UNC Charlotte bioinformatics and genomics expert shares insights on the cyclosporiasis outbreak

As federal and state health officials continue investigating one of the nation’s largest recorded cyclosporiasis outbreaks, questions remain about how the parasite spreads, why identifying contaminated food sources is so challenging and what advances in genomics and bioinformatics could mean for future outbreak detection.

Carol Grotnes Belk Distinguished Professor of Bioinformatics and Genomics and codirector for CIPHER Dan Janies discusses these topics as more confirmed illnesses are reported across the United States and investigators continue to analyze the outbreak as new data emerges.

What is cyclosporiasis, and why is it causing outbreaks in the United States?

Cyclospora is a human parasite typically transmitted when raw produce is contaminated by water containing feces or unwashed hands of agricultural handlers.The parasite is not new and emerges every summer in the U.S. However, the current situation is exceptionally severe. Public health agencies are tracking an inordinately large spike in cases across 34 states, driven by a major multistate outbreak.

• Cyclosporiasis is an intestinal illness caused by the parasite Cyclospora cayetanensis.
• Cyclospora is difficult to wash off produce as it transmits as microscopic sticky hard-coated capsules (termed oocysts) containing the parasites’ offspring (termed sporozoites).
• Cases occur due to ingestion of contaminated produce domestically and during travel abroad.
• The coating of the oocysts adheres to crevasses in produce.
• Cryptosporidium species are related, but distinct parasites that are mostly transmitted in swimming pools, water parks and splash pads. The foodborne outbreak in the summer of 2026 is not caused by Cryptosporidium species.

What are the symptoms of cyclosporiasis?

Symptoms begin about two days to two weeks after exposure and may last for several weeks if untreated and can include:

• watery diarrhea (often prolonged)
• loss of appetite
• weight loss
• abdominal cramping
• bloating
• nausea
• fatigue
• low-grade fever (sometimes)

How is Cyclospora transmitted and does it spread from person-to-person?

Cyclospora is not typically spread directly from person to person because the parasites’ offspring must mature in the environment before becoming infectious. Offspring in newly excreted oocysts are immature and noninfectious.

Under favorable environmental conditions such as warm, moist soil or water, maturation of the offspring to an infectious state in the oocyst (termed sporulation) generally takes one to two days outside the human host. This environmental maturation step reduces the likelihood of direct transmission between people.

Has a source causing the outbreak been identified?

The Food and Drug Administration is conducting an investigation of the sources.
The outbreak is widespread in 34 states and there are likely several food sources of Cyclospora.

Does washing produce help prevent the illness and are there particular foods that the public should stop eating?

Fresh produce consumed raw, such as leafy greens, herbs, berries, green onions, snap peas, and essentially any fruits and vegetables grown close to or in the ground, have been associated with historical outbreaks. It is not feasible to wash the sticky oocysts from the crevasses of produce.

• It is advisable to cook produce and heat it to at least 158 °F (70°C).
• If you are eating raw produce, eat peelable fruits and wash your hands after handling the peel.

Use safe drinking water and follow proper food handling and hygiene practices.
Also, preventing contamination of water used during the growing and processing of produce is essential for reducing outbreaks.

Do farms have protocols in place to test for microscopic parasites on leafy vegetables?

Farms do not typically test for Cyclospora. However, under U.S. federal law, the FDA Food Safety Modernization Act regulations apply to both the United States and Mexico for U.S.-bound produce. The U.S. FDA does require farms to monitor agricultural water for the bacterium Escherichia coli which can indicate fecal contamination. Depending on the water source, this monitoring involves annual risk assessments or seasonal culture testing. In outbreaks, advanced genomics are used for investigations to trace the pathogen to the source.

How did Cyclospora evade surveillance procedures in this latest outbreak?

This summer’s Cyclospora outbreak highlights several blind spots in our food safety system. First, the parasite has a tough outer capsule that makes it immune to the standard chlorine washes used to clean produce. Routine farm testing rarely catches the parasite. The lag of days or weeks from ingestion of Cyclospora to cyclosporiasis diseases makes investigations to trace the parasite to its source difficult. By the time patients develop symptoms and doctors order the highly specialized tests needed to properly diagnose the parasite, the contaminated produce has likely been eaten or thrown away.

What makes Cyclospora different from other foodborne pathogens, and why is it so challenging to prevent?

Cyclosporiasis is a challenging foodborne disease because the biology of the parasite takes time for the outbreak to unfold.

Contaminated produce can be widely distributed before the source of contamination is recognized and interventions are put in place. Additionally, the parasites’ sticky oocysts are a game changer and force us to rethink cleaning produce.

Can wastewater testing be conducted to determine if a community is affected by Cyclospora?

During this extensive 2026 summer outbreak, public health agencies have relied on clinical fecal testing and supply chain tracking rather than widespread wastewater surveillance for several reasons.

For viruses like SARS-CoV-2 or polio, wastewater testing is useful because reverse transcription quantitative polymerase chain reaction (rt-qPCR) can catch the virus before large numbers of people show symptoms. A person has to already be heavily symptomatic with cyclosporiasis to shed the Cyclospora parasite into the wastewater.

Testing wastewater for parasites is significantly harder than testing for viruses. Parasite oocysts are larger and sturdier, and get trapped in sewage sludge easily, requiring tedious extraction methods. Agencies generally prioritize their limited rt-qPCR testing resources on testing actual patients and trace-back sampling on suspected farms.

Has Cyclospora been detected in major cities in North Carolina, or surrounding areas, and how many cases have been reported?

Yes, Mecklenburg has 19 confirmed cases and Cabarrus County has one. In contrast, there are over 370 confirmed cases in the Triangle area, mostly in Wake County. The rate of case growth in the Triangle is concerning.

How can the public be certain that food at a restaurant is safe to eat?

My advice is to eat cooked or peeled produce at home for a while.

What is the key to prevention?

Water with feces contaminates fresh produce during irrigation, washing or processing, making contaminated irrigation water an important catalyst for outbreaks of Cyclospora.

Looking ahead, what advances in research or technology could improve how we detect and respond to outbreaks like these?

Technologies to test for clean water that are widely deployable in low-resource settings will help to stop Cyclospora at its origins in the field. Widely deployable examples include:

• dead-end ultrafiltration with polymer fiber filters that can be hooked up to a standard field pump
• smartphone microscopy to see the oocysts
• field-ready molecular tests to detect the oocysts

Written by: Dan Janies