​Spring 2022

Even as SARS-CoV-2 has taken the world by storm, other pathogens have continued their own inexorable spread and evolution in the past two years. For public health laboratories, finite capacity—staff time, equipment, reagents and other resources—has necessitated difficult decisions and creative solutions to keep abreast of both existing and emerging pathogens.

by Jill Sakai, PhD, writer

Even as SARS-CoV-2 has taken the world by storm, other pathogens have continued their own inexorable spread and evolution in the past two years. For public health laboratories, finite capacity—staff time, equipment, reagents and other resources—has necessitated difficult decisions and creative solutions to keep abreast of both existing and emerging pathogens.

“The pandemic brought a wholesale pivot of our healthcare infrastructure toward managing this novel and devastating disease,” said Tim Southern, PhD, director of the South Dakota Public Health Laboratory. As clinic visits and non-essential care dropped, so did some laboratory testing demands. But fewer tests does not necessarily mean fewer infections. In some cases, he added, “now we’re seeing that there was some collateral damage from being so COVID-focused.”

Communities have continued to grapple with recurring outbreaks, such as sexually transmitted infections and gastrointestinal pathogens, and are now in the midst of an active influenza season. Some places have seen growing emergence of antibiotic-resistant Candida auris and other organisms. As the pandemic enters its third year, public health laboratories are drawing on a variety of strategies to keep up with a full gamut of pathogens amid ongoing COVID-19 testing needs.

Clear Focus

When there is always too much work to do, setting clear priorities is essential—which often means getting external guidance on what not to do, said Megan Crumpler, PhD, HCLD, director of the Orange County Public Health Laboratory in California. Their administration helped them prioritize specific public health groups rather than tasking their laboratory with mass community COVID-19 testing.

“Now we’re down to about 900 to 1,000 samples a week, so it’s become manageable,” she said.

It also means knowing what’s most critical.

“Some things we can put off—maybe syphilis for a day or so—and we wouldn’t impact our turnaround time,” said Shane Sevey, virology and immunology manager of the Oregon State Public Health Laboratory. “You start with the most important results that need to get out that day, and then you kind of work backward.”

National and regional reference laboratories, for example, have to maintain those testing responsibilities regardless of a pandemic.

“We can’t say, ‘well, there’s COVID, we can’t do [National Influenza Reference Center] testing;’ or ‘sorry, there’s COVID, we can’t do [Antibiotic Resistance Laboratory Network] work.’ That’s just not an option,” said Allen Bateman, PhD, MPH, D(ABMM), director of the communicable disease division of the Wisconsin State Laboratory of Hygiene. “We’re the only lab in the state that can do rabies testing and the level of tuberculosis testing that we do. That’s what we should be and need to be focusing on.” The state health department has been a key partner in setting and holding those priorities. “There has never been higher testing capacity, ever, for any other test than [there is now] for COVID-19,” Bateman added. “Massive COVID testing is not our role anymore.”

In South Dakota, Southern and his staff work closely with the Office of the State Epidemiologist and the Office of Disease Prevention Services to set testing priorities.

“The communication between those three principal teams—epidemiology, laboratory and disease prevention—is absolutely critical to determine what tests we need to escalate in importance, and what we can deescalate or send to someone else,” he said. That helped them manage immediate needs and stay focused on surveillance, outbreak detection and facilitating investigation.

Through creative use of some federal funding, the South Dakota team is reinforcing laboratory infrastructure to help absorb some of the additional testing and surge attributed to both COVID-19 and non-SARS-CoV-2 pathogens. Part of that process has also involved helping other clinical laboratory partners develop programs and infrastructure that can support public health needs, such as supporting matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for tuberculosis testing and opening a BSL-3 facility in a clinical reference laboratory.

Plan, Plan, Plan—But Don’t Get Too Attached

Public health laboratories are accustomed to planning for short-term outbreaks. But maintaining surge capacity during a prolonged public health emergency is a different beast, one that takes meticulous planning paired with the flexibility to scrap and rework those plans at a moment’s notice.

“Coordinating and planning—that’s the bottom line,” said Vanda Makris, a microbiologist in the Oregon laboratory. “You have an action plan. And then the next day, something changes, and you have to make adjustments.”

Good communication among personnel allowed them to coordinate and triage the most pressing needs.

“Oftentimes people may feel comfortable juggling multiple benches, so maybe they’re doing chlamydia, gonorrhea and our serologies at the same time and, as they have downtime, they’ll bounce from one instrument to the other,” Sevey said.

It helped that laboratory personnel had to work in person throughout the pandemic, Bateman said, because that facilitated the quick communication and discussion needed to adapt to daily needs and situations.
“We can walk down the hall and immediately touch base.”

Planning also has to happen at the instrumentation and supply level. Resource limitations sometimes necessitated some influenza samples being triaged for later analysis, said Kirsten St. George, PhD, MAppSc, director of the virology laboratory at the Wadsworth Center in New York. And in South Dakota, a surge in syphilis—with cases rising more than 1000% between 2019 and 2021—prompted a new public health campaign aimed at improving healthcare for vulnerable populations that has brought an influx of specimens to the public health laboratory for sexually transmitted infection (STI) testing.

“There’s been a mad dash for syphilis reagents of all kinds,” Southern said. “We have learned that we have to be very mindful of the amount of reagents and supplies that we keep. We’ve also brought on some new instrumentation and we’re really thinking about how we’re going to approach syphilis in the future, so that we can better accommodate a surge like what we’re seeing now.”

Find Efficiencies…

To stretch capacity as much as possible, Southern and others are turning to systems with higher throughput and automation wherever possible.

“The surge in syphilis is really pushing us towards automation of some of the algorithms that we use,” he said. Crumpler echoed this, saying that shifting STI testing from a traditional manual assay to the more automated reverse sequence screening algorithm helped the Orange County laboratory maintain syphilis testing throughout the pandemic.

The Wisconsin team has shifted a lot of their COVID-19 testing to more automated instruments as well, a move that enables anyone from the serology team to step in and help if the virology staff are needed elsewhere—which has proven especially beneficial during the first season of concurrent influenza and COVID-19. At Wadsworth, too, St. George said, “Significant efforts have been made in recent years to develop and implement more automated testing platforms and more multiplexed assays that provide concurrent test results for multiple respiratory agents simultaneously.”

The Oregon laboratory is similarly ramping up use of a multiplex assay, BioFire, to streamline testing for a panel of gastroenteritis-associated pathogens. In collaboration with the US Centers for Disease Control and Prevention (CDC) and APHL, they are also helping develop a new, next-generation sequencing assay for norovirus as a faster, higher throughput replacement for traditional Sanger sequencing.

In some cases, increased efficiency has even enabled new capabilities. Prior to the pandemic, the Orange County laboratory had started testing some clinical samples for C. auris by 16S sequencing, a multi-step, labor-intensive process. In mid-2020, demand began to increase and despite the throes of COVID-19 testing, the laboratory added C. auris outbreak testing and PCR screening to facilitate patient transfers between facilities. In 2021, the team switched to a MALDI platform to speed up the confirmation process. For PCR screening, they obtained an instrument, collaborated with CDC and the Washington State Public Health Laboratory to get specimens for validation of the assay, and went live in September, becoming the first local laboratory in California to offer this type of testing.

Although demand still far exceeds their capacity, Crumpler said, Orange County is hoping to receive funding through the CDC’s Strengthening HAI/AR Program Capacity (SHARP) program and is now working with the state of California to figure out how to increase capacity for resource-intensive C. auris point prevalence surveys.

Oftentimes, it’s more than just the testing itself that backs up. The detail-oriented, hands-on work of sample accessioning, preanalytical data entry and result reporting can also create bottlenecks. In Oregon, a LIMS administrator added barcoding and automated parts of their reporting platform, slashing the time needed to create and check reports. The improvements have also decreased the human error that comes with manually handling hundreds or thousands of samples, said Laura Tsaknaridis, a microbiologist in the laboratory.

“Now it’s so automated that it’s very difficult to get a specimen switched up or get the wrong accession number in there. That’s helped out a lot.”

…But Build in Redundancies

Despite the need to keep workflows as streamlined as possible, an element of strategic redundancy can help maintain operations throughout the volatile circumstances of a prolonged pandemic. Overwhelming demand and shifting manufacturer priorities have created ongoing supply challenges. And when gonorrhea and chlamydia tests, for example, use the same platforms as COVID-19 tests, completing a day’s work takes careful planning and allocation of available resources.

Diversification was a hard lesson learned from the pandemic, Southern said.

“For our non-COVID-19 programs, sometimes we need to be able to pivot between different platforms” to ensure that something is always up and running despite inconsistent supply chains. That represents significant investments in infrastructure, training and time, as scientists must establish proficiencies and competencies in redundant assays and complete additional validation and verification testing. But, he added, “those kinds of strategic changes will allow us to [handle] surge in other areas beyond COVID-19.”

Cross-training staff can also help fine-tune a laboratory’s effective capacity day-to-day. Wisconsin has shifted much of its COVID-19 testing to more automated instruments and trained their full serology team on those instruments, so they are able to step in if the virology staff are all unavailable. Similarly, virology staff can shift over and help with STI testing if needed. Such contingency planning has become even more pressing as Omicron sweeps the country, to manage both testing demands and the likelihood that some staff may be out sick or caring for family members.

Take Care of Your People, and They’ll Take Care of You

To keep things running, “it comes down to having an amazing crew,” Sevey said.
“If people weren’t willing to come in and they weren’t passionate about what they did—I don’t know where we would be at this moment. We just have exceptional people working in public health.”
In the early stages of the pandemic, many laboratories adopted an all-hands-on-deck approach, with personnel stepping into new roles where possible to prioritize COVID-19 testing. But as other needs returned, staff have largely resumed their regular duties.

“We were trying to hire new people,” Bateman said. But “government systems don’t move at the speed of a pandemic.”

Like most public health laboratories, Oregon implemented overtime and extended work weeks to get more done with the same number of employees—stopgap measures that have now stretched on for years.
“We kind of scrambled, like everyone else in the country, to bridge these gaps. And they’re still there,” Sevey said, echoing a common sentiment. Many temporary positions are now expiring, and filling specialized needs, such as informatics, can be especially hard.

Workforce issues are nothing new for Southern—“we traditionally have a very difficult time recruiting staff to central South Dakota”—and the pandemic’s challenges have refocused his attention on honing his existing team’s skills, coordination and morale. The efficiencies and collegiality born out of the COVID-19 response will boost the group moving forward, he said.

“We’re focusing on resiliency, self-care, making sure that we all have a little bit of juice left in the tank to get us over that next whatever—the next week, the next month, the next testing campaign, the next surge,” Southern said. “I want to do the best I can to take care of that small team of mine, because there’s great power in what they can do. If I can keep culture and morale high in the laboratory, I know we’ll be able to navigate months [or even] another year of really difficult COVID and non-COVID programming.”