What Happens to Your Gut During Cyclospora Treatment?

Treating a cyclospora infection often means a course of antibiotics, and for many patients, that’s where the thinking stops. But according to Bruce Hirsch, M.D., an infectious disease specialist at Northwell Health who serves on the Peggy Lillis Foundation’s Medical Advisory Council, what happens to the gut during that treatment matters just as much as clearing the original infection.

Antibiotics like Bactrim, the standard treatment for cyclosporiasis, don’t just target the parasite causing symptoms. They also reduce the diversity of normal gut bacteria, opening the door to opportunistic infections like Clostridioides difficile (C. diff), a serious and sometimes dangerous complication that can develop after the original illness has already started to improve. Hirsch breaks down who’s most at risk, what warning signs to watch for and how to support gut health during recovery.

Most people being treated for cyclospora right now are taking antibiotics without giving much thought to what those antibiotics are doing to their gut. What happens to the microbiome during a course of antibiotic treatment, and why does that matter for recovery?

Bruce Hirsch, M.D.: Cyclospora causes a wide range of clinical severity. Many people with minor symptoms will not require antibiotics. Those with weakened immune systems and the very young and very old are vulnerable to the severe, prolonged diarrhea associated with cyclosporiasis. The antibiotic of choice is sulfamethoxazole-trimethoprim (aka Bactrim). For those allergic to Bactrim, the anti-parasitic agent nitazoxanide can be used.

As with other antibiotics, Bactrim reduces the diversity of normal bacteria in the gastrointestinal (GI) tract. With antibiotics, the gut becomes more vulnerable to opportunistic infections. C. diff can grow out in the intestine and cause a severe toxic colitis.

Most persons will recover from cyclospora. Resuming a healthful diet as soon as feasible will help improve gut health.

Who is most at risk of developing C. diff after taking antibiotics for something like cyclospora, and what are the warning signs people should know?

BH: People with extensive exposures to antibiotics and other gastrointestinal problems, particularly inflammatory bowel disease, are at highest risk. C. diff infection announces itself with a change of character of worsening GI symptoms. The diarrhea of C. diff tends to have a particular bad smell. Diarrhea can get worse after initial improvement. The abdominal cramps and overall malaise can be severe with C. diff.

There is a difference between diarrhea from the cyclospora infection itself and diarrhea that signals something has gone wrong after treatment. How does a patient know when lingering or returning symptoms are worth a call to their doctor?

BH: The course of the illness changes with the complicating C. diff infection. After modest improvement, any sudden worsening should prompt a call for medical evaluation.

What does antibiotic stewardship mean in practice for someone who has just been prescribed antibiotics for a gastrointestinal infection, and what questions should they be asking their provider?

BH: Doctors should use the most focused antibiotics for the shortest time necessary for treatment in call cases.

Once someone has finished their antibiotic course and is feeling better, what can they actually do to help restore their gut microbiome and reduce the risk of complications down the road?

BH: Resuming a healthy diet as soon as feasible will help. Many people have temporary lactase deficiency after a GI infection and may have difficulty with dairy. Some foods provide a probiotic benefit that can restore a healthy gut microbiome, such as kefir, Greek yogurt, sauerkraut, kimchi, pickled vegetables, tempeh and kombucha tea. Modest and gradually increasing amounts of beans and legumes give a prebiotic boost.