Source of 'explosive diarrhea' illness remains mystery as cases surge

A summer surge of an explosive diarrhea-causing illness has left health officials and the public searching for answers as cases of the parasitic infection surpass the 1,000 mark.

Federal and state investigators have yet to determine a common cause for multiple clusters of cyclosporiasis, a stomach-churning condition caused by a parasite commonly found on fresh produce. While it often spikes during the summer, with the Centers for Disease Control and Prevention defining cyclosporiasis "season" as May 1 to Aug. 31, the size and nature of the outbreaks have the CDC and Food and Drug Administration looking to pinpoint its origins.

Past outbreaks have proven difficult to track, as tools used for other common foodborne illnesses like E. coli and listeria aren't useful for the cyclospora parasite. While the last such outbreak sickened upward of 1,000 people, federal health agencies were never able to identify one source.

With new recalls and outbreaks announced almost daily, the enduring mystery surrounding the so-called diarrhea parasite begs the question: Why is it so hard to track?

How outbreaks are usually tracked - and why it doesn't work with cyclosporiasis

Most clusters of foodborne illness and infectious disease today are traced via whole genome sequencing (WGS), a technique in which the unique genetic code of a pathogen is tested and compared to establish a unique "fingerprint." This DNA "fingerprinting" lets scientists determine whether germs making people sick are closely related, helping investigators connect cases and trace outbreaks to a common source.

WGS is highly effective at extracting exact details to confirm the origin of an outbreak and related illnesses, like the cases of E. coli currently associated with blueberries sold at Publix. It can also help identify a single contaminated ingredient within a larger dish, like the onions linked to a 2024 E. coli outbreak that traced back to McDonald's Big Macs, or a common manufacturer, like the specific Jarratt, Virginia Boar's Head plant that produced the meats at the center of a deadly 2024 listeria outbreak.

Unlike bacterial foodborne pathogens such as E. coli and listeria, however, cyclospora is not routinely tracked using WGS. Cyclosporiasis's parasitic nature poses a challenge, as it generally does not give investigators enough clean parasite DNA to work with.

Whole genome sequencing works best when investigators can obtain large amounts of pure DNA from a pathogen. That's difficult with cyclospora, a parasite that can't be routinely grown in a lab and is often present in very small quantities in stool samples. One CDC study, published in the Journal of Clinical Microbiology, found that roughly 20% of submitted cyclospora specimens failed genotyping.

Because the parasite is difficult to culture and commonly seen in low quantities in stool samples, the CDC instead relies on a different sequencing system that targets select genetic markers. While the technique has proven highly accurate, not every sample contains enough parasite DNA to generate a usable genetic profile, making it an often slower process than tracking an outbreak via WGS.

The last major cluster of cases investigated by the FDA relied on epidemiologic and traceback evidence, not sequencing, to identify it. The 2025 outbreak sickened nearly 1,000 people across 37 states before FDA and CDC investigators pegged parsley as the likely source; even so, no specific brand, grower, or supplier was ever publicly identified.

Tracking contaminated foods is also a challenge with cyclosporiasis

The incubation period of cyclosporiasis, or the time between a person being exposed to a pathogen and showing symptoms, is relatively long, averaging one week but ranging from two days up to two weeks and beyond, according to the CDC.

Because of this, food safety attorney Bill Marler explained, it is harder for people to identify what could have made them ill. Part of the tracing process involves sick people answering questions about their recent movements and diet. In a perfect scenario, everyone interviewed by health officials recalls one or two common foods, grocery stores or restaurants in their recent past, giving investigators a lead on where to look next.

With an incubation period that can last two weeks plus, narrowing things down becomes more cumbersome.

"The longer (incubation) is, the harder it is for people to remember what they ate," Marler told USA TODAY. "Another confounding factor is you ask someone what they ate, but there's been so many outbreaks of cyclospora linked to different products, it's hard to bore into what ingredient it was."

In other words, no one food sticks out like a red flag when mentioned in such a list.

Health departments may also be lagging when it comes to keeping on top of domestically acquired cases, Marler said, as cyclospora was previously considered a problem that primarily arose from imported crops. In the last decade, however, it has increasingly become a U.S. issue.

"That is something that public health and the fresh food and vegetable industry have got to get their heads around," he said. "Because you're going to have these spikes in outbreaks in summer months and they're just going to get more frequent, and we need to get a handle on it so we don't have 'explosive diarrhea July' every year."

Why declaring a source may take a while, even if health officials have a hunch

As of Thursday, July 9, federal and state health departments have said publicly that they do not yet have evidence of a common denominator or indication of one multistate outbreak. But even if they have a hunch, said Marler, the public won't know about it for a while.

"When you have a hard bug to figure out, like cyclospora, it takes a lot longer (to trace). It takes a lot more time and a lot more legwork," said Marler. "As an attorney, if I can find two clusters of cases at, say, two restaurants that carry the same raspberries, then I'll say, 'Oh, that's probably it.' But health departments have much higher standards for naming a product or restaurant - it's almost 'beyond a reasonable doubt'."

The CDC is likewise only updating its centralized dashboard for this outbreak once a month, something that isn't entirely unusual, especially for an illness that is not reportable in every U.S. state.

Generally speaking, state health departments track their own numbers and then feed them back to the CDC at specific times. But with something as rapidly evolving as cyclosporiasis, this data can get outdated quickly. Currently, the CDC dashboard, last updated June 16, lists only 145 cases nationwide and none in Michigan. Michigan, on the other hand, reported more than 700 cases to USA TODAY as of July 7.

Pair this with a significantly pared-down staff at both CDC and FDA, thanks to budget cuts and firings, and states that have lost health funding through new legislation or expired COVID-era boosts, and you have the makings of a long investigation, said Marler.

What you can do now based on what we know

In the meantime, Americans can look to past outbreaks and general food safety tips to avoid getting sick, even when we don't know where exactly cases are coming from.

Cyclosporiasis cases have been linked to an assortment of fresh fruits, vegetables and herbs, including bagged salad mixes and kits, fresh cilantro, basil and parsley, raspberries, snow peas and green onions. The most common vehicle is unwashed produce, which can become naturally contaminated with fecal matter during growing and processing through soil, irrigation systems, proximity to livestock and exposure to tainted surfaces.

State health departments have issued guidance for avoiding the spread of cyclosporiasis, including:

• Avoid consuming food or water that may be contaminated with feces. Avoid drinking or cooking with untreated water.
• Wash your hands with soap and water after using the bathroom and before, during and after food prep.
• Wash all food prep surfaces, including utensils, cutting boards and countertops, before and after use.
• Wash and peel vegetables before eating them; scrub produce with skins like melons and cucumbers well; and cut away damaged or bruised areas on fruits and vegetables before preparing and eating them.
• Refrigerate prepared fruits and vegetables as soon as possible (within two hours).
• Cook your food when you can; heating food to 158 degrees Fahrenheit or higher kills Cyclospora.

This article originally appeared on USA TODAY: Source of 'explosive diarrhea' illness remains mystery as cases surge

Reporting by Mary Walrath-Holdridge, USA TODAY / USA TODAY

USA TODAY Network via Reuters Connect

Copyright Reuters or USA Today Network via Reuters Connect

This story was originally published July 9, 2026 at 9:07 PM.