NEW YORK – As demand for testing has soared during the SARS-CoV-2 pandemic, many labs with little experience in infectious disease or molecular testing have added such assays to their offerings.
And while instrument and reagent shortages have dominated discussions of the challenges laboratories faced in ramping up SARS-CoV-2 testing, lab information systems (LIS) have also proved a major chokepoint.
In a recent survey of healthcare systems by consulting and lab optimization firm Accumen, labs identified LIS resources as one of the major challenges they currently face, with more citing this as an issue than the supply chain problems that have hampered SARS-CoV-2 testing efforts.
A major source of lab LIS challenges is the fact that for many facilities SARS-CoV-2 testing requires them to handle considerably higher test volumes than they were previously. This creates strains at multiple points throughout the process, but especially so where the lab's internal routines make contact with the outside world — taking in samples and reporting out results.
Philippe Flamant, vice president of solutions engineering at Elmwood Park, New Jersey-based healthcare data firm Ellkay, said that since the pandemic hit his company has seen labs scrambling to implement fully electronic sample accessioning systems to help them handle the increased test volumes.
"A small laboratory has maybe three to five [people in accessioning], and if they crest anywhere over 600 samples [per day] they are drowning," he said. "They are calling in the CIO and the CEO to sit in and help with accessioning."
Bridget Ketron, a sales executive at Ellkay, said she had seen this firsthand at a customer lab.
"People were accessioning 12 to 18 hours a day at one of our labs in the south where COVID was high and the CIO, the CEO, the COO all were accessioning along with [regular staff] for 12 to 18 hours a day because they were all manual," she said.
Flamant cited the case of a Connecticut lab that was having to turn away SARS-CoV-2 testing business because they couldn't accession the samples quickly enough.
"It was a throughput problem in accessioning," he said. "They didn't have the infrastructure in place to [accession] more than 600 samples per day. They would have had to just keep hiring every day — throw another human at it, throw another human at it."
"The need to get [accessioning] to be 100 percent electronic and not have to relabel specimens when they come into the lab and let them just go directly into the lab has never been more important," he added.
Even labs that did have fully electronic accessioning systems could run into problems if those systems weren't tailored to the higher-throughput demands of SARS-CoV-2 testing, Flamant said. "You're an esoteric genomics laboratory that is used to doing whole-genome sequencing. The [system] will ask you all the very detailed questions that you want when you are trying to do genomic testing, but it doesn't work when you are trying to just do COVID tests. You can't take seven minutes to place one order."
The volume challenges were compounded by the fact that SARS-CoV-2 testing was also being done in a variety of environments outside traditional healthcare settings that labs don't typically interact with and with which their LISs may not be easily able to interface.
"You had to be able to quickly onboard cohorts of patients, whether that be a staff member, an employee, a student, an actual patient," Flamant said. "A lot of LISs are not made for that."
The other end of the process, reporting results, has also been difficult for labs not accustomed to dealing with this kind of testing. "Many people still rely on fax, on couriers, on manual processes for getting results back, and you need something that can get it back to providers a lot faster," Flamant said.
Samir Ahmetovic, senior enterprise account executive with Tucson, Arizona-based Sunquest Information Systems, likewise said that taking in samples and reporting results were two areas he had seen labs struggle on the LIS side of things.
"COVID testing orders are coming in through the system and they are going to have to receive the samples and run them, and that is going to have to be done manually unless they have a solution there," he said. "And then on the back end, when they have to send the results back, that is also going to be a manual process. If you're looking at 50 samples a day, you can handle that manually. You can call the physicians, you can fax over the results. But when you start scaling up into the hundreds and thousands of tests per day, you have to have an automated, IT solution."
Clinical labs handling routine testing likely have systems in place to handle this kind of volume, said Joe Nollar, AVP of product development at San Diego, California-based revenue cycle management and lab informatics firm Xifin. However, he noted, a wide range of lab types including specialty and esoteric labs have added SARS-CoV-2 testing to their offerings.
"The labs we have seen who have been expanding rapidly into COVID testing have been really all over the map in terms of the types of labs," he said. Xifin recently released its LIS 7 system, which is designed in part to help labs handle higher testing volumes.
"A lot of what we've been doing with laboratories who said, hey, we need to start running COVID-19 PCR tests, is to make sure they have the capability to accession those cases quickly, to process them in batches, and then result them in batches with the ability to view and sort the results in large batches so they can focus on the cases that are positive and automatically sign out the negative cases," Nollar said.
Labs equipped to handle high-volume testing might not have had the LIS resources needed for high-volume molecular testing, Ahmetovic said.
"There are some [anatomic pathology] systems out there that could handle some level of molecular testing, but they are basically using workarounds to let an existing [LIS] handle a molecular workflow that it wasn't built for," he said. "And then you have other labs that have no information system for molecular at all and are just using Excel."
Ahmetovic said the complexity of molecular testing, which involves keeping track of multiple specimens in different sample wells on different plates across multiple steps of an assay, has led to demand for molecular specific LISs that labs can purchase and plug into their larger LIS.
Nollar agreed, noting that the LIS requirements for molecular workflows are somewhat unique.
"The procedures in place for doing DNA extraction and amplification and having the right quality assurance steps in place, batching to the right instrumentation, the liquid handlers and real-time PCR devices and then producing those results and allowing the technologists to review and report those results at high volumes are all very important," he said. "That is very different from, say, your more standard clinical and toxicology workflows."
Ahmetovic added that the interest in pooling approaches to SARS-CoV-2 testing adds another level of complexity that some labs may not be well equipped to handle.
Additionally, because molecular testing has not traditionally been as high-throughput a business as it has become during the pandemic, some LISs tailored to molecular workflows may still include manual steps that can create bottlenecks for labs, he said.
"A lot of these functionalities or needs weren't really thought about because molecular volume is usually not very high, so a lot of systems are going to have these gaps or are going to have to address these types of gaps," he said.
Another capability many LISs were not necessarily designed with in mind is reporting results from high-volume molecular testing to authorities like state and federal public health organizations. This has been further complicated by the fact that many labs that were previously primarily local or regional businesses are now receiving samples for SARS-CoV-2 testing from around the country.
"All of a sudden [labs] went from being in one state to being in 50 states," Flamant said. "That is where it has really been challenging. You've been dealing with your state, but now you have to go and deal with all of these other states. I've been on the phone on Saturdays and Sundays and late at night, 11, midnight, 1AM, with [officials in] California, Florida, Massachusetts, you name it."
Nollar and Ahmetovic both said that even before the pandemic, demand had been increasing for better LIS tools for handling molecular testing, which is one of the fastest growing areas in the laboratory.
Ketron added that demand remains strong among labs that have moved into SARS-CoV-2 testing, as well, though she noted that the type of customer is changing somewhat.
"At first it was a lot of reference laboratories, and now we're seeing more institutions and colleges and universities who are trying to do student testing and things like that," she said. "We are seeing clientele that we have never seen before."
Flamant said many customers have also begun to anticipate how their testing needs may change moving into the fall and winter.
"This summer it was just like, we have to have something, we have to go," he said. "Now it is, we know a second wave is coming. We need to not just run PCR for COVID but start thinking about adding flu and respiratory panels, too. It's less chaotic now, more it's time to plan for tomorrow."