What Cyclospora does inside the gut and how it gets there

What Cyclospora does inside the gut and how it gets there

NPR |
By
Pien Huang
Published August 2, 2026 at 5:00 AM EDT

This summer, tiny Cyclospora parasites have wreaked havoc on the digestive systems of thousands of people in the U.S

It’s the biggest outbreak of this parasite the U.S. has ever seen. In a July 28 update, the Centers for Disease Control and Prevention counted 45 states reporting cases of cyclosporiasis — the disease caused by the parasite

Michigan is ground zero for cyclosporiasis, where more than 10,000 people have eaten something, likely lettuce, contaminated with microscopic pods containing Cyclospora parasites

These parasites rely on the digestive tracts of humans — and only humans — to reproduce. To get there, they’ve likely been hitching rides on crops from places where the parasite is relatively common, to the unwitting mouths of hungry people across the U.S. Their complex biology contributes to why they’re so hard to kick, leading to infections that can last for weeks or months

A lifecycle that requires the human gut

On the surface of an herb, vegetable or berry, Cyclospora parasites lie dormant in pods — called oocysts — that are virtually invisible to the human eye. “It would take about a hundred of them, linked end to end, to fit across the head of a pin,” says Vernon Carruthers, professor of microbiology and immunology at the University of Michigan Medical School

Once swallowed by a human, the oocysts make their way down the esophagus, to the stomach and then the intestines. “The [oocysts] respond to signals in the gut, like body temperature, probably bile, digestive enzymes. This causes the parasites to be released,” Carruthers says

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The parasites go straight for the lining of the small intestine, where they burrow in, taking over the cells to make copies of themselves. “These grow from just a few of the parasites we would take in, to millions of parasites replicating inside our intestinal cells,” Carruthers says

After a while, some of those parasites begin to differentiate into egg- and sperm-like forms, which combine to form new microscopic oocysts — a process that can happen millions of times at the height of infection. “This is truly remarkable, given that the sperm must find the eggs inside infected cells that are blanketed by a mucus layer,” Carruthers says

This whole process messes with the intestinal lining. “[The parasite is] entering those host cells, replicating in those cells, producing its life cycle within those cells. And that process eventually destroys the cells,” says Joel Barratt, a molecular parasitologist and associate professor at Emory University School of Medicine who used to lead a lab team at the CDC that responded to parasitic outbreaks

Hardy pods in human excrement

As the parasites injure the cells lining the small intestine, they reduce nutrient absorption and lead to widespread damage, causing the hallmark symptoms of cyclosporiasis, such as nausea and diarrhea, Barratt says

A single milliliter of that diarrhea can contain around a thousand of these parasitic pods, Carruthers says

As far as scientists can tell, people only get sickened by Cyclospora when they inadvertently ingest these pods in food or water contaminated with traces of human waste

But not when the waste is fresh. “When [the oocysts are] immediately shed, they’re not infectious,” Barratt says. “They have to sit out there in the environment and mature.”

The science isn’t clear on how long it takes for them to become infectious. It could be days or weeks; it may be affected by the seasons

The parasite can enter the food system from tainted dirt or irrigation water, or germy hands handling the produce. It might be further spread by the industrial washing process, where many pieces of produce are rinsed in the same water

The Cyclospora pods are hardy: They can remainold temperatures

Infections can linger

Inside the body, Cyclospora infections can last for weeks or months. “It’s much more complex than the typical viral stomach bug that you can pass in a day or two,” says Dr. Bobbi Pritt, a microbiologist at Mayo Clinic and director of its Clinical Parasitology Laboratory

A combination of certain antibiotics — sold under the brand names Bactrim, Septra or Cotrim — can help by stopping the parasites from replicating and giving the immune system a better chance to clear them, Carruthers says

Cyclosporiasis isn’t typically fatal, and people’s bodies seem to get better at fighting it off in places where the parasite is more common, including tropical and subtropical regions

Where Cyclospora is endemic, studies have found that “it tends to be younger people who get the symptomatic infections; older people don’t tend to get symptomatic infections,” Carruthers says. “That would imply that you can build up some immunity to it, but that it may take several exposures to do that.”

It’s a “mystery” why this is a big outbreak year

In the U.S., Cyclospora has been causing more suffering in recent years

Cyclosporiasis outbreaks detected in the U.S have been “up and down a little bit, kind of choppy,” after large outbreaks in 2018 and 2019, Barratt says. “But this year it’s just going straight through the roof.”

One major reason for cyclosporiasis outbreaks in the U.S. is the imported food supply. “We’re getting produce and other food materials from all around the world. Many of these are endemic countries where people don’t have access to good sanitary facilities,” Pritt says. Human waste containing Cyclospora “gets into the groundwater or it contaminates the plants that are being grown directly.”

Still, it’s a mystery why cyclosporiasis cases in the U.S. are so widespread this year. “It might just have been bad luck,” Pritt says, “with a large dose that was put into products that just happened to be high consumables,” destined for big chain restaurants like Taco Bell, whose shredded lettuce from Taylor Farms in central Mexico has been linked as onely recalled that product on July 17

Public health authorities are still working to figure out additional another culprit, according to the state health department

In the meantime, health officials recommend washing and cooking fresh vegetables to cut your risk of a gut-busting infection