When cyclospora escalated from a routine annual nuisance to the largest nationwide outbreak in recorded history, clinical laboratories stepped up. By quickly adapting existing artificial intelligence (AI) tools, educating physicians, and, in one memorable case, motivating staff with a pizza party after an all-hands-on-deck call, laboratorians were able to successfully manage the summer onslaught.
“It’s crazy. And [it was] almost like COVID all over again,” said Bobbi S. Pritt, MD, MSc, DTMH, FCAP, FASTMH, FAAM, chair of the division of clinical microbiology at the Mayo Clinic.
Here’s how clinical laboratories met the moment.
Cyclospora cayetanensis is a parasite that usually spreads through food and water that is contaminated by human feces. Typically, the U.S. sees between about 2,500 and 4,500 cases a year, with cases peaking in summer since outbreaks are typically linked to contaminated fruits and vegetables.
This year, however, the outbreak has been exponentially worse, with 15,716 laboratory confirmed cases by mid-August, according to the Centers for Disease Control and Prevention (CDC), resulting in 828 hospitalizations and two deaths. The CDC also reported an additional 11,841 cases that either had not been laboratory confirmed or required further investigation to determine whether these patients acquired the parasite in the country or abroad.
Cyclospora is not an easy parasite to test for either. In response to the outbreak, clinical laboratorians couldn’t spin up mass antigen and PCR testing options, as they did during the worst of the COVID pandemic. The traditional test for cyclospora is microscopy, “which is lab intensive, almost like an art form,” said Ann T. MacIntyre, DO, MHS, FIDSA, senior medical director of infectious diseases at Quest Diagnostics. “You can’t mass produce skilled parasitologists overnight.”
The Mayo Clinic usually gets orders for about 70 cyclospora tests a month in the summer, said Pritt. But this July alone, they received over 11,000. As the Mayo Clinic is the reference laboratory for the state of Michigan, much of that workload involved testing samples for the Michigan Department of Public Health — and Michigan had the worst of the outbreak with 14,277 confirmed cases as of mid-August, according to the Michigan Department of Health and Human Services.
The Mayo Clinic started out trying to handle the load with their usual staff, who would perform a modified safranin stain. But as the laboratory became inundated, Pritt knew they had to do something. “We started asking for overtime and put out a plea, not just to microbiology but to all laboratories in lab medicine and pathology,” she said.
She actually didn’t mean to send the email to all of those labs, but she’s glad that she did. As a result, they even got volunteers from hematopathology for tasks that were seemingly unrelated to that specialty. “If you really just needed somebody who is willing to sit in a biosafety cabinet and process stool specimens, they don’t really need to be a microbiologist,” she said. She organized a pizza party for all the people who helped clear out the cyclospora backlog.
Anisha Misra, PhD, medical director for mycology and parasitology at the Cleveland Clinic, said they detected that the cyclospora surge was coming based on a 3-day span in late June. “We knew pretty early prior to anything being in the media,” she said. They usually get one cyclospora test request a day in the summer months. By the middle of July, they were getting 400 daily.
It required radical rethinking of how they process samples, as overall they usually only conduct about 4,000 ova and parasite (O&P) tests a year, which is not that high of a volume. This year, as of mid-August, they’d conducted 6,589 tests for cyclospora. “To get 6,000 samples within a span of 30 days is quite a large volume, even for us,” Misra said. “And this is just for cyclospora. A lot of our stool testing increased as well, including O&P and on some days microsporidia.”
The Cleveland Clinic also increased their staff, with microbiologists and process teams stepping in to help their parasitologists. “Other sections could help with processing or slide making because it is a very laborious process,” she said. “It was all hands on deck to keep up with those volumes.”
When Pritt saw the Mayo Clinic still wasn’t making a dent in their backlog, they looked to AI. Before the outbreak, the Mayo Clinic had already done a short pilot study on using AI to detect cyclospora in 20 positive and 20 negative samples. Then during the outbreak they ran another study on 250 positives and 250 negatives. “Compared to manual detection, [AI] detected another 15 positives we missed out on,” she said, referring to samples that had a low positive. Once Pritt’s lab implemented this AI approach, they made sure to confirm every positive result manually.
The Cleveland Clinic also started using AI in mid-July when cases were peaking. Their goal was to get results to clinicians in an average of 44 hours, so that patients who tested positive could be treated with trimethoprim-sulfamethoxazole, which is a very effective combination antibiotic. Providing quick results also helped to support antibiotic stewardship and ensure that clinicians were not giving the antibiotic to patients who eventually tested negative. But even with increased staffing help, “we were not going to be able to meet that turnaround time without the help of AI,” said Misra.
The Cleveland Clinic had already validated trichrome staining for cyclospora detection but had to validate modified acid test staining during the outbreak. “We ran over 1,000 specimen slides so that we could pivot to using AI for modified acid-fast stained slides,” she said. This enabled them to keep getting physicians results within 44 hours after specimen receipt by the lab. “We’re really proud of this average turnaround time,” she said.
Misra also noted that it was an AI tool for trichrome staining that led them to “guess something was going on” and realize back in June that a cyclospora outbreak was ramping up.
Educating clinicians about cyclospora testing was an important part of handling the outbreak this summer, said MacIntyre. At the start, “no one knew where it was emanating from or how large it would become, but we had to start educating the physicians or clinicians ordering the testing,” she said.
Quest had to educate clinicians, for example, that cyclospora is not included on a routine O&P test and may not be on gastroenterological PCR panels. They also had to tell clinicians that, even though the standard is to order, not one, but three O&P tests anytime they encounter a parasite, that was not appropriate for cyclospora.
“We have to really look into what is reality in modern outpatient medicine and how to develop a bridge between the two so we can avoid delayed diagnosis,” MacIntyre said. Quest also made sure clinicians weren’t over-testing, or if they were still ordering other kinds of parasite tests, that these were needed. For example, since cyclospora can take weeks to treat, patients can have co-infections during the treatment period that clinicians also need to test for.
And in some cases, Quest had to address logistical problems that could potentially prevent clinicians from ordering the right test. For example, Quest sometimes found that cyclospora testing simply wasn’t an option in a healthcare system’s digital catalogue. “It’s a complex clinical landscape,” MacIntyre said.
Pritt said that the Mayo Clinic did face some supply chain issues, and they had to be creative to keep going. For cyclospora testing, they accept specimens that are fresh frozen, or preserved in Ecofix, or two-vial stool sample collection kits. When some of their partners said they couldn’t get fixatives for stool samples, Pritt’s lab told them to get a “clean conical vial and make your own 10% formalin,” she said. This worked since most laboratories can get a hold of formalin.
“It’s so hard to predict what the supply chain’s going to be,” she said.
Being prepared and having backups helped the Cleveland Clinic get through the worst of this summer’s outbreak, said Misra. They had alternatives that were already validated in case they ran out of anything, whatever that anything might be. “We just had to maneuver, and moved a lot of backup products,” she said.
Overall, she thinks the Cleveland Clinic “did an incredible job of collaborating and pulling help from other places,” she said, and that “AI showed its strength when we hit those exponential volumes.”
Collaboration was important beyond just getting help from other laboratories, too, Misra added. “It’s really important to keep in constant conversation with primary clinicians and stakeholders,” she said. “We were able to care for our patients early, before we even thought of [cyclospora]. I don’t think any of us were expecting it to turn out as big as it was going to be. If there’d been any delays we probably wouldn’t have been able to test or pivot like we did.”
Jen A. Miller is a freelance writer who lives in Audubon, New Jersey. +Bluesky: @byjenamiller.bsky.social
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