Blastocystis hominis: How helpful are Antibiotics?

blastocystis hominis natural treatment options byron bay herbalist australian naturopathic treatment for parasites

You have found gut infection and now are considering antibiotics for Blastocystis. There has been a debate in the literature as to whether Blastocystis is pathogenic or not. Some consider it pathogenic and others list the huge amount of infected individuals that show no symptoms. The truth of the matter may be somewhere in the middle with the subtype or strain of bug and the host immunity.  

One paper summed it up quite nicely. ‘The infection’s onset depends on the interaction between the virulence of parasites and host’s immune competence (1)’

While there are many cases of infected people showing no symptoms the evidence that Blastocystis can take on a pathogenic role is growing. Along with nonspecific symptoms including

  • Diarrhoea
  • Abdominal pain
  • Flatulence

There is also the cancer concern to consider as well. Blastocystis subtypes in certain environments have been shown to increase the proliferation of colorectal cancer cells (2). Now we also need to consider the gut’s environment and diet in the progression of cancer as well so don’t take this evidence as a sure thing.

Other pathogenic tendencies have been observed including the production of proteases (3). Proteases are enzymes that cleave our immunoglobulin A (IgA) antibodies which we produce to protect ourselves from these pathogens. Many parasites share this trait and produce a range of protease enzymes that damage the host including Entamoeba histolytica and Giardia duodenalis (4).

Further Reading


Efficacy of Antibiotics for Blastocystis – Metronidazole

There are a number of recommended antibiotics for Blastocystis but the front line therapy for Blastocystis is a drug called metronidazole, brand name flagyl. Some doctors I have seen swear by this antibiotic and almost don’t believe me when I tell them it didn’t work. Who can blame them. If you haven’t been keeping up with the literature coming out then it is understandable not to know that there has been a massive increase in antibiotic resistance among a number of different pathogens. As I’ve written about before Helicobacter pylori is a great example of this idea with a sharp rise in antibiotic resistant strains emerging (5).

A clinical trial published back in 2001 showed that metronidazole seemed reasonably effective looking at different antibiotics for Blastocystis. Even then, when you looked a bit closer at the results you might scratch your head. They showed 80% of the patients treated with the antibiotic had cleared it in the first month compared to only 3% in the placebo arm. When they did a follow up 6 months after the antibiotic treatment they found that the number of cleared patients dropped from 80% down to 48%. There are two scenarios that could explain this massive drop.

  1. Using the recommendedantibiotics for Blastocystis the patient had cleared the infection with metronidazole. They were then reinfected at a later date and came back positive on the stool test.
  2. The stool tests actually missed the Blastocystis infection the first time, possibly due to the low numbers, and caught it the second time. This is known as a false negative and can really confuse the situation, sending you down the wrong track.

Just last week a paper was published in Parasitology Research covering two different case studies. In these case studies patients were administered the standard metronidazole for Blastocystis sp. infections. To me it wasn’t surprising that the antibiotics didn’t work. Here in Byron Bay, Australia, where Blastocystis is rampant I have heard more cases of failed eradication with antibiotics than I care to count. The interesting and concerning aspect of this study was the effect that metronidazole had on the cyst count of the Blastocystis population. These two case studies reported a higher cyst count and more severe symptoms after taking flagyl. Here I would start to question certain antibiotics for Blastocystis as this happened to me quite dramatically.

The paper concluded ‘The two studies uniquely demonstrate for the first time a cyst count as high as fivefold more than the original cyst count before treatment and show an exacerbation of GI symptoms despite treatment’  


To Treat or Not to Treat?

This is the major debate in the scientific community. One paper suggested that patients with no symptoms and a low cyst count should skip treatment and that those experiencing gastrointestinal symptoms or skin issues with a higher cyst count should attempt to treat the infection (6). There may even be a link between the different forms that Blastocystis spp. can take with one study showing that the amoeboid form producing more protease enzymes thus being more pathogenic.

With that said it is important to stop and take stock. If you have come back with a positive stool test for Blastocystis as I did then take a moment to consider a few points.

  • Gastrointestinal symptoms – bloating/flatulence/diarrhoea/distention
  • Skin issues – urticaria/hives/rashes
  • Possible wheat, fructose or dairy sensitivities
  • Nutrient deficiencies
  • Sleep quality

All of these points and more can be contributing to your symptom profile and each one must be ruled in our ruled out.

All of my gastrointestinal symptoms have resolved even though my stool tests still come back positive for a Blastocystis infection. I attribute this to the two herbal antimicrobial treatments I’ve been through, the probiotics and prebiotics I’ve been working with to improve my gut flora and some herbal medicines (Chinese medicine and western herbal medicine) designed to support my immune system.

Have you tried antibiotics for Blastocystis? What were your results? Share your thoughts below.


References and Resources

  1. Eradication of Blastocystis in humans: Really necessary for all?
  2. Blastocystis sp. subtype 3 triggers higher proliferation of human colorectal cancer cells, HCT116
  3. Degradation of human secretory immunoglobulin A by Blastocystis
  5. Antibiotic treatment for Helicobacter pylori: Is the end coming?
  6. A Placebo-Controlled Treatment Trial of Blastocystis hominis Infection with Metronidazole
  7. Exacerbated symptoms in Blastocystis sp.-infected patients treated with metronidazole: two case studies
  8. Blastocystis: To Treat or Not to Treat.
  9. Amoebic forms of Blastocystis spp. – evidence for a pathogenic role
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  1. hello I had this bug about 6 years ago . Dr put me on flagyl for at least 4 weeks, didn’t help at all.3 months later after having chronic diharea I got onto a triple antibiotic from usa. This worked. Now my 20 year old daughter has it. We’ll go the natural way this time.

    1. Thanks for sharing your experience Donn. I am not surprised that Flagyl failed. It is good to know that the triple therapy worked. For the natural approach I have been seeing good success with a combination of a handful of different herbs (coptis, garlic, oregano etc).

      Circle back and let me know how your natural treatment goes!

  2. Hi Todd —

    I was just diagnosed with same two parasites as you! I’ve traveled the world from the Mediterranean to India/Nepal and symptoms started showing 2 months after I returned home. Though, I also could’ve caught here in the US (I’m quite outdoorsy).

    I have all the symptoms you’ve described above, the bloating is the most uncomfortable. I’m quite desperate for a solution.

    I’ve had it for about 5 months now and I’ve tried Flagyl and Bactrim to no avail. I’ve also been taking probiotics. Buying prebiotics now based on your suggestion.

    I’m also considering a round of Paromomycin

    Please let me know, if you have any other suggestions.

    I read a paper where a US traveler who came from nepal had it for 5 years and tried dozens of antibiotics to no avail.

  3. Hi, I found out I had blasto about 6-7 months ago and after a holistic month long parasitic cleanse ( which didnt work) + 10 days of 1500mg metronidazole, my bloating + constipation and horrible eczema like widespread skin rash got better by 90%.
    my gut is still better but not 100% but my skin has started acting up. Im 34 and I have never had chronic issues like this till 2020 when I first started showing all the gastro symptoms of painful cramps, flatulence.. Now i have widespread food sensitivities and this has made me miserable. I am lost and I have no idea what to do anymore because trusting american health system has been very very hard. Please help!

    1. Hi Arpana, with those symptoms I would rule in/out SIBO instead of chasing after blastocystis. You may have resolved the bacterial overgrowth with your protocol and are left with the gut damage that needs attention. For patients with your symptoms I would run a SIBO breath test and a leaky gut (IP) test and treat what came back.
      Hope that helps!

  4. Oh I guess I should mention I am from Nepal. Born and raised, never had skin and gut issues like this all my life while I lived there. I couldve picked this up from back home ( i doubt it) or in the US ( where I live now) or the solomon islands when I was visiting in 2019.. I did once drink water from a tap on this remote island in the solomon islands ( which I have never in my life done) so I am guessing it must be that? Or contaminated restaurant food in the US?

  5. sorry to flood your comments.
    the most difficult and chronic symptom I have is the skin rash – eczema. It was so bad at some point in 2021 ( post covid vaccine as well) that I thought I couldnt make it another day for about 3-4 months…I really could use any and all the help there is to cure this once and for all. It’s very hard when doctors tell you you have an autoimmune issue, or eczema and that its a life sentence of sorts when I know that there is something thats causing this.. Blasto being it.

  6. Hello Todd!
    After two months of having your same symptoms, I was diagnosed with blastocystis two weeks ago. A doctor prescripted me 10 days of flagyl (1500 mg a day). On day 6 of treatment I was doing great, but on day 7 I had bad stools again, and day 9 was hell: vomiting, abdominal cramping, severe diarrhea and shaking. I suspended my treatment and felt my body was asking me to desintoxicate myself of so many antibiotics. I don’t want to take strong medicines ever again. Today has been better, I have drank herbal teas, been in calm and eating very healthy food. This has been a tough lesson for me in which I only want homeopathic and natural remedies from now on.

  7. Hi Todd!
    I have 2 parasites which i’ve had for quite a while now. I have blastocystis and dientamoeba. I took flagyl (3 a day for 7 days) which didn’t work. They are both still there. Any tips?

  8. Have you heard about the triple therapy colonic infusion? They infuse several anti-protozoan agents inside the colon. I read that it has a 100% eradication rate. I’ve seen it only done in Australia. What are your thoughts on this treatment? I think the real reason this parasite is so hard to eradicate is because in part it lives in the large intestine, which I presume is a harder to reach place for medications and also probiotics.

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