Illustration by Laurie Hawton
tick-tok
Back in the early 1980s, a basic microscope was the only real technology Wilhelm “Willy” Burgdorfer had at his disposal when he discovered the culprit of Lyme disease. Through it, he spotted disease-causing bacteria shaped like corkscrews (spirochetes) in black-legged ticks.
Since then, those black-legged ticks (deer ticks, to a Minnesotan) and their disease have proliferated. The Centers for Disease Control and Prevention estimates the number of Lyme disease cases in the United States to be more than 10 times higher than the number of actual reported cases, which is around 476,000 each year. And black-legged ticks, previously relegated to places like Connecticut and northern Minnesota, now make their homes in a much wider swath of the country, likely due to climate change.
Much tick research is still slow and painstaking, using technology akin to Burgdorfer’s microscope—like dragging sheets through the woods to count ticks one at a time or even examining the number of ticks on mice and chipmunks. The specimens are often frozen at −80 degrees Celsius so that researchers can take their time counting ticks or testing them for disease, so data often isn’t available until after the worst of the season is over.
But during the pandemic, when much research was put on hold or pivoted, a couple of University of Minnesota professors stumbled across a preprint from a lab in the UK that inspired them to brainstorm how they could use a nanopore sequencer, a new piece of technology that is already transforming many aspects of health care. Nanopore sequencing of DNA and RNA can provide real-time data to help doctors identify cancerous tumors during surgery or provide surveillance of COVID-19 and mpox (monkeypox).
“Because of the pandemic, we were at home thinking about how to use it,” says Peter Larsen, a College of Veterinary Medicine assistant professor. “We thought, Wait a second; we could do this and this and this—and one of the things was that we could leverage it for ticks. We started doing some initial experiments and confirmed that we could do it and it worked well, which led us to put together an NIH proposal.”
With a $3.4 million grant now in hand and tick season ramping up, Larsen and School of Public Health assistant professor Jon Oliver are putting the candy-bar-sized sequencer to use at various tick surveillance spots in the metro area and across the state.
To get data on-site in real time, the researchers need to create a mobile lab. Evan Kipp, a PhD student in the Department of Veterinary and Biomedical Sciences who works with Oliver and Larsen, showed me how it’s done using a fly as an example in the lab back in March. Even witnessing the process firsthand, it’s still hard to imagine how the delicate work can be conducted in the field. For instance, Kipp says, they have to spray down a pop-up tent with disinfectant to create as sterile an environment as possible. And all of the gear they need packs down into a couple of suitcases. A battery pack keeps the computer running long enough to sequence the samples and generate results in real time.
But it’s worth it. “Being able to generate data on-site is huge,” Kipp says, noting that other technology involves shipping the samples off and waiting months for the data.
Within minutes, the machine starts spitting out lines of data from the fly sample via a computer that’s the equivalent of “a really powerful gaming computer,” according to Larsen. The new technology isn’t just faster—it found three billion base pairs or “rungs” on the fly’s DNA ladder in 24 hours—the process also allows researchers to identify not only every pathogen a sample is carrying but also the exact species they’re testing.
Nanopore sequencing flips the script a bit, Larsen explains. Using PCR technology, you identify what you’re looking for and run tests for those specific one, two, or three things. So, there isn’t a comprehensive understanding of all the pathogens circulating within ticks, he says. But with the new technology, researchers get all the data, unleashing the potential to find things they weren’t even looking for.
“We could take a series of ticks and ask, ‘What are all the viruses present in this sample of ticks?’” says Larsen. “We could sequence all the viruses, [figure out the strains], and say, ‘OK, here’s Powassan [a virus that causes a rare, but serious, disease].’ It gives you a much more global view of the tick pathogen landscape.”
So, for example, if the team goes out looking for Lyme disease, the researchers might end up finding a different pathogen that no one knew was circulating. That could direct them to adapt their fieldwork to focus on a more specific geographical area and also use less-powerful but more-available technology, like PCR, more effectively by knowing what pathogens to look for.
“It’s not only a real-time view, but you can also adapt your fieldwork in real time,” Larsen says. “You start to see a signal of concerning bacteria or a virus in a certain area, and you can go back and concentrate in that area to get samples.”
Photo by Chris Cooper. Used with permission from the UMN School of Public Health.
nanopore-sequencer
Not a Motorola flip phone that fell out a car window: This is a nanopore sequencer. The pocket-size tech is revolutionizing tick research.
What It Means for Tick-borne Disease in Minnesota
Nanopore sequencing is already changing the game in other health applications. For example, it can detect new COVID-19 variants in wastewater. One study showed it could reduce the use of broad-spectrum antibiotics by tailoring specific antibiotics to surgery patients. It could be used to test specific locations where mosquitoes themselves could be treated to reduce malaria, says Oliver. For instance, researchers could look for antimalarial-resistance genes in the field, which could inform control strategies: If risky malaria is in the area, then it would be high priority to treat mosquitoes there.
Imagine this future: Before you head Up North for the weekend, you check the tick forecast and get an accurate read on whether you’re likely to encounter any arachnids carrying disease agents (not all do!). Or you find an attached tick and bring it to the nearest walk-in clinic to get it scanned for disease agents on the spot. Or a doctor treating a patient for an unknown tick-borne disease is able to determine exactly which pathogen is causing the havoc or where multiple pathogens are present.
That’s all within the realm of possibility using nanopore sequencing.
Better prevention and diagnosis would be a huge game changer, researchers say, given that one of the biggest dangers of tick-borne diseases is not identifying the disease or not doing so fast enough to start effective treatment. Often, Larsen says, there are situations where folks go undiagnosed, and sometimes people have multiple, simultaneous infections.
“They think it’s a tick-borne disease, but they don’t know what it is,” he says. “This opens Pandora’s box. We showed that using this approach, you can find co-infections. Let’s say there are four pathogens present. They show up—bing, bing, bing, bing.”
Treatments vary from disease to disease, so accurate diagnosis is essential to recovering from the handful of tick-borne diseases common in Minnesota. Lyme disease is harder to treat after a delay, and untreated cases can turn into serious, and sometimes fatal, conditions.
The technology should also help researchers understand the changing nature of ticks. Decades ago, it was rare to see a black-legged tick outside of very specific locations, such as the extreme eastern border of the state in the St. Croix River area. Since about 1990, however, they have spread westward to every forested county in Minnesota. That’s partially due to changing climates, experts think, but there’s also evidence that bacteria inside ticks could affect their ability to survive in different habitats, Oliver says.
Now, says Oliver, they can look into the microbiome of a tick and potentially figure out what helps it survive. “There’s some evidence that infection with the bacteria that causes Lyme disease may help ticks resist drier environments,” Oliver says. “And the bacteria that cause anaplasmosis may help ticks survive colder temperatures. And other thousands of species of bacteria that we have no idea about.”
Not to mention viruses, Larsen adds, which could be living in ticks—some that may even be able to spill over into humans.
What’s Next
While Minnesota is a hotbed for both ticks and tick research, it’s not the epicenter to look for emerging pathogens in ticks. That would be Kansas, one of two places in the world where several types of tick species and rodent species converge. (The other is in Central Asia.) So, next summer, Oliver and Larsen plan to take their technology on the road.
For now, Minnesotans still need to follow the standard precautions: Know when to look for ticks (while the season is getting longer, June and July are still prime months) and where to be especially careful (forested areas, leaf litter). Wearing bug spray with permethrin and long sleeves and pants tucked into socks while hiking can be helpful. Wearing white helps you spot ticks during a tick check after being outdoors.
Fortunately, all of this coincides neatly with a Lyme disease vaccine by Pfizer, which is progressing through clinical trials. Ticks will likely always roam Minnesota’s woods, but Lyme disease and tick checks could, someday, become a thing of the past.
