Infectious Disease | NeuMoDx

Shifting gears in clinical testing

At the beginning of the COVID-19 pandemic, the first public health lab in Michigan to run PCR tests processed about 90 samples a day. By the time Omicron hit, it processed 2,700. But how did they manage to keep up with testing needs? Especially when the nation faced massive testing kit shortages?

Linoj Samuel, Ph.D. remembers the exact date his lab began running COVID-19 PCR tests: March 16, 2020.

As the division head for clinical microbiology at the Henry Ford Health System (HFHS), he’d seen a lot of pathogens pass through the lab during the past 14 years, from strep A and B and influenza to RSV, bacterial pneumonia, and tuberculosis.

A board-certified medical microbiologist, Samuel says the lab functions 24/7 because “we believe that microbiology samples are time-sensitive, and getting those sample results back in a quick and timely manner is critical to patient care and outcomes. And especially in terms of infectious diseases, bacteria and viruses degrade over time. So we make sure we process samples around the clock.”

That core practice became more important than ever on that day in March 2020.

The samples were from patients who’d been hospitalized for pneumonia. The lab techs pipetted the manual assay recommended by the CDC—the first lab in Michigan to do so. At the time, only three people on staff had the training to do manual testing.

“It was very challenging because we had to work extra hours around the clock,” says Moroj Altaweel, a medical technologist in the microbiology lab for the past six years. “I would barely get a few hours of sleep and then come back.” 

They completed the first 30 tests in about three hours. “I remember standing there looking over the shoulder of a lab tech as the first results came in and thinking, ‘Wow,’” recalls Dr. Samuel. “A significant chunk of that first batch were positive for COVID.”

The Clinical Microbiology Lab at Henry Ford Health System was the first public health lab to identify a COVID-19 positive case in the state in 2020. What followed was an unprecedented onslaught of testing needs. “What we had to do was really get creative and innovative,” says Division Head Samuel Linoj, Ph.D. And while the staff struggled to keep up with the skyrocketing number of lab samples, they were also dealing with the impact of COVID-19 on their personal lives. But a shift in testing methods – from manual to automated – helped with the burden. 
We had to deliver results in a timely manner because people were afraid. Not just patients, but health care providers. 
Linoj Samuel, Ph.D., Division Head, Clinical Microbiology Lab, Henry Ford Health System

Global shortages

Four days later, the team began running out of reagents, nasopharyngeal swabs and viral transport medium (VTM), reflecting global shortages. At that point, the lab was still able to process about 90 manual samples a day, using swabs that had to be 3D printed and filling vials by hand. The lab prioritized the sickest patients in the ICU, says Altaweel, who was pulling triple shifts when testing was at its peak. “The patients don’t ever see us, but we are here to help doctors with their diagnoses,” she says.

For Kareem Rofoo, manager of the microbiology lab and a 17-year veteran of HFHS, the pandemic was right in his home: His daughter caught the virus in that early phase, before there were vaccines or medications. With his presence at the lab essential to the lab’s continuing operation, and his wife working at the hospital, Rofoo and his wife had little choice but to isolate themselves from their daughter, who quarantined upstairs in their home. Every day, they gave her the food they’d cooked for her on disposable plates.

Meanwhile, tests were returned to the lab in higher and higher numbers. A shocking number of them were positive for COVID-19.

“We were told time and again that keeping testing up and running was a critical aspect of managing what limited resources there were on the frontlines—sample collection, outpatient centers, urgent care or emergency rooms were getting slammed at that time. Keeping the testing pipeline up and running was absolutely critical to the delivery of effective patient care,” Samuel says.

And it wasn’t just patients who needed testing: “Another critical part of keeping the health care system going was employee testing so that we had nurses and doctors who were tested and cleared to work in the units.” 

Linoj Samuel, Ph.D.
Linoj Samuel, Ph.D., is the division head for clinical microbiology at the Henry Ford Health System (HFHS) and an ABMM (American Board of Medical Microbiology) certified medical microbiologist with a Ph.D. in Microbiology and Immunology from the University of  Arizona in Tucson. He is drawn to the ever-evolving nature of his field. “You're never standing still. Neither are the pathogens. They're constantly changing. This isn't one of those fields where you settle in for the long haul. You have to really always reinvent yourself with new technology with new developments.”
We were dealing with thousands of samples every day that we knew had an extremely high level of virus.
Linoj Samuel, Ph.D., Division Head, Clinical Microbiology Lab, Henry Ford Health System

Keeping testing up and running

It was around then that Samuel thought of the NeuMoDx, a high-throughput automated PCR platform located in a hospital research lab.

“When we first got the NeuMoDx platform, we had two of them—the NeuMoDx 288 and the NeuMoDx 96,” Altaweel says. “We started getting other platforms at that time, but the NeuMoDx took a lot of our work volume.”

“We went from doing a couple hundred samples a day to close to 2,700 samples daily” using six testing platforms when Omicron hit greater Detroit in early 2022. They returned 90% of the results within 24 hours. “Keep in mind that a lot of national reference labs were backed up almost seven to ten days for results, and that was really not helpful to management of patients in real time,” Samuel points out. “We sustained a 24-hour turnaround time almost throughout the entire pandemic.”

“It changed things significantly,” he says. “When we brought NeuMoDx on board, we were able to slowly ramp up capacity and really expand on testing. And it meant not just faster results, but it meant that we could expand the patient population. It wasn't just the sickest patients who we were testing anymore. We could test additional employees and patients in outpatient settings. We really needed to do that to get a handle on this disease.”

The WHO has identified antimicrobial resistance (AMR) as one of the biggest challenges facing medicine. Traditional methods of AMR testing can take up to three days to identify resistance markers. That’s why there’s been a trend in clinical microbiology towards more molecular-based testing, which offers improved sensitivity, specificity and faster turnaround times. “With molecular-based testing, you can have those results upfront and you're able to make sure that you're using the right antibiotics,” Saumel says. “I think that's a positive change that is going to benefit patients in the long term. You're making sure that you're doing the right things from an infection control standpoint to limit the spread of those highly resistant organisms.”
We are now seeing a transition to molecular based testing because of improved sensitivity, specificity, better turnaround times. And that's going to benefit patients in the long term.
Linoj Samuel, Ph.D., Division Head, Clinical Microbiology Lab, Henry Ford Health System

Lessons learned

Now that the COVID-19 burden on the HFHS lab has eased up a bit, the lab can shift its focus to some of the recurring pathogens prevalent in the metro Detroit region.

They’ll use the lessons of the pandemic going forward. “Masks are a useful tool, and vaccines are powerful tools,” says Rofoo. “I think telehealth will be the new norm from now on. So will diversifying testing platforms, diversifying the supply chain, cross-training between shifts and prioritizing testing. All these I think we have learned from COVID.”

And for Samuel, that includes making it clear that lab techs are some of the unsung heroes of the pandemic.

“You hear about nurses all the time – and more power to them. They do an incredible job,” he says. “But I think that most of the country is unaware that there are lab techs behind the scenes with highly specialized training who are working 24/7. For many folks, the lab is a black box that no one sees and no one knows. But what we do is critical to the delivery of healthcare. A huge proportion of medical decision making relies on lab results. And during the pandemic, we were on a different kind of frontline. We were handling hundreds of thousands of highly infectious samples that in the early days that we knew nothing about. We did the best we could under the circumstances. I'm proud of the way our staff stepped up and put themselves on the line to do what needed to be done for their patients.”

Clinical testing
The global supply chain suffered major lapses during the pandemic, with essential components for molecular testing suddenly becoming unavailable. Labs all over the world scrambled for swabs and reagents. The team at HFHS had to get innovative and created lab-made kits with 3D-printed swabs and self-filled vials for collection. “An army of lab personnel” assembled the components into testing kits “so that our providers on the front lines had the tools they needed to collect the samples for COVID,” Dr. Samuel says. They sent thousands of these lab-made kits throughout the HFHS system.

June 2022