously, Chinese exporters were required only to have CE certification to indicate that their goods conformed to the health and safety standards required for sale in the European Economic Area, SCMP added.
In a joint statement issued March 31, China’s Ministry of Commerce, General Administration of Customs (GAC), and the National Medical Products Administration said the new rule applies to all companies seeking to export test kits, face masks, protective clothing, ventilators, and infrared thermometers.
Spain
Discontinues Use of Rapid Diagnostic Tests from Bioeasy
The new rules came after health authorities in Spain stopped using a rapid diagnostic test (RDT) kit that required a nasopharyngeal (NP) swab to collect specimens to diagnose patients for the SARS-CoV-2 virus, saying the test kits from Shenzhen Bioeasy Biotechnology were unreliable. Turkey also rejected the Shenzen Bioeasy test kits after finding similar problems, according to The Middle East Eye. Ukraine and Georgia also bought kits from Bioeasy, according to published reports.
The low accuracy rate of the Bioeasy coronavirus test kits raises questions about the rapid rate of development for new tests in the United States and worldwide, said Michael Noble, MD, FRCPC, Chair of the University of British Columbia (UBC) Clinical Microbiology Proficiency Testing program and the UBC Program Office for Laboratory Quality Management, in Vancouver.
“There’s
an inherent problem with building a test during a crisis,” Noble said in an
interview with Dark Daily. “Clinical laboratory test developers are
being forced into building tests in a hurry, and the highest likelihood is that
they will fail because these tests take a lot of time if the aim is to get them
right.
“When
a company or a lab feels the need to go too fast, it is likely to take
shortcuts,” he added. “And every time a shortcut is taken, an opportunity for
error is created.
“Also,
the federal Food and Drug Administration (FDA) may be going too fast to issue
emergency use authorizations (EUAs). If laboratory test developers and the FDA
go too fast, then both could make mistakes,” Noble noted.
“The lesson for labs in the United States and everywhere is you can’t go too fast and you don’t want to go too slow either,” Michael Noble, MD (above), Chair of the University of British Columbia Clinical Microbiology Proficiency Testing Program, told Dark Daily. “Instead, you need to proceed as quickly as you can, but also take as long as you need to ensure you follow all the steps accurately.” (Photo copyright: The Dark Report.)
Bioeasy
Questions Whether Tests are Being Used Correctly
On
March 27, SCMP reported that Shenzhen Bioeasy would send new kits to
ensure that “patients get the best diagnostics” and to “ensure the test kits’
sensitivity and specificity.” The company also raised questions about whether
the tests were used properly and promised to send a video explaining how those
administering the tests should collect specimens using NP swabs.
“As
it [is a] rapid test kit, following the protocol is very important,” the
company added, according to SCMP.
Last
week, Zhu Hai, a manager at
Shenzen Bioeasy, said reports that the test kits had a low accuracy rate were
untrue, SCMP reported. A more detailed explanation would be given via
official Chinese government channels, he added.
Shenzen
Bioeasy also issued a statement about the tests, saying, “The production export
of our CE products to Spain has been done according [to] regulations. All
Bioeasy COVID-19 rapid test [kits] are officially CE-IVD approved, so we are free
to [export] and sell in [the EU],” SCMP reported.
The company exported 337,000 tests to South Korea and more than 420,000 test kits to at least 10 countries, including Italy, Qatar, and Ukraine, the company added. It had five million such kits under production, the company said.
Spain
Purchased More than Half a Million Bioeasy Test Kits
One
of the first publications to report the inaccuracy problems was El País, a Spanish
language daily newspaper in Madrid.
The
Shenzen Bioeasy tests functioned much like pregnancy tests, the newspaper
wrote. Once the sample is taken, the NP swab is diluted and placed into a
cartridge with a lined test strip showing whether the result is positive,
negative, or invalid. “The tests detect the presence of antigen and the result is obtained in 10
or 15 minutes,” El País wrote.
Based
in part on a claim that the medical laboratory test kits have an 80% accuracy
rate, the government purchased 640,000 kits to screen health workers and the
elderly. If the Chinese tests were of sufficient quality, negative or doubtful
results would require a confirmatory molecular diagnostics test, the
newspaper added.
The
Chinese embassy in Spain also responded, saying on Twitter on March 26 that
the country’s National Medical Products Administration had not approved the
tests, and that they were not included in the medical supplies the Chinese
government sent to Spain, SCMP reported. “The Chinese Ministry of
Commerce offered Spain a list of approved suppliers, in which Shenzhen Bioeasy
Biotechnology was not included,” the embassy added.
After
the low accuracy rates were reported, the Spanish government said it ordered
€432 million (US$468 million) worth of medical supplies from China, 5.5 million
test kits, 550 million face masks, and 950 ventilators, SCMP added. But
none of the kits in this order were from Shenzen Bioeasy, the government said.
SCMP quoted Professor Leo Poon
Lit-man, BSc, MPhil, DPhil, FFPH, an expert in the SARS-CoV-2 coronavirus
who helped design a testing protocol for the COVID-19 illness, and who is a
Professor and Division Head of the Division of Public Health Laboratory
Sciences at The University of Hong Kong. A claim of 80% accuracy
for a test using nasal swabs was perplexing, because such tests are known to be
inaccurate, Poon said. “It would be dangerous if it’s used on a large scale,
since patients who are supposed to be positive might not be detected,” he
added.
Pathologists
and clinical laboratory scientists know there are many reasons why a clinical
laboratory test can be unreliable or inaccurate. For example, during the
production of a batch of tests, one step in the manufacturing process may have
gone awry and that problem was not detected before those tests were shipped to
a medical laboratory.
Unfortunately,
when lab tests are proved to be “unreliable” or inaccurate, the public or the
medical laboratory profession seldom learn the reasons for these problems and
what steps were taken to resolve them.
Cloud-based platform—IDseq—shows potential to track the causes and spread of infectious diseases worldwide using metagenomic data
Here’s the latest example of how big data and related technologies can give physicians—as well as microbiologists and clinical pathologists—a new tool for understanding infectious disease and tracking outbreaks anywhere in the world. This project is being funded and organized by well-known Silicon Valley entrepreneurs.
The project is known as IDseq. It was announced recently in a press release issued by Chan Zuckerberg Biohub (CZ Biohub), Chan Zuckerberg Initiative (CZI), and the Bill and Melinda Gates Foundation. IDseq is a platform designed to support global disease surveillance and prevention. It will make use of gene sequencing and analysis of metagenomic data. This data will be made accessible to the global medical community.
The system leverages the power of cloud computing to streamline the process of transmitting and analyzing metagenomic data, as well as sharing results with other platform users.
“That will be incredibly valuable. Information sharing is one of the most powerful public-health interventions in an outbreak,” Jennifer Gardy, PhD, an epidemiologist at the University of British Columbia, told The Atlantic.Designed by Engineers to Be Easily Used by Healthcare Providers and Medical Laboratory Technicians
Coverage in The Atlantic notes that IDseq isn’t the first tool to offer similar features. Joseph DeRisi, PhD, a biochemist at the University of California San Francisco and co-president of CZ Biohub, states, however, that IDseq is one of the first designed by a large team of engineers, security experts, and other tech and medical researchers.
Many tools see their origins in academic research and are less friendly to those without advanced academic expertise. The research team’s goal, according to DeRisi, is for IDseq “To enable people in under-resourced areas to do what we’ve been trying to do in San Francisco.”
“It’s easy for us to sit in our labs dreaming up tools and platforms,” Jennifer Gardy, PhD (above), an epidemiologist at the University of British Columbia, told The Atlantic. “But we need to make sure we’re designing them in a way that makes sense to the doctors, nurses, lab techs, and epidemiologists out there in an outbreak.” (Photo copyright: Michelle Thorpe/University of British Columbia.)
Two Trials Show Promise for IDseq Use
While the software is already available for free as a collection of open source tools, the IDseq platform is now in a “soft launch” phase. The Bill and Melinda Gates Foundation is funding training for clinicians at CZ Biohub’s labs in San Francisco through its Grand Challenges Explorations Initiative.
However, the platform has already achieved success in two noted scenarios—one at Dhaka Shishu Hospital in Dhaka, Bangladesh, and another in Tororo District Hospital in Uganda. Both used the system to analyze the samples of children admitted for fevers for which they found no known cause.
In the Dhaka cases, Senjuti Saha, PhD, a microbiologist from Child Health Research Foundation, used the platform to trace unexplained cases of meningitis to an earlier chikungunya virus outbreak. Saha explained to The Atlantic that her colleagues previously thought chikungunya could not cause meningitis. The platform found otherwise, allowing her to analyze a further 478 samples and detect an additional 17 cases of potential chikungunya-related meningitis.
In the Uganda cases, the researchers used metagenomic next-generation sequencing (mNGS) data and the IDseq platform to investigate unknown causes of fever in children.
“As progress is made toward elimination of malaria in sub-Saharan Africa, it will be increasingly important to understand the landscape of pathogens that account for the remaining burden of morbidity and mortality,” researchers state in their study, currently in early access at bioRxiv. “The use of mNGS can contribute importantly to this understanding, offering unbiased identification of infecting pathogens.”
Wide-Spread Use of IDseq Not Without Challenges
While an article in Medium by Charles de Bourcy, PhD, Software Engineer at Chan Zuckerberg Initiative, outlines how the IDseq platform can process up to 480GB in approximately 10 minutes, it doesn’t account for the initial data input, which can be daunting.
For areas with weak infrastructure and/or slow connection speeds, this could add significant delays as medical laboratories and healthcare workers at remote sites attempt to transfer data to the nearest IDseq-enabled location. Saha told The Atlantic, “If the transfer is too slow or the data too large, we just [ship] hard drives.”
Sequencing requirements create additional concerns. Bulky equipment and the skills required to run sequencers could limit the ability to use the IDseq platform to analyze and share results. Clinicians might also face difficulties in sourcing sequencing reagents due to customs and supply chain concerns.
Finally, the platform still requires an expert to interpret findings. “IDseq is an excellent tool, but it needs to be paired with people who have substantive knowledge to guide its use,” Saha told The Atlantic.
Regardless of these issues, Saha believes IDseq can help remote/resource-challenged medical labs chase diseases. “It doesn’t solve all the problems, but it means that groups like ours don’t have to spend time to build up [sequencing] capacity. And anything is better than nothing.”
IDseq might offer an excellent opportunity for microbiology laboratories, clinical laboratories, and medical researchers around the world to share data surrounding outbreaks, track disease on global and community level, and better determine the strains and probable sources of infectious diseases.
Improved diagnostic technologies and more sophisticated software tools allow innovative clinical lab managers to more precisely measure the accuracy of their lab’s analytical results
VANCOUVER, BRITISH COLUMBIA, CANADA—In this beautiful port city, a national gathering of clinical laboratory and anatomic pathology experts convened last week and tackled serious issues concerning the accuracy and integrity of the diagnostic test results produced by labs in Canada and other developed nations.
One big take-away from this meeting was that the bar is being raised for the quality of the lab test results produced by a medical laboratory. Issues of bias, variability, and inaccuracy that accompany the technologies and methods used by clinical laboratories and anatomic pathology groups were front and center during all three days of the meeting. (more…)
