New artificial intelligence model agrees with interpretations of human medical technologists and microbiologists with extraordinary accuracy
Microbiology laboratories will be interested in news from Brescia University in Italy, where researchers reportedly have developed a deep learning model that can visually identify and analyze bacterial species in culture plates with a high level of agreement with interpretations made by medical technologists.
They initially trained and tested the system to digitally identify pathogens associated with urinary tract infections (UTIs). UTIs are the source for a large volume of clinical laboratory microbiological testing.
The system, known as DeepColony, uses hierarchical artificial intelligence technology. The researchers say hierarchical AI is better suited to complex decision-making than other approaches, such as generative AI.
In their Nature paper, the researchers explained that microbiologists use conventional methods to visually examine culture plates that contain bacterial colonies. The scientists hypothesize which species of bacteria are present, after which they test their hypothesis “by regrowing samples from each colony separately and then employing mass spectroscopy techniques,” to confirm their hypotheses.
However, DeepColony—which was designed for use with clinical laboratory automation systems—looks at high-resolution digital scans of cultured plates and attempts to identify the bacterial strains and analyze them in much the same way a microbiologist would. For example, it can identify species based on their appearance and determine which colonies are suitable for analysis, the researchers explained.
“Working on a large stream of clinical data, and a complete set of 32 pathogens, the proposed system is capable of effectively assisting plate interpretation with a surprising degree of accuracy in the widespread and demanding framework of urinary tract infections,” the study authors wrote. “Moreover, thanks to the rich species-related generated information, DeepColony can be used for developing trustworthy clinical decision support services in laboratory automation ecosystems from local to global scale.”
“Compared to the most common solutions based on single convolutional neural networks (CNN), multi-network architectures are attractive in our case because of their ability to fit into contexts where decision-making processes are stratified into a complex structure,” wrote the study’s lead author Alberto Signoroni, PhD (above), Associate Professor of Computer Science, University of Brescia, and his researcher team in their Nature paper. “The system must be designed to generate useful and easily interpretable information and to support expert decisions according to safety-by-design and human-in-the-loop policies, aiming at achieving cost-effectiveness and skill-empowerment respectively.” Microbiologists and clinical laboratory managers will want to follow the further development of this technology. (Photo copyright: University of Brescia.)
How Hierarchical AI Works
Writing in LinkedIn, patent attorney and self-described technology expert David Cain, JD, of Hauptman Ham, LLP, explained that hierarchical AI systems “are structured in layers, each with its own distinct role yet interconnected in a way that forms a cohesive whole. These systems are significant because they mirror the complexity of human decision-making processes, incorporating multiple levels of analysis and action. This multi-tiered approach allows for nuanced problem-solving and decision-making, akin to a seasoned explorer deftly navigating through a multifaceted terrain.”
DeepColony, the researchers wrote, consists of multiple convolutional neural networks (CNNs) that exchange information and cooperate with one another. The system is structured into five levels—labeled 0 through 4—each handling a different part of the analysis:
At level 0, the system determines the number of bacterial colonies and their locations on the plate.
At level 1, the system identifies “good colonies,” meaning those suitable for further identification and analysis.
At level 2, the system assigns each good colony to a bacterial species “based on visual appearance and growth characteristics,” the researchers wrote, referring to the determination as being “pathogen aware, similarity agnostic.”
The CNN used at this stage was trained by using images of 26,213 isolated colonies comprising 32 bacterial species, the researchers wrote in their paper. Most came from clinical laboratories, but some were obtained from the American Type Culture Collection (ATCC), a repository of biological materials and information resources available to researchers.
At level 3, the system attempts to improve accuracy by looking at the larger context of the plate. The goal here is to “determine if observed colonies are similar (pure culture) or different (mixed cultures),” the researchers wrote, describing this step as “similarity aware, pathogen agnostic.” This enables the system to recognize variants of the same strain, the researchers noted, and has the effect of reducing the number of strains identified by the system.
At this level, the system uses two “Siamese CNNs,” which were trained with a dataset of 200,000 image pairs.
Then, at level 4, the system “assesses the clinical significance of the entire plate,” the researchers added. Each plate is labeled as:
“Positive” (significant bacterial growth),
“No significant growth” (negative), or
“Contaminated,” meaning it has three or more “different colony morphologies without a particular pathogen that is prevalent over the others,” the researchers wrote.
If a plate is labeled as “positive,” it can be “further evaluated for possible downstream steps,” using MALDI-TOF mass spectrometry or tests to determine susceptibility to antimicrobial measures, the researchers stated.
“This decision-making process takes into account not only the identification results but also adheres to the specific laboratory guidelines to ensure a proper supportive interpretation in the context of use,” the researchers wrote.
Nearly 100% Agreement with Medical Technologists
To gauge DeepColony’s accuracy, the researchers tested it on a dataset of more than 5,000 urine cultures from a US laboratory. They then compared its analyses with those of human medical technologists who had analyzed the same samples.
Agreement was 99.2% for no-growth cultures, 95.6% for positive cultures, and 77.1% for contaminated or mixed growth cultures, the researchers wrote.
The lower agreement for contaminated cultures was due to “a deliberately precautionary behavior, which is related to ‘safety by design’ criteria,” the researchers noted.
Lead study author Alberto Signoroni, PhD, Associate Professor of Computer Science, University of Brescia, wrote in Nature that many of the plates identified by medical technologists as “contaminated” were labeled as “positive” by DeepColony. “We maximized true negatives while allowing for some false positives, so that DeepColony [can] focus on the most relevant or critical cases,” he said.
Will DeepColony replace medical technologists in clinical laboratories any time soon? Not likely. But the Brescia University study indicates the direction AI in healthcare is headed, with high accuracy and increasing speed. The day may not be far off when pathologists and microbiologists regularly employ AI algorithms to diagnose disease.
Representatives from almost 50 different clinical laboratories, professional associations, and societies came together this week to align efforts to expand the supply and retention of qualified laboratory scientists
FORT WORTH, TEXAS—Last week, representatives from a broad cross section of clinical laboratories, lab and pathology associations, public health laboratories, and lab regulatory bodies gathered specifically to identify ways to expand the number of skilled lab professionals.
COLA organized the “Workforce Action Alliance Summit,” a one-day gathering of key clinical laboratory stakeholders who share a common interest in developing initiatives that would directly increase the number of individuals choosing to pursue a career in laboratory medicine.
This is not a new problem, as the lack of trained laboratory scientists across all scientific disciplines has been acute for many years.
In a communication sent to invited participants, COLA’s CEO, Nancy Stratton, and COO, Kathy Nucifora, described the objective of the summit, writing:
“Clearly a call to collective action is required if we are to address the impending clinical laboratory workforce shortage. The past three years have demonstrated the significance of a resilient laboratory infrastructure, not only for the daily care of millions of Americans, but also during the global pandemic. The numerous efforts currently underway to resolve the shortage are unquestionably a component of the solution. Many, however, believe that these efforts are insufficient to close the gap between the projected number of new entrants into the profession, the rate at which those currently in the profession are departing, and the future demand for laboratory testing.”
Robert L. Michel, Editor-in-Chief of Dark Daily’s sister publication The Dark Report was a participant at COLA’S workforce summit. The Dark Report regularly profiles clinical laboratory organizations that have developed innovative and productive initiatives designed to increase the number of students choosing to train as medical technologists (MTs), clinical laboratory scientists (CLSs), medical laboratory technologists (MLTs) and other skilled lab positions.
In materials distributed at the summit, the ongoing gap between demand for skilled lab professionals and the supply was illustrated thusly:
“The US Department of Labor estimates 320,000 bachelors and associates degreed laboratory professionals are working in the United States. If each of those professionals worked a standard 40-year career, the natural annual attrition of 2.5% would require 8,000 new professionals to maintain their current numbers. This exceeds the current output of accredited educational programs by more than 1,000 annually.”
Case Studies of Success
Over the course of the day, participants at the summit heard about the successes of certain laboratory organizations designed to get more students into training programs, supported by the educational courses required for them to become certified in their chosen area of laboratory medicine. These case studies centered around several themes:
Obtaining funding specifically to establish an MT/CLS training program to increase the number of candidates in a region. One example involved ARUP Laboratories and its success at working with a local Congressional representative to get a $3 million federal grant funded as part of a larger legislative package.
The medical laboratory scientist (MLS) program at Saint Louis University (SLU) worked with Quest Diagnostics to launch an accelerated bachelor’s degree program. The 16-month program combines online academic courses with intensive hands-on learning and clinical experiences in Quest’s Lenexa, Kansas, laboratory. The first students in this accelerated degree program began their studies in the spring semester of 2023.
By rethinking the structure of its existing didactic and experiential learning structure, NorthShore University HealthSystem’s MLS program, located at Evanston Hospital north of Chicago, doubled its enrollment capacity.
During the afternoon, working groups addressed ways that lab organizations can collaborate to increase recruitment and retention of laboratory scientists across all disciplines of lab medicine. This input was synthesized into action planning for the three priorities that can lead to expanding the lab workforce.
By day’s end, several working groups were organized with specific next steps. COLA is taking the lead in managing this initiative and giving it momentum. All clinical laboratory professionals and pathologists are welcome to participate in the Workforce Action Alliance (WAA). Anyone wishing to learn more can contact COLA by clicking here, calling 800-981-9883, or by visiting https://education.cola.org/contact-us-page.
Program launched by a Rochester-area technical center is intended to provide early study for students interested in a career in clinical laboratory medicine
Acute shortages of clinical laboratory staff across all types of skills is one of the big stories of this new year. It is also triggering unconventional approaches to reach students in high school and interest them in careers as medical technologists (MTs). One such example is a high school in New York that now offers a top-level medical laboratory program designed to create interest—then train—high school students for a career in laboratory medicine.
“With the acute shortage of medical technologists, this effort by one high school to reach students early and encourage them to pursue a career in clinical laboratory medicine should be of interest to all laboratory professionals,” said Robert Michel, Editor-in-Chief of Dark Daily and its sister publication The Dark Report.
“Our juniors and seniors in high school will learn about 60 employable laboratory skills,” said Jim Payne (above), a Medical Laboratory Assisting and Phlebotomy program instructor at WEMOCO. “They learn not only medical laboratory skills, but [the skills] are transferable to biotechnology, to chemical labs, food labs, environmental labs, research, forensics, and so on. The goal is each individual student comes out skilled in all 60 skills.” Clinical laboratories may want to explore creating similar programs with high schools in their own areas. (Photo copyright: Twitter.)
Dynamic Curriculum of Clinical Laboratory Skills
During the first year of the WEMOCO program, students learn skills that Jim Payne, a Medical Laboratory Assisting and Phlebotomy program instructor at WEMOCO, stated he learned in college. These include:
The students also learn the theories and techniques behind phlebotomy and how to perform blood draws (venipuncture).
Students spend 40 hours drawing blood samples from real patients in local medical laboratories and can earn a certification as a Phlebotomy Technician after completing the necessary coursework.
During the second year of the program, students learn college-level:
They also receive their certifications in American Red Cross CPR/AED and First Aid and spend 80 hours actually working in local clinical laboratories. Upon completion of the second year of coursework, students can earn a certification as a Certified Medical Laboratory Assistant.
“In both cases, they can get jobs straight out of the program,” said Payne in the CLP podcast. “But a lot of our grads go on to college for medical laboratory careers.”
Overcoming Vocational School Stigma
Recruiting students into the program was initially challenging as some of the negative stigma surrounding non-traditional coursework had to be overcome. Vocational education is now referred to as career and technical education and the WEMOCO program is more academically focused than previous vocational studies. Students can obtain some college credits when completing the two-year program.
“With my students, when we are teaching them how to do the math around making laboratory solutions, for example, that requires algebra,” Payne explained. “And they have to actually make something with the algebra and suddenly it starts to make a lot more sense than the way that they were taught in a traditional high school.”
In addition, some students interested in the program struggled in a typical high school environment due to lack of direction, according to Payne. However, when those same students found their focus, discovered a passion, and were motivated and challenged, they flourished.
Originally, Payne gave a talk to potential enrollees. But he found there was more interest if students were given a hands-on experience at their first exposure to the program. He also lets current students interact with interested students and allows them to answer any questions in a student-friendly manner.
“Students who are interested in the program come in, they get lab coats on, they get gloves on, and they are then told a story about a case and have to perform a few experiments to try to determine what is wrong with a patient. They actually do things,” Payne explained.
Multiple Career Paths in Clinical Laboratories upon Graduation
One advantage to completing the two-year WEMOCO program is that students can explore all the different careers in clinical laboratory medicine and are offered opportunities to work in medical laboratory situations. Phlebotomy students perform 40 hours of work in a blood lab with a goal of performing 50 successful sticks, although many students perform more than that.
“I have students who are under the age of 18 drawing blood on real patients with real samples with these companies’ trainers. It’s like they have been hired,” Payne said. The medical laboratory assistant work is broken up into increments of two hours a day over the course of several months.
Another benefit to the WEMOCO program is that students are prepared for a job right out of high school, which pleases both the students and the parents. Many graduates of the program go on to college to study different fields within the clinical laboratory profession.
Attracting Young Students to the Clinical Laboratory Profession
Payne believes it is important to get young kids interested in the medical laboratory profession in the lower grade levels. His suggestions for stoking that level of interest include:
Developing programs that are age-appropriate but contain medical laboratory concepts.
Outreach programs where clinicians talk to students in the lower grades to spark interest.
Outreach programs where kids can perform simple experiments like staining onions and seeing results.
Telling stories and explaining the roles labs play in helping patients.
Holding field trips where students visit local clinical laboratories and observe medical laboratory professionals.
Opportunities for students to shadow medical laboratory technicians so the kids can imagine themselves in the profession.
Participating in local activity day/career day events.
He also believes that clinical laboratory professionals should promote their field at every opportunity.
“The biggest thing is actively advocating for the profession. Any chance I get, I’m going out and trying to talk to anyone about the clinical laboratory. Try to have some statistics in your back pocket or other things that can be a good talking point and make a powerful statement to people,” Payne suggested.
Determining unique ways to garner interest in the medical laboratory profession is a crucial step in mitigating staffing shortages. Clinical laboratory leaders may want to participate in community outreach programs and serve as advocates for their profession.
The 2023 conference comes as clinical laboratories, diagnostics companies, and anatomic pathology practices wrestle with budgets that are strained by inflation, supply chain woes, and the faltering financial performance of parent hospitals and health systems. Meanwhile, lab hiring managers continue to face a severe staffing shortage of diagnostics employees.
“The current twin trends of hospitals losing money and labs struggling to maintain adequate staffing is without parallel in my 30 years of covering the clinical laboratory, diagnostics, and pathology sectors,” said Robert Michel, Founder of the Executive War College and Editor-in-Chief at Dark Daily. “This is a perfect storm that threatens the ability of labs to sustain high-quality testing services in a financially-sustainable manner. At the 2023 Executive War College, we are going to help participants get through this predicament by giving them innovative insights and best-in-class expertise they can take back and implement in their clinical labs and pathology groups.”
“Staffing and supply chain difficulties are not the only burdens facing clinical laboratories,” said Robert Michel (above), Founder of the Executive War College on Diagnostics, Clinical Laboratory, and Pathology Management. “Equally stressful forces are altering how providers, payers, and healthcare consumers access medical laboratory testing and pay for those services.” (Photo copyright: The Dark Intelligence Group.)
Earning New Revenue Will Take Center Stage at 2023 Executive War College
The full agenda for the 2023 Executive War College has not yet been released, but attendees can expect to see keynote presentations and sessions devoted to pressing topics in the diagnostics and laboratory industries. Among them is how to best position the clinical lab as a growing revenue source.
“With financial pressures mounting, we intend to present cutting-edge advice from innovative clinical laboratories, diagnostics companies, and pathology practices about how they earn new revenue—whether that be through creating business opportunities in the community, uncovering new test reimbursements, or using technology to improve existing processes,” Michel explained.
Last spring’s gathering of the Executive War College featured 10 keynotes, 55 sessions, and three post-conference workshops. Participants at the upcoming 2023 Executive War College conference can expect a similar bonanza of educational and professional development options, as well as collaborative networking breaks, luncheons, and receptions.
“The chance to meet innovative peers from across the country, share lab-related challenges with them, and compare effective solutions makes the Executive War College a cost-effective investment for any laboratory administrator, executive, or business-minded pathologist,” Michel added.
Diagnostics Services Will Be Better Reflected at 2023 Conference
For the first time, the conference’s moniker directly reflects the diagnostic work associated with clinical laboratories and pathology groups.
“Long-time attendees will notice that we tweaked the Executive War College’s full title to emphasize ‘diagnostics.’ That term is an important addition,” Michel noted.
“In the recent past, ‘clinical laboratory’ and ‘anatomic pathology’ were terms that sufficiently described the profession of laboratory medicine,” he continued. “However, a subtle but significant change has occurred in recent years. The term ‘diagnostics’ has become a common description for medical testing, along with other diagnostic areas such as radiology and imaging.”
Keep an eye on the conference’s website, ExecutiveWarCollege.com, for updates about the upcoming program and to see the session topics and speakers as they are confirmed and announced.
“The Executive War College is the top gathering for lab leaders to learn from the profession’s best innovators and gain insights they will need to keep their laboratories at the cutting edge of clinical excellence in a financially sustainable manner,” Michel concluded.
Register today to ensure places for you and your management team at the 2023 Executive War College on Diagnostics, Clinical Laboratory, and Pathology Management. Click here for early registration discounts.
Staffing specialists advise medical laboratories to expect shortages to continue
Clinical laboratory and pathology group managers are keenly aware of the Great Resignation and how it has affected lab industry staffing and recruiting. Medical technologists (MTs) and clinical laboratory scientists (CLSs) are in particularly short supply and some experts do not see this critical shortage waning anytime soon.
In an exclusive interview with Dark Daily, Maggie Morrissey, Director of Recruiting and Staffing Services at Lighthouse Lab Services, explains the multi-faceted problem labs are facing meeting recruitment goals, and how understaffing can lead to bigger matters regarding morale and job satisfaction.
Based in Charlotte, N.C., Lighthouse Lab Services is a medical laboratory consulting and recruiting firm that employs 150 people and services more than 1,500 medical laboratory clients.
In July, Lighthouse released the results of its 2022 Survey on Wage and Morale Issues among Medical Laboratory Professionals. The collected data from 1,112 respondents found that only 27% indicated their clinical laboratories were adequately or well-staffed. Forty percent of respondents believe their labs were moderately understaffed while an additional 33% felt their labs were significantly understaffed.
The primary reasons, according to Lighthouse, for staffing shortages can be attributed to:
The number of schools offering medical technology programs has decreased.
People have been retiring at a higher rate than most industries.
It is difficult to become a medical technologist/clinical laboratory scientist.
There are hurdles to jump through to become a medical technologist.
Medical technology is not a well-known field.
“[Eastern Carolina University] told us they don’t have anyone graduating from the [medical technology] program this year because of COVID. There are all these issues exacerbating the problem,” said Maggie Morrissey (above), Director of Recruiting and Staffing Services at Lighthouse Lab Services, in an exclusive interview with Dark Daily. “Making it more attractive starts at the school level. People need to be introduced to the science of medical technology. It’s not something that many students know exists as a career.” This lack of interest in training programs is a major reason for the severe shortage of medical technologists on staff at clinical laboratories around the US. (Photo copyright: Lighthouse Lab Services.)
Stagnant Pay, Low Morale, Lack of Appreciation in Clinical Labs
“The major issue that we see with medical labs across the country is that they are understaffed,” Morrissey stated. “That tracks to low morale. It’s a major issue for laboratories because when a lab is understaffed and everyone is working very hard, lab staff may not feel appreciated and their morale starts to wane, which snowballs into larger issues.”
Morrissey pointed out that individuals who work for different sized clinical laboratories have dissimilar grievances about their jobs.
“Pay continues to be a concern for all, but benefits are also important,” she said. “Pay and lack of benefits, like not being able to get time off, not having a 401K, and not having health insurance are hurdles for people working in smaller labs.”
Professionals working in medium-sized and larger labs are also concerned about pay, but they have other complaints as well.
“They feel like they are a cog in the machine and feel underappreciated,” Morrissey said. “What we hear a lot from people who work in the clinical labs of large hospitals is that they feel unappreciated by those working in other departments.”
Too Few MT/MS Training Programs to Meet Demand
According to Forbes, the US currently has a shortage of approximately 20,000-25,000 medical technologists. The approximately 338,000 technologists working in the country equate to about one technologist per 1,000 people, which translates to a vacancy rate of 7% to 11% in almost every region.
Forbes also reported that medical technologists in the US had performed approximately 13 billion laboratory tests annually before the COVID-19 pandemic. However, the pandemic added 997 million SARS-CoV-2 diagnostic tests to the existing workload.
Intensifying the problem is that currently there are only 240 medical technologist and medical scientist training programs in the US, which represents a 7% decrease since 2000. Forbes notes there are some states that have no such training programs at all.
“Having the opportunity to train to be a medical technologist is an important thing,” Morrissey said. “More universities and community colleges need to offer associate’s and bachelor’s degrees in medical technology.”
However, even with an increase in available degrees, few students are enrolling in those programs.
Morrissey suggests that clinical lab professionals contact local educational institutions to inform them of the need for medical technology degrees and determine if they can do anything to help start such training programs.
“If you are a medical laboratory in an area that doesn’t have a school that offers a degree in medical technology, I would recommend banging down the doors of community colleges to see how you can get that type of program into place,” she proposed. “It really benefits you. It is really about getting those schools to realize there is a need for medical technologists.”
Morrissey added that schools are beginning to re-add medical technology programs to their curriculum. This may translate into more available MTs and CLSs to work in clinical laboratories and relieve some of the staffing shortages.
Laboratory Automation, More Federal Lobbying Could Help
Automating some medical laboratory operations could present another solution to staffing dilemmas.
“Automation will help a little bit,” she said. “A significant number of labs are adding automation—either at the technology or collection level—so they don’t need as many technologists to run the lab.”
Additionally, regionalization of clinical labs could help with staffing issues because high volumes of samples can allow for the streamlining of staff.
“Some integrated delivery networks (IDNs) that have multiple hospitals within a city or metro area are regionalizing their clinical laboratories and using couriers to transport the samples being collected, resulting in better efficiency and productivity,” she said.
Morrissey also believes there is room for lobbying for the occupation of medical technology at both the state and federal levels. She compared the clinical laboratory profession to how the nursing profession dealt with shortages in the past.
“Nursing is in all hospital and doctor groups,” she explained. “They have very large organizations that are advocating for them at the federal and state level and labs need more of that.”
Clinical Lab Recruiting Reverting to Pre-COVID Qualifications
Though more people are testing themselves for COVID at home, Morrissey says the need for more clinical laboratory professionals will not subside any time soon.
“Before COVID, there was a huge increase in requests for toxicology reports due to drug testing and screening,” she explained. “COVID caused those needs to go away, not because people didn’t need those things, but because everyone was focusing on COVID. If an individual is not going into work, does he or she really need a monthly drug screen? The needs shifted during COVID and now they are shifting back.”
During the COVID-19 pandemic, medical labs were more willing to train individuals who had some lab experience or a background that would indicate they could perform the job duties. It is probable that recruiters will start to have more stringent requirements for potential lab employees, reverting back to pre-COVID qualifications.
Nevertheless, Morrissey believes staffing shortages for medical laboratories will continue.
“In the short term, in the next one to three years, I think it is going to get worse before it gets better,” she said. “In the medium term, automation in clinical laboratories will probably ease the staffing shortage quite a bit. Potentially, we will see more medical technology training programs pop up as the staffing shortages become a better-known issue.”
