My Approach to Diagnosing and Treating Parasite Infections

Many people don’t realize how common parasites are or how often they’re behind chronic symptoms like bloating, fatigue, and digestive issues. In my practice, I see a large number of patients who’ve been treated for conditions like small intestinal bacterial overgrowth (SIBO), irritable bowel syndrome (IBS), and Candida overgrowth, yet they still don’t feel better.

But when we take a deeper look, testing will often reveal the underlying cause: a parasitic infection.

Because this is such a frequent pattern in my patients, I want to share how I approach these cases. So let's start by looking at the tests I use most often to uncover these infections.

Testing for Parasite Infections and Gut Imbalances

Before we dive into treatment, I want to review one of the main tests I use in patients with gut issues: the Gastrointestinal Microbial Assay Plus (GI-MAP) stool test. This test detects and measures the different bacteria, fungi, viruses, and parasites with a single stool sample.¹

By using this test, we can learn what organisms are present in the gut and what their levels are. The GI-MAP stool test also checks for issues related to digestion, inflammation, immune function, and metabolism within the gut.

I order this test on many of my patients–even those without overt gastrointestinal (GI) symptoms. This is because issues in the gut can contribute to or even cause illness in other areas of the body. So looking at the gut is always a great place to start.

And when it comes to diagnosing parasitic infections, the GI-MAP stool test looks for several different parasites and parasitic worms (helminths) including: 

  • Blastocystis hominis

  • Chilomastix mesnili

  • Cyclospora spp

  • Dientamoeba fragilis

  • Endolimax nana

  • Entamoeba coli

  • Pentatrichomonas hominis

  • Hookworms

  • Roundworms

  • Whipworms

  • Tapeworms

You can read more about the different types of disease-causing parasites in my last blog.

Sometimes I also refer patients to get a comprehensive exam from a parasitologist. Dr. d‘Angelo offers a lab service where patients can order their own microscopic examination of their stool. This test often yields better results than using PCR testing like the GI-MAP. I highly recommend this lab especially if patients tell me they have a history of travel and gastrointestinal illness while they were traveling.

You can learn more about this testing at the link below:

Overall, we don’t have one perfect test for everything. Testing of the GI track is controversial because testing is only able to capture what exits the GI tract in the form of your stool. Because of this, we believe we’re often missing certain organisms that aren’t in the stool on that particular day and in that particular sample. 

For example, worms are very difficult to find on testing because they usually don’t like to exit the host they’re living in. So this makes it difficult to get them to show up in many of the stool tests we have available. 

My hope is that, at some point, there will be a better way to microscopically see what’s living in our GI tract inside the tissue itself. But for right now, we’re testing and also going off of clinical signs and symptoms to help guide us. 

My Top Two Treatments for Parasitic Infections

If we find a parasitic infection through a stool analysis, treatment depends on which organisms are present and how they’re affecting the body. I typically combine pharmaceutical and herbal strategies, with my most frequent pharmaceutical choices being Nitazoxanide and Paromomycin.

1) Treating Parasites with Nitazoxanide

Nitazoxanide is the most common medication I use to treat certain parasitic infections. It's a thiazolide antiparasitic agent that was first approved for use in the United States in 2004. It's been shown to be effective at treating the parasitic species Giardia, Cryptosporidium and Entamoeba. I also use it to treat Blastocystis hominis, which I see a lot in my practice and most commonly with patients who have chronic SIBO.

Overall, people tend to tolerate Nitazoxanide well, but there are some side effects to be aware of, including:²⋅³

  • Diarrhea

  • Upset stomach

  • Nausea

  • Headaches

  • Abdominal pain

When used to treat Giardiasis and Cryptosporidiosis, the dose for adults is usually 500mg every 12 hours for 3-14 days.² It's available in both oral tablets and liquid suspension.

2. Paromomycin to Treat Parasitic Infections

My second most-used antiparasitic treatment is Paromomycin. This medication is classified as an antibiotic, but it functions specifically as an amebicide–meaning that it kills amoeba-type parasites in humans (entamoebas).⁴

In my practice, I mainly use Paromomycin to treat Entamoeba, a disease-causing (pathogenic) parasite known to cause dysentery. However, I also use it for species that are non-pathogenic, meaning that they don't cause acute illness. These organisms include:

  • Entamoeba coli

  • Endolimax nana

  • Pentatrichomonas hominis

  • Dientamoeba fragilis

There’s some debate in the medical community about whether these non-pathogenic strains need to be treated. According to the Center for Disease Control (CDC), non-pathogenic Entamoebas don't need to be treated because they don't cause acute illness.⁵ However, based on my education, which includes training from parasitologist Raphael d’Angelo, MD, these parasites need to be treated. 

These organisms may not cause overt illness, but they take up space in the GI tract. When this happens, it leaves less space for healthy normal flora to thrive and support our bodies. 

Paromomycin was recently removed from many standard pharmacies in the United States due to low demand. However, it's still available through compounding pharmacies.⁶

The dose varies depending on the parasite that's being treated. But for treating Entamoeba histolytica, the dose is 25 to 35 mg/kg/day in three divided doses for 5-10 days.⁴

Side effects of paromomycin are usually mild and include:

  • Abdominal cramps

  • Diarrhea

  • Heartburn

  • Nausea

  • Vomiting

We Must Restore Gut Flora When Treating a Parasitic Infection

A healthy gut depends on a delicate balance of bacteria: your normal flora. Infections, recurrent antibiotic use, and chronic inflammation can throw that balance off, especially when parasitic infections are involved.

Many of my patients with parasitic infections have imbalances in their normal gut flora, which usually presents as an overgrowth of the normal flora to harmful levels. To treat this, I often use Berberine. 

Berberine is a plant-based compound that's been used for more than 1,000 years in traditional Chinese medicine to combat parasites, bacteria, and fungi. In several studies, Berberine has been proven to be effective at killing many harmful bacteria including Streptococcus agalactiae⁷ and Staphylococcus aureus.⁸

Beyond its anti-bacterial properties, Berberine has powerful benefits for gut and immune health. Berberine has been shown to:⁹

  • Reduce harmful inflammation in the GI tract

  • Support the health of gut-associated immune cells

  • Restore balance of the normal gut flora after treatment of a parasitic or bacterial infection

Berberine has also been studied for its positive effects on other conditions like:⁹

  • Obesity

  • Diabetes

  • Inflammatory bowel disease (IBD)

  • Atherosclerosis (plaque build-up in the walls of arteries)

  • Alzheimer's disease

  • Rheumatoid arthritis

  • Cardiovascular disease (a group of conditions that affect the heart and blood vessels in the body)

Fungal Infections Should Be Treated Alongside Parasites and Bacteria

Whenever we treat parasitic or bacterial infections in the gut, fungi like Candida albicans must also be considered. The GI-MAP stool test checks for fungal infections, but even if the results come back negative, antifungal support is still a necessary part of the treatment plan.

That’s because parasites, fungi, and bacteria all work together in the gut. In fact, these different organisms often work together to form protective layers called biofilms. These biofilms are made up of different bacteria, fungi, and sometimes viruses, and they line the gut to help one another survive.¹⁰

To truly clear parasitic infections and support healing, we need to treat all of these organisms together. If we don't do this and instead focus our treatment on only one type of infection, like a parasite or bacteria, this can cause a worsening imbalance of the other organisms in the gut.

And when these imbalances occur, such as overgrowth of the fungus Candida albicans, this results in persistent infection and inflammation in areas like the gut, sinuses, and mouth.¹¹⋅¹²

Could a Parasitic Infection Be the Missing Piece?

If you’ve been struggling with chronic digestive issues despite being treated for GI conditions, it may be time to consider a deeper look into your gut health.

Functional Medicine tests like the GI-MAP stool test or Parawellness Research are some of the most comprehensive tools I’ve used to uncover what’s really going on in the gut. These tests help identify parasites, bacterial imbalances, and fungal imbalances that may be contributing to your symptoms–even if you don’t have obvious GI complaints.

If you’re curious whether a parasitic infection or an imbalanced gut microbiome could be behind your symptoms, you may benefit from one of these tests. Click the link below to schedule an appointment with me and find out if this testing is right for you.

It could be the first step toward finally getting answers and healing your gut.