Funded by the CDC, the program hopes to alleviate personnel shortages in Baltimore area clinical labs while also producing a knowledge base for lab managers nationwide
Clinical laboratory managers struggling to fill vacant phlebotomy and accessioning positions will be interested to learn about a pilot program being conducted by the City of Baltimore and the University of Maryland School of Medicine to train people “for employment in hospital laboratories, phlebotomy draw sites, and reference laboratory processing centers,” according to The Elm, a publication of the University of Maryland, Baltimore.
The 14-week “Mayor’s Workforce Development Program” began on April 19 and will continue through the end of July. Participants meet twice a week for lectures and experience working with specimens in actual medical laboratories or in a “hybrid learning environment,” The Elm reported.
“I came up with the idea of doing cross-training for laboratory people and public health people in case there is another pandemic,” explained Lorraine Doucette in an exclusive interview with Dark Daily. Doucette, who is managing the pilot program, is an Assistant Professor and Medical Laboratory Science Program Director, Department of Medical and Research Technology, University of Maryland School of Medicine.
“There is already a huge shortage of laboratory people, but an enormous amount left in droves during the pandemic because they got physically burned out. Some just could not do the work anymore because of things like carpal tunnel syndrome and repetitive stress injuries,” she added.
“I’m confident that all 15 or 16 students who complete this workforce program will be employed within weeks of finishing as accessioners,” said Lorraine Doucette (above), Assistant Professor and Medical Laboratory Science Program Director, Department of Medical and Research Technology, University of Maryland School of Medicine, in an exclusive interview with Dark Daily. “This has been so successful. This is making a difference in people’s lives. This is changing them from being unemployed to actually having a career in a clinical laboratory. They love it. They are so proud of themselves.” (Photo copyright: LinkedIn.)
CDC Funding Part of National Program to ‘Enhance’ Clinical Lab Workforce
The collaboration is part of a CDC project titled, “Enhancing US Clinical Workforce Capacity.’ Doucette will receive a total of one million dollars over the course of three years to facilitate the program in stages.
“It is not necessarily an old-fashioned grant where they just gave me a pile of money,” Doucette told Dark Daily. “The CDC works with me constantly via reports and Zoom meetings.”
This CDC project is designed to both cross train clinical laboratory professionals in public health, clinical chemistry, microbiology, and hematology, as well as to train individuals in the workforce development program to become laboratory accessioners.
“They are going to be qualified to work as an accessioner in any local hospital,” Doucette noted. “The people who pick up the lab samples out of the tube system are the accessioners and there is a huge shortage of them also. We’re teaching them the basics so the more advanced lab personnel can perform the higher-level work.”
Students in the program learn all about lab safety and the proper handling of lab samples as well as proper data entry, professionalism, and how to communicate with medical and laboratory personnel. They work with urine and blood samples and fabricated spinal fluid samples.
“They are taught about the different tubes, what the anticoagulants are, what makes each tube unique, why you can’t mix samples, balancing a centrifuge, and how to properly put on and remove safety gear like lab coats, gloves, and goggles,” Doucette explained.
The Mayor’s Workforce Development Program is free for Baltimore residents looking for employment via the workforce office. The only requirements for enrolling are having a high school education and being fully vaccinated.
Phlebotomy and Additional Cross-training to Be Added
Doucette would eventually like to add a phlebotomy segment to future training sessions. “We would like to develop an additional partnership with BCCC (Baltimore City Community College) for the phlebotomy piece. That would definitely increase the people and the program’s marketability,” she said. “They could not only draw the blood, but they could also process the sample.”
After assessing the success of the current program and determining what did and did not work, there will be an additional training session held in the fall. Next year, there will be more sessions held for individuals in the workforce program and cross-training classes for current clinical laboratory professionals.
The strategy for the third year of the grant includes sharing the specifics of the program with medical laboratory professionals via the CDC’s free OneLab REACH platform. This portion includes the online delivery of documentation such as training sheets, lab exercises, Microsoft PowerPoint presentations, and videos used in both the accessioning and cross-training coursework.
“We’re going to do the OneLab REACH,” Doucette said. “I’m going to be putting it all online and marketing it all around the country in stages and increments. I will be going to a lot of professional society meetings and talking to lab managers to help them understand the concept of how this all benefits them.”
This unique collaboration between the City of Baltimore and University of Maryland School of Medicine, funded by the CDC, should help alleviate some of the clinical laboratory worker shortages that exist in the Baltimore area. Hopefully, the effort will result in additional knowledge, resources, and tools to assist medical lab managers across the country to recruit and retain talented, highly-skilled workers.
Another study in the United Kingdom that also used genomic analysis to understand drug-resistant Shigella produced findings that may be useful for microbiologists and medical laboratory scientists
From the onset of an infectious disease outbreak, public health officials, microbiologists, and clinical laboratory managers find it valuable to trace the origin of the spread back to the “index case” or “patient zero”—the first documented patient in the disease epidemic. Given the decreased cost of genomic analysis and improved accuracy of gene sequencing, infectious disease researchers are finding that task easier and faster than ever.
One recent example is a genomic study conducted at University of Washington (UW) in Seattle that enabled researchers to “retrace” the origin and spread of a “multidrug-resistant Shigellosis outbreak” from 2017 to 2022. “The aim of the study was to better understand the community transmission of Shigella and spread of antimicrobial resistance in our population, and to treat these multi-drug resistant infections more effectively,” the UW scientists stated in a new release.
Shigellosis (aka, bacillary dysentery) is a highly contagious disease of the intestines that can lead to hospitalization. Symptoms include fever, stomach cramps, diarrhea, dysentery, and dehydration.
“Additional analysis of the gut pathogen and its transmission patterns helped direct approaches to testing, treatment, and public health responses,” the UW news release states.
Usually prevalent in countries with public health and sanitation limitations, the “opportunistic” Shigella pathogen is now being seen in high-income countries as well, UW reported.
“You can’t really expect an infectious disease to remain confined to a specific at-risk population. [Shigella infections are] very much an emerging threat and something where our public health tools and therapeutic tools have significant limitations,” infectious disease specialist Ferric Fang, MD (above) told CIDRAP News. Fang is a UW professor of Microbiology and Clinical Laboratory Medicine and a corresponding author of the UW study. (Photo copyright: University of Washington.)
Generally, Shigella infects children, travelers, and men who have sex with men (MSM), the CDC noted.
The UW researchers were motivated to study Shigella when they noticed an uptick in drug-resistant shigellosis cases in Seattle’s homeless population in 2020 at the beginning of the COVID-19 pandemic, Center for Infectious Disease Research and Policy News (CIDRAP News) reported.
“Especially during the pandemic, a lot of public facilities were closed that homeless people were used to using,” infectious disease specialist Ferric Fang, MD, told CIDRAP News. Fang is Professor of Microbiology and Laboratory Medicine at University of Washington and corresponding author of the UW study.
The researchers studied 171 cases of Shigella identified from 2017 to 2022 by clinical laboratories at Harborview Medical Center and UW Medical Center in Seattle. According to CIDRAP News, the UW researchers found that:
46% were men who have sex with men (MSM).
51% were people experiencing homelessness (PEH).
Fifty-six patients were admitted to the hospital, with eight to an intensive care unit.
51% of isolates were multi-drug resistant (MDR).
Whole-Genome Sequencing Reveals Origin
The UW scientists characterized the stool samples of Shigella isolates by species identification, phenotypic susceptibility testing, and whole-genome sequencing, according to their Lancet Infectious Diseases paper. The paper also noted that 143 patients received antimicrobial therapy, and 70% of them benefited from the treatment for the Shigella infection.
Whole-genome sequencing revealed that two strains of Shigella (S. flexneri and S. sonnei) appeared first in Seattle’s MSM population before infecting the PEM population.
The genomic analysis found the outbreak of drug-resistant Shigella had international links as well, according to CIDRAP News:
One S. flexneri isolate was associated with a multi-drug resistant (MDR) strain from China, and
S. sonnei isolates resembled a strain characteristic of a current outbreak of MDR Shigella in England.
“The most prevalent lineage in Seattle was probably introduced to Washington State via international travel, with subsequent domestic transmission between at-risk groups,” the researchers wrote.
“Genomic analysis elucidated not only outbreak origin, but directed optimal approaches to testing, treatment, and public health response. Rapid diagnostics combined with detailed knowledge of local epidemiology can enable high rates of appropriate empirical therapy even in multidrug-resistant infection,” they continued.
UK Shigella Study Also Uses Genomics
Another study based in the United Kingdom (UK) used genomic analysis to investigate a Shigella outbreak as well.
Motivated by a UK Health Security Agency report of an increase in drug-resistance to common strains since 2021, the UK researchers studied Shigella cases from September 2015 to June 2022.
According to a paper they published in Lancet Infectious Diseases, the UK researchers “reported an increase in cases of sexually transmitted S. flexneri harboring blaCTX-M-27 (an antibiotic-resistant gene) in England, which is known to confer resistance to third-generation cephalosporins (antibiotics),” the researchers wrote.
Their analysis of plasmids (DNA with genes having antibiotic resistance) revealed a link in two drug-resistant Shigella strains at the same time, CIDRAP News explained.
“Our study reveals a worsening outlook regarding antimicrobial-resistant Shigella strains among MSM and highlights the value of continued integration of genomic analysis into surveillance and research,” the UK-based scientists wrote.
Current challenges associated with Shigella, especially as it evades treatment, may continue to demand attention from microbiologists, clinical laboratory scientists, and infectious disease specialists. Fortunately, use of genomic analysis—due to its ongoing improvements that have lowered cost and improved accuracy—has made it possible for public health researchers to better track the origins of disease outbreak and spread.
Screening and analysis of ocean samples also identified a possible missing link in how the RNA viruses evolved
An international team of scientists has used genetic screening and machine learning techniques to identify more than 5,500 previously unknown species of marine RNA viruses and is proposing five new phyla (biological groups) of viruses. The latter would double the number of RNA virus phyla to 10, one of which may be a missing link in the early evolution of the microbes.
Though the newly-discovered viruses are not currently associated with human disease—and therefore do not drive any current medical laboratory testing—for virologists and other microbiologists, “a fuller catalog of these organisms is now available to advance scientific understanding of how viruses evolve,” said Dark Daily Editor-in-Chief Robert Michel.
“While scientists have cataloged hundreds of thousands of DNA viruses in their natural ecosystems, RNA viruses have been relatively unstudied,” wrote four microbiologists from Ohio State University (OSU) who participated in the study in an article they penned for The Conversation.
The OSU study authors included:
Ahmed Zayed, PhD, research scientist, Dept. of Microbiology, OSU.
Matthew Sullivan, PhD, Professor of Microbiology and Director of the Center of Microbiome Science at OSU.
“RNA viruses are clearly important in our world, but we usually only study a tiny slice of them—the few hundred that harm humans, plants and animals,” explained Matthew Sullivan, PhD (above), Director, Center of Microbiome Science, in an OSU news story. Sullivan led the OSU research team. “We wanted to systematically study them on a very big scale and explore an environment no one had looked at deeply, and we got lucky because virtually every species was new, and many were really new,” he added. (Photo copyright: University of Ohio.)
RNA versus DNA Viruses
In contrast to the better-understood DNA virus, an RNA virus contains RNA instead of DNA as its genetic material, according to Samanthi Udayangani, PhD, in an article she penned for Difference Between. Examples of RNA viruses include:
One major difference, she explains, is that RNA viruses mutate at a higher rate than do DNA viruses.
The OSU scientists identified the new species by analyzing a database of RNA sequences from plankton collected during a series of ocean expeditions aboard a French schooner owned by the Tara Ocean Foundation.
“Plankton are any aquatic organisms that are too small to swim against the current,” the authors explained in The Conversation. “They’re a vital part of ocean food webs and are common hosts for RNA viruses.”
The team’s screening process focused on the RNA-dependent RNA polymerase (RdRp) gene, “which has evolved for billions of years in RNA viruses, and is absent from other viruses or cells,” according to the OSU news story.
“RdRp is supposed to be one of the most ancient genes—it existed before there was a need for DNA,” Zayed said.
The RdRp gene “codes for a particular protein that allows a virus to replicate its genetic material. It is the only protein that all RNA viruses share because it plays an essential role in how they propagate themselves. Each RNA virus, however, has small differences in the gene that codes for the protein that can help distinguish one type of virus from another,” the study authors explained.
The screening “ultimately identified over 44,000 genes that code for the virus protein,” they wrote.
Identifying Five New Phyla
The researchers then turned to machine learning to organize the sequences and identify their evolutionary connections based on similarities in the RdRp genes.
“The more similar two genes were, the more likely viruses with those genes were closely related,” they wrote.
The technique classified many of the sequences within the five previously known phyla of RNA viruses:
But the researchers also identified five new phyla—including two dubbed “Taraviricota” and “Arctiviricota”—that “were particularly abundant across vast oceanic regions,” they wrote. Taraviricota is named after the Tara expeditions and Arctiviricota gets its name from the Arctic Ocean.
They speculated that Taraviricota “might be the missing link in the evolution of RNA viruses that researchers have long sought, connecting two different known branches of RNA viruses that diverged in how they replicate.”
In addition to the five new phyla, the researchers are proposing at least 11 new classes of RNA viruses, according to the OSU story. The scientists plan to issue a formal proposal to the International Committee on Taxonomy of Viruses (ICTV), the body responsible for classification and naming of viruses.
Studying RNA Viruses Outside of Disease Environments
“As the COVID-19 pandemic has shown, RNA viruses can cause deadly diseases. But RNA viruses also play a vital role in ecosystems because they can infect a wide array of organisms, including microbes that influence environments and food webs at the chemical level,” wrote the four study authors in The Conversation. “Mapping out where in the world these RNA viruses live can help clarify how they affect the organisms driving many of the ecological processes that run our planet. Our study also provides improved tools that can help researchers catalog new viruses as genetic databases grow.”
This remarkable study, which was partially funded by the US National Science Foundation, will be most intriguing to virologists and microbiologists. However, clinical laboratories also should be interested in the fact that the catalog of known viruses has just expanded by 5,500 types of RNA viruses.
While working to increase turn-around-times for STAT tests, Florida’s first coronavirus patient arrived, requiring SMH’s clinical laboratory team to adapt its plans
Despite the COVID-19 pandemic, the clinical laboratory team at 839-bed Sarasota Memorial Hospital, part of the Sarasota Memorial Health Care System (SMH) in Sarasota, Fla., not only implemented a new automated microbiology system, it also installed a new mass spectrometry analyzer, along with new instruments to support large volumes of SARS-CoV-2 testing.
How SMH’s microbiology laboratory team accomplished this while shelter-in-place directives in Florida caused many patients to stop visiting emergency departments and physicians’ offices—and as hospitals and medical laboratory facilities restricted access to staff and essential personnel—provides useful lessons for pathologists and clinical laboratory managers.
“Florida reported its first positive SARS-CoV-2 infection on March 2, marking the beginning of an outbreak that continues today,” he noted, adding, “This created the need to support the hospital in identifying infected patients in Sarasota County by having the microbiology lab acquire and set up more instruments. Also, the micro lab needed space for a new mass spectrometry analyzer to speed up pathogen identification this year.
In the same TDR interview, Olevia Fulkert, Microbiology Technical Supervisor at SMH said the microbiology lab had to reconfigure its layout to be prepared for the new COPAN system. “Our team had to arrange space for these new instruments, while protecting the space needed for the microbiology automation.”
“The WASPLab (above) literally went right into the middle of the busiest area of our lab,” said SMH’s Director of Laboratory Services, Harold Vore, MS, MT. “That’s the room we call COVID central, because that’s where we process all SARS-CoV-2 specimens.” SMH’s medical laboratory team began this implementation in the early months of the COVID-19 pandemic and relied on Lean processes to accomplish its goals. (Photo copyright: Sarasota Memorial Health Care System.)
Return of the ‘Snowbirds’
In August, SMH’s microbiology laboratory staff was busy validating the WASPLab instruments so the lab would be ready to process patient specimens when Florida’s snowbirds—out-of-state residents who arrive for the winter—return to Sarasota.
Vore knew several elements would be required for SMH’s microbiology automation project to succeed:
He had to assure the microbiology lab’s staff that adding automation would not cause any loss of jobs.
Timing of the implementation was critical, because lab test volume rises in the winter when tourists and part-time residents return.
Lean methods would be important because lab staff was familiar with them and they would help the vendor to arrange the physical layout and workflow to optimize productivity, reduce errors, and decrease turnaround times.
Vore needed documentation that showed automating the microbiology lab met and exceeded the return-on-investment projections he and his lab team used to persuade health system administrators of its value.
According to Vore, to date the installation has gone smoothly. “The staff in the microbiology lab has been phenomenal,” he commented. “They have continued to do what they always do, while at the same time we’re installing this large new system right in their midst.
“And they did not complain. In fact, they were eager to make progress in improving production,” he continued. “That attitude is common among our laboratory staff, because we saw the same thing happen when we automated our core lab.”
Increasing Microbiology Lab Capacity without Increasing Staff
Vore estimates automation will expand SMH’s microbiology laboratory capacity by up to 40%. “We measure that 40% in terms of the number of plates our techs can read per day with the WASPLab versus how we did it manually with our existing staff,” he explained. “We may still need to increase some staff. But even without adding staff, we thought we could move the peg further down the road in terms of throughput and improve our turnaround time too.
“We cannot make bacteria grow any faster and yet our specimen volume continues to increase,” he noted. “That makes automating microbiology the right strategy. Also, if we hadn’t automated the core lab starting in 2015, we might not have been able to handle the increased volume that we saw last year and this year’s additional surge in COVID-19 tests.”
How Lean Helped with the Implementation
Workflow in microbiology has traditionally been mostly manual. Therefore, combining Lean and automation can generate substantial benefits for a lab. “By definition, the design of the WASPLab is Lean,” Vore explained. “By that I mean the person who touches each specimen the least wins. That’s why the WASPLab is designed the way it is. Once we load a specimen in the front end, theoretically, no one needs to touch those plates until the testing is complete.”
“That’s the ideal we’re trying to reach,” he added. “At the moment, we still need to pull the plates to, as we say, ‘pick them.’ But we just introduced a way to improve that part of the process.
Adding Mass Spectrometry
“Along with the microbiology automation, we now read specimens digitally and we tell the machine to take a certain plate off so we can spot it,” Vore continued. “To speed up that process, we got some additional funding and bought a mass spec analyzer that uses MALDI-TOF to identify pathogens. Now we get the boost from the WASPLab, and we also use mass spec to cut six hours off our first read,” Vore added.
“The WASPLab and the mass spec give us higher quality incubation and better harvest of pathogens. Once we spot the plate, the mass spec can identify the pathogen in about two minutes,” he said.
“After going live with the mass spectrometry in August, we’ve made huge progress versus the normal process, where we would plate the specimen manually under a hood and then put the specimen in the incubator and pull it out to read 24 hours later,” he said.
“That whole step-by-step process to identify the pathogen could take 48 hours,” he continued. “But now we can move to a 24-hour, seven-day-a-week operation, where we can do first-in-first-out of pathogens in about 18 hours. That cuts six hours off the time to do the first plate read. Then we can spot it and get a result from the mass spec in two minutes. The impact for patient care can be tremendous.
“In a recent case, for example, we had to identify a specimen from an infant and used the mass spec to identify salmonella in two minutes,” Vore noted. “Normally that would take at least a day or more. That’s what I mean about making tremendous impact on patient care by using automation in microbiology.”
Clearly, this would be a challenging project for any medical laboratory to complete during the best of times, let alone during the early months of the COVID-19 pandemic. But through determination, the use of Lean, and a positive approach, SMH’s microbiology lab team implemented the first WASPLab in the state of Florida. And it will improve SMH’s ability to care for patients for years to come.
Researchers believe new findings about genetic changes in C. difficile are a sign that it is becoming more difficult to eradicate
Hospital infection control teams, microbiologists, and clinical laboratory professionals soon may be battling a strain of Clostridium difficile (C. difficile) that is even more resistant to disinfectants and other forms of infection control.
A WSI news release states the researchers “identified genetic changes in the newly-emerging species that allow it to thrive on the Western sugar-rich diet, evade common hospital disinfectants, and spread easily.”
Microbiologists and infectious disease doctors know full well that this means the battle to control HAIs is far from won.
“C. difficile is currently forming a new species with one group specialized to spread in hospital environments. This emerging species has existed for thousands of years, but this is the first time anyone has studied C. difficile genomics in this way to identify it. This particular [bacterium] was primed to take advantage of modern healthcare practices and human diets,” said Nitin Kumar, PhD (above), in the news release. (Photo copyright: Wellcome Sanger Institute.)
Genomic Study Finds New Species of Bacteria Thrive in
Western Hospitals
In the published paper, Nitin Kumar, PhD, Senior Bioinformatician at the Wellcome Sanger Institute and Joint First Author of the study, described a need to better understand the formation of the new bacterial species. To do so, the researchers first collected and cultured 906 strains of C. difficile from humans, animals, and the environment. Next, they sequenced each DNA strain. Then, they compared and analyzed all genomes.
The researchers found that “about 70% of the strain collected specifically from hospital patients shared many notable characteristics,” the New York Post (NYPost) reported.
Hospital medical laboratory leaders will be intrigued by the
researchers’ conclusion that C. difficile is dividing into two separate
species. The new type—dubbed C. difficile clade A—seems to be targeting
sugar-laden foods common in Western diets and easily spreads in hospital
environments, the study notes.
“It’s not uncommon for bacteria to evolve, but this time we actually see what factors are responsible for the evolution,” Kumar told Live Science.
New C. Difficile Loves Sugar, Spreads
Researchers found changes in the DNA and ability of the C.
difficile clade A to metabolize
simple sugars. Common hospital fare, such as “the pudding cups and instant
mashed potatoes that define hospital dining are prime targets for these strains”,
the NYPost explained.
Indeed, C. difficile clade A does have a sweet tooth. It was associated with infection in mice that were put on a sugary “Western” diet, according to the Daily Mail, which reported the researchers found that “tougher” spores enabled the bacteria to fight disinfectants and were, therefore, likely to spread in healthcare environments and among patients.
“The new C. difficile produces spores that are more
resistant and have increased sporulation
and host colonization capacity when glucose or fructose is available for
metabolism. Thus, we report the formation of an emerging C. difficile
species, selected for metabolizing simple dietary sugars and producing high
levels or resistant spores, that is adapted for healthcare-mediated
transmission,” the researchers wrote in Nature Genetics.
Bacteria Pose Risk to Patients
The findings about the new strains of C. difficile bacteria
now taking hold in provider settings are important because hospitalized
patients are among those likely to develop life-threatening diarrhea due to
infection. In particular, people being treated with antibiotics are vulnerable
to hospital-acquired infections, because the drugs eliminate normal gut
bacteria that control the spread of C. difficile bacteria, the
researchers explained.
According to the Centers for Disease Control and Prevention (CDC), C. difficile causes about a half-million infections in patients annually and 15,000 of those infections lead to deaths in the US each year.
New Hospital Foods and Disinfectants Needed
The WSI/LSHTM study suggests hospital representatives should
serve low-sugar diets to patients and purchase stronger disinfectants.
“We show that strains of C. difficile bacteria have continued to evolve in response to modern diets and healthcare systems and reveal that focusing on diet and looking for new disinfectants could help in the fight against this bacteria,” said Trevor Lawley, PhD, Senior Author and Group Leader of the Lawley Lab at the Wellcome Sanger Institute, in the news release.
Microbiologists, infectious disease physicians, and their
associates in nutrition and environmental services can help by understanding
and watching development of the new C. difficile species and offering
possible therapies and approaches toward prevention.
Meanwhile, clinical laboratories and microbiology labs will
want to keep up with research into these new forms of C. difficile, so
that they can identify the strains of this bacteria that are more resistant to
disinfectants and other infection control methods.
