Cyclosporiasis is an intestinal infection caused by the microscopic parasite Cyclospora cayetanensis, usually caught from contaminated fresh produce rather than from other people. Fishtown Medicine treats it with a 7 to 10 day course of trimethoprim-sulfamethoxazole after specifically requesting the right stool test, since routine panels often miss the parasite.
TL;DR: Cyclospora is a microscopic parasite that spreads through contaminated fresh produce rather than from person to person. It causes watery, often explosive diarrhea that can drag on for weeks and come and go in waves, which is what sets it apart from a 2-day stomach bug. The catch is that a routine stool test usually misses it, so the parasite has to be asked for by name. Once it is found, a 7 to 10 day course of the antibiotic trimethoprim-sulfamethoxazole clears it. The summer of 2026 brought one of the largest U.S. outbreaks on record, most of it traced to fresh produce.
You have been sick for 2 weeks now. The diarrhea eased for a day or two and you thought you were through it, and then it came right back. You are tired in a way that sleep does not touch, your appetite is gone, your jeans are looser, and the bug that was supposed to last a couple of days has taken over most of a month. Maybe you already went to an urgent care, gave a stool sample, and were told everything came back normal.
What I want you to know is that a normal-looking workup does not mean nothing is wrong. A weeks-long, relapsing case of watery diarrhea after a summer salad or a plate of fresh herbs has a specific short list behind it, and near the top of that list right now is a parasite called Cyclospora. It is one of the few causes of prolonged diarrhea that a standard test will walk right past unless someone thinks to look for it directly.
What is cyclospora, and how do you catch it?
Cyclospora is short for Cyclospora cayetanensis, a single-celled parasite too small to see, and the illness it causes is called cyclosporiasis. You catch it by swallowing the parasite in food or water that was contaminated with trace amounts of infected stool, almost always fresh produce that is eaten raw. Past U.S. outbreaks have been tied to basil, cilantro, raspberries, blackberries, snow peas, bagged salad mixes, and lettuce.
Here is the part that surprises most people. Cyclospora does not spread from person to person the way a stomach virus does. When the parasite first leaves the body, it is not yet infectious. It has to sit in the environment for days to weeks, under the right warmth and moisture, before it matures into a form that can make the next person sick. That biology is why cyclosporiasis moves through the food supply rather than through a household, and why one contaminated field can sicken people in a dozen states at once while your family at home stays fine.
It also explains the calendar. In the United States, cases cluster in the spring and summer, which is when the growing and harvest conditions line up. If you came down with stubborn diarrhea in July after a farmers market haul or a restaurant salad, the season itself is a clue.
What are the symptoms of cyclosporiasis?
The symptoms of cyclosporiasis usually start about a week after you eat the contaminated food, though the window runs anywhere from 2 to 14 days. The hallmark is frequent, watery diarrhea that can come on suddenly and feel explosive. Around it you tend to see a cluster of other complaints:
- Loss of appetite, and often several pounds of unintended weight loss
- Bloating, cramping, and a lot of gas
- Nausea, though outright vomiting is less common
- A low-grade fever or a flu-like, wiped-out feeling
- Fatigue that lingers even on the better days
Two features separate cyclospora from the usual summer stomach bug. The first is the timeline. A viral gastroenteritis or a bout of norovirus tends to hit hard and burn out within 1 to 3 days. Cyclospora, left untreated, can last from a few days to a month or longer. The second is the pattern: it often relapses, easing off for a day or two and then returning, sometimes more than once. That stop-and-start rhythm over weeks is the single most useful thing you can tell a doctor, because very few things behave that way.
Why did my stool test come back normal?
Because the standard test was almost certainly not looking for this parasite. Cyclospora is hard to find, for two reasons that stack on top of each other.
First, the routine stool ova-and-parasite exam does not reliably catch it. Cyclospora needs special stains or ultraviolet fluorescence microscopy to be seen, and those are not part of the ordinary panel most labs run. On top of that, the parasite is shed in low numbers and only on and off, so even the right test can come up empty on a single sample and need to be repeated.
Second, the newer multiplex stool PCR panels, the ones that test for a whole menu of gut pathogens at once, do not all include a Cyclospora target. Plenty of them do not. So a patient can get a modern, thorough-sounding molecular panel, have it come back negative, and still have cyclosporiasis the whole time.
This is why the Centers for Disease Control and Prevention (CDC) tells clinicians to specifically request testing for Cyclospora when the story fits, rather than assuming a general panel covered it. The test has to be named. If you have had watery diarrhea for more than a few days this summer, that one sentence to your doctor, "could this be Cyclospora, and can we test for it directly," can be the difference between another normal result and an answer.
In my practice, prolonged diarrhea is never just "a bug that's taking a while." When something has run past a week and keeps circling back, I stop treating it as a waiting game and start asking what the routine tests were never built to see. Cyclospora is a textbook example of a diagnosis you only make if you go looking for it on purpose.
How is cyclospora treated?
Cyclosporiasis is treated with a specific antibiotic: trimethoprim-sulfamethoxazole, usually written as TMP-SMX. For most healthy adults that means a 7 to 10 day course, and people generally start feeling better within the first few days of starting it. Unlike a viral stomach bug, cyclospora does not dependably clear on its own, and even when symptoms fade they can relapse, so finishing the full course matters.
A few practical points that come up often:
- Fluids and electrolytes are half the battle. Weeks of watery diarrhea pull out water, sodium, and potassium faster than most people replace them. Rehydrating steadily with electrolytes, more than plain water, is what keeps this from becoming the reason you land in an emergency room. Our guide on hydration and electrolytes covers how to do it well.
- A sulfa allergy changes the plan. TMP-SMX contains a sulfonamide, so it is off the table if you have a true sulfa allergy. The honest reality in 2026 is that no alternative works as well; options like nitazoxanide or ciprofloxacin are used, but their track record against this parasite is weaker. That trade-off is worth a careful conversation rather than an automatic substitution.
- A weakened immune system means closer follow-up. People who are immunocompromised, from HIV, a transplant, or immune-suppressing medications, can get sicker, relapse more, and need a longer course with tighter monitoring.
- Antibiotics disrupt the gut too. A course of TMP-SMX plus a parasite that has been irritating your gut lining for weeks can leave digestion off for a while afterward. Rebuilding is its own step, which we walk through in antibiotics and gut health.
Get Real Answers
Tired of being told your labs are 'normal'? Dr. Ash digs deeper.
How do you prevent cyclospora, and does washing produce work?
Prevention is honest but imperfect, and it helps to know the limits going in. Washing fresh produce under running water is still worth doing and does lower your risk, but it does not reliably remove Cyclospora. The parasite is sticky and clings to the surface of leaves and berries, and no amount of rinsing scrubs all of it away. Just as important, the sanitizing tricks people trust for other germs do not apply here: chlorine and produce washes do not kill this parasite. Heat does. Cooking contaminated produce destroys Cyclospora, which is why a sauteed version of the same vegetable is safer than the raw one during an active outbreak.
What that means in practice:
- Follow the recalls. When public health officials name a contaminated product, take it seriously and check what is in your fridge against the recall. During an outbreak, the FDA and CDC recall notices are the most current source of what to avoid.
- Cook it when you can. For higher-risk produce during outbreak season, particularly fresh herbs and leafy greens, cooking is the one step that truly clears the parasite.
- Be extra careful if you are immunocompromised. If your immune system is suppressed, this is the season to lean toward cooked produce and to be choosier about raw salads and garnishes from unknown kitchens.
- Safe water still matters. Contaminated water can carry it too, so the usual travel-water precautions apply if you are heading somewhere with a higher burden. Our travel medicine page covers pre-trip planning.
For Philadelphians, none of this means giving up the best part of summer. The herbs from the Italian Market, the berries at Headhouse and Clark Park farmers markets, the salads that make July worth it, all of it stays on the table. It means knowing which items are under recall in a given week, cooking the higher-risk ones when an outbreak is active, and taking a weeks-long case of diarrhea seriously instead of waiting it out.
How big is the 2026 cyclospora outbreak?
The summer of 2026 has brought an unusually large wave of cyclosporiasis. As of mid-July, the CDC had logged several thousand laboratory-confirmed domestic cases with thousands more still under investigation, far above the roughly 249 cases reported by the same point the prior year. Among people with known outcomes, close to 9% have been hospitalized, and no deaths have been reported. Much of the activity has been linked to fresh produce, and in mid-July 2026 a supplier recalled iceberg lettuce sourced from central Mexico after it was tied to a multistate cluster.
Numbers like these move week to week, so the value of an outbreak is not the exact count. It is the reminder that this is circulating right now, that it is landing people in the hospital for dehydration, and that the people getting diagnosed are the ones whose doctors thought to look. If your illness fits the pattern, this is the summer to ask directly.
How Fishtown Medicine approaches a prolonged gut infection
At Fishtown Medicine, a case of diarrhea that has run past a week gets treated as a question to answer instead of a clock to run out. The value of direct primary care here is speed and specificity: you can tell me the timeline and the meals the same day, I can order the stool test that names Cyclospora rather than the generic panel that skips it, and if it is positive I can start trimethoprim-sulfamethoxazole without another round of appointments. If dehydration is the pressing risk, a home visit for a membership patient can handle fluids and reassessment at your doorstep instead of a night in an emergency room.
Just as much of the work is connecting the dots. A weeks-long, relapsing gut illness gets waved off as stress, a lingering virus, or a new case of irritable bowel far too often. Part of my job is to hold the whole timeline in view, match it against what is circulating in Philadelphia this season, and separate a treatable parasite from a chronic label you did not earn. If your gut has been off for a while and no one has given you a straight answer, our guide on gut health is a good companion read, and the fastest path is simply to tell me what is going on.
Contact a physician promptly if you have:
- Watery diarrhea lasting more than a few days, or diarrhea that keeps returning in waves
- Signs of dehydration: dizziness on standing, a dry mouth, dark urine, or urinating much less than usual
- Blood in the stool, a high fever, or severe abdominal pain
- Any prolonged gut illness while pregnant or immunocompromised
- Diarrhea after travel to a tropical or subtropical region
If you are in the Philadelphia area and looking for a physician who will take a weeks-long stomach illness seriously and test for the right thing, tell Dr. Ash what is going on at Fishtown Medicine.
Key Takeaways
- Cyclospora is a parasite caught from contaminated fresh produce and does not pass person to person, and it clusters in spring and summer in the United States.
- Its signature is watery, sometimes explosive diarrhea that lasts weeks and relapses, which separates it from a 1 to 3 day viral stomach bug.
- Routine stool tests and many GI PCR panels miss it, so Cyclospora has to be requested by name.
- The treatment is a 7 to 10 day course of trimethoprim-sulfamethoxazole, plus steady rehydration; a sulfa allergy needs a different, less effective plan.
- Washing produce lowers but does not remove the risk, chlorine does not kill it, and cooking does; following recalls matters most during an outbreak.
- The 2026 U.S. outbreak is one of the largest on record, so a matching illness this summer is worth testing for directly.
Related at Fishtown Medicine
- Philadelphia Seasonal Illness Tracker: what is circulating in Philly right now
- Norovirus strategy: the stomach bug that cyclospora is often mistaken for
- Travel medicine in Philadelphia: pre-trip planning and traveler's diarrhea
- Gut health: rebuilding after a prolonged gut infection
- Hydration and electrolytes: staying ahead of dehydration
Scientific References
- Centers for Disease Control and Prevention. Domestically Acquired Cyclosporiasis Cases in Multiple U.S. States, 2026. CDC Health Alert Network (HAN) Health Advisory. https://www.cdc.gov/han/php/notices/han00531.html
- Centers for Disease Control and Prevention. Clinical Overview of Cyclosporiasis. https://www.cdc.gov/cyclosporiasis/hcp/clinical-overview/index.html
- Centers for Disease Control and Prevention. About Cyclosporiasis. https://www.cdc.gov/cyclosporiasis/about/index.html
- Ortega YR, Sanchez R. Update on Cyclospora cayetanensis, a food-borne and waterborne parasite. Clinical Microbiology Reviews. 2010;23(1):218-234.
- Almeria S, Cinar HN, Dubey JP. Cyclospora cayetanensis and Cyclosporiasis: An Update. Microorganisms. 2019;7(9):317.
Frequently Asked Questions
Common Questions
Deep-Dive Questions
Ready when you are
Dr. Ash reads every intake himself, and answers questions personally - usually within a few hours.
