I think I have C Diff: Now what?

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1. Find a doctor you trust to handle your health and that accepts the administrative aspect of the medical system.

2. Be informed. Research issues and medications so you can have efficient conversations.

3. Be prepared. Make a list of your symptoms and your questions. For example, “Could it be ____? "What do you think it is?" "What else could it be?" “What are my treatment options?” “What about?”

4. If you need a referral to a specialist, research specialists and draft wording for a potential referral.

5. If you are not certain about a particular treatment, explain why. Perhaps your doctor will calm your fears or can suggest an alternative. Be careful with this. I told my dentist I didn’t want Amoxycillin, and he gave me an alternative that made me sick. Sometimes it is best to “go with the flow”. (Note 2)

6. Consider going to a naturopath for subclinical issues. A GI Map or similar test can take a deeper dive into gut issues if the doctors cannot find a medical diagnosis or for generic “post-infectious irritable bowel syndrome” (PI-IBS). In my case, I had E. Coli and Klebsiella bacteria after Vancomycin and the doctors called it PI-IBS.

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Your GP, GI doctor, and/or IDD may ask you to perform various tests or try different treatments. Ask questions, and keep things efficient to promote a good working relationship with your doctor.​

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GI - gastrointestinal

GP - General Practitioner / family physician

IDD - infectious diseases doctor

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Note 2 - On the other hand, I deferred my colonoscopy because I was getting better and was afraid to do the colonoscopy prep. Luckily, it was clear when I eventually did it a year later. Also, I stopped taking Cipro and Flagyl because they caused sharp pain in my stomach. 

Please check out the Mayo clinic website:

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https://www.mayoclinic.org/diseases-conditions/c-difficile/symptoms-causes/syc-20351691

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It is a very scary thing to "Google" your symptoms. Yes, it is good to know what you are up against. Then you can face what you fear or find out that it isn't real. See Diet and Naturopathic treatment for some things you can do to decrease your symptoms and improve your chances of fully recovery.

To be tested for C. Difficile infection, you must be symptomatic. When I was diagnosed in January 2020, doctors would not test me for C. Difficile bacteria unless I had at least 3 loose stools per day (diarrhea).

​​The two main types of testing in Ontario are the GDH by EIA, and the PCR test. The GDH by EIA is the most common. A third type of test is more accurate, but is not offered as a general rule.

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The GDH by EIA (a lab test of your stool sample (poop)) is the most common C Diff test and has two parts:

1. Is the C. diff protein detected in your stool?

​        a. If Yes go to 2.

        b. If No, the toxins A/B text (or in Toronto, the toxin B test) will not be performed.

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2. Are the C. diff toxins A/B (or toxin B) detected in your stool?

        a. If yes, this is indicative of C. difficile infection (symptomatic - but your doctor still has to diagnose you).

        b. If no, you might be a "carrier" or have dormant C. difficile bacteria.​​

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The lab will generally not test a sample unless it is watery.

You can be diagnosed with a mild, moderate, or severe C Difficile infection. Your doctor will diagnose you based on:

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- a stool test, such as a "GDH by EIA" or PCR test, and

- an assessment of your symptoms.

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For me, I was glad to get diagnosed quickly.

• Fidaxomycin (Dificid)—a newer antibiotic reducing recurrence risk, may require insurance approval and patient assistance.

• Vancomycin tablets—a potent antibiotic killing most bacteria in the colon.

• Fecal Microbiota Transplant (FMT)—a poop transplant from a healthy, screened donor such as a family member who has undergone proper screening. This is the only treatment known as a "cure", but it is not warranted for every C Difficile infection. FMT is available in Ontario after two recurrences of a C Difficile infection. Mount Sinai hospital in the US may provide FMT for a severe CDI that did not respond to antibiotics within two days. There are many hospitals in Canada and the US that run FMT programs, and you can always ask your doctor if this is an option for you.

• Rebyota—a screened microbiome therapy (patient support may be available). Similar to FMT and is given easily via enema.

• VOWST is in fact not intended for treatment, but to prevent recurrence (pills, taken 2-4 days after finishing antibiotics). Rebyota and VOWS are considered "LBPs" (Live Biotherapeutic Products)

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Tips on Treatments

• There are mixed experiences with all treatment types.

• S. Boulardii, a yeast-based probiotic, can be taken daily and survives antibiotics.

• Other probiotics may assist recovery or recurrence prevention (e.g., HMF Replete, HMF Forte, Align).

• Naturopathic support is an alternative if antibiotics are not preferred, but sometimes antibiotics are necessary.

• Manuka honey is sometimes suggested for its antibacterial properties, though it is costly and may increase cravings for sugar.

• Metronidazole is omitted due to less favourable outcomes, but may be considered with trusted medical advice.

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Treatments Being Tested / Clinical Trials

• Ibezapolstat—phase 2B clinical trials in the US.

• CRS3123—a narrow-spectrum antibiotic for C Diff.

• Clinical trials and university studies on the microbiome are ongoing.

• Additional resources and treatment options can be found via CDiff.org (Peggy Lillis Foundation).

When I realized that antibiotics had not worked, and I still had symptoms that made me think I still had C Difficile, I revolutionized my diet and found a naturopath. My father found a good naturopath in our town, and drove me there since I was so tired. I thank God for my family who helped me through a difficult; although the bulk of the recovery was on my shoulders, family and friends helped in key ways.

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The first naturopath I saw, Dr. JP, prescribed me a "weed and seed" protocol; we would "weed" the bad bacteria from my gut on weekends (Saturday and Sunday), and from Monday-Friday "feed" the good bacteria using certain probiotics and "Slippery Elm".

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Speak to your own naturopath before trying anything, in case what worked for me does not work for you.

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I also found out from Dr. NC, another Naturopathic Doctor, that I no longer had a C Difficile infection but I had excessive Klebsiella and E Coli bacteria. This combination mimics C Difficile, but without the blood; however, by this point my digestive symptoms were improving, and Dr. NC wanted me to gain weight before trying to attack the E Coli, I added 1/4 teaspoon cinnamon at some meals daily to fight the E Coli, but otherwise fought Anorexia and re-learned to digest food. SON Formula pills are amino acid/protein pills that I used when I was at a dangerously low weight despite eating as much I felt able to.

The below is a summary of how I changed my diet when I realized I still felt poorly after my antibiotic treatment. More information about my dietary changes are in the separate page about diet.

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​Diet was an important part of my recovery, including the following habits:

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• no sugar, fat, salt, or spice

• no caffeine or alcohol

• ⁠get a dietician

• join a food support group (if appropriate)

  • I did because I thought, “If I don’t eat, the bacteria don’t eat” – so I was starving and sometimes binged on various foods and therefore needed help knowing how, when, and what to eat.​

• manage diarrhea​

• high nutritional value

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My philosophy was: 

• starve the C Diff

• overwhelm the C Diff with an army of good bacteria - probiotics. Many people say that FMT is the best probiotic, but it is hard to access.

​I remember eating greasy chicken and potatoes at a lunch buffet next door to my doctor's office. It was delicious, but I remember thinking that it was the last restaurant meal I was going to eat for a long time. If I wanted to get better, I had to put the work in, including cooking my own food.

Remember, that your body is different than mine, but there are general principles that I strongly believe in (avoiding sugar and sweeteners). What worked for me might help you think about what will work for you.

[Coming soon.]​

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[Coming soon.]

​​​FMT can be risky, but lifesaving.

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FMT is hard to access, and alternatives are available: "Live biotherapeutic products (LBPs)" such as Rebyota (delivered easily by enema) or VOWST (used to prevent recurrence). These products may not work as well as FMT, but have been screened by medical authorities. Recent discussions (2025) with the Peggy Lillis Foundation wondered why FMT is classified as an experimental drug instead of having its own category like blood does.

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Some people prepare a kit to perform FMT at home, but never do the FMT because they get better from other treatments like I did. I was strict with my diet, improved my sleep and mental health, and had friends, family and a support group helping and praying for me, besides all of the doctors, naturopaths and dieticians I saw.​

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The information in this web site is based on the research and experience of the author, who recovered from C Diff at home in 2020.