Stool Testing – My Personal GI Results CDSA + PCR

byron bay herbalist naturopath gut health specialist australian gut testing functional medicine todd mansfield

My interest in Functional Medicine and health in general came about from a very selfish place.  Living in the Byron Bay hinterlands at the age of 27, for the first time in my life, I experienced the first symptoms that developed into long term (2 years +) IBS. Don’t get me started on IBS, or irritable bowel syndrome. It is not the actual underlying issues, simply a description of the symptoms!

After going to the doctor’s office and getting their very limited stool test it turned out I had Blastocystis hominis. Unfortunately conventional medicine doesn’t have the best approach to many GI infections. The standard antibiotics are increasingly ineffective and have some nasty side effects.

So what to do? Looking into the different healing modalities I came across Functional Medicine and haven’t looked back. Even though my original motivation was from a selfish place it has evolved into something else. I came to realise that if I struggled to find a solution to my personal health issues that many other people must be in the same boat. Hence the creation of Fully Functional. I’m eager to share my learnings and hopefully it helps anyone in the same boat.


Onto My Test Results

It took me two years to actually commit to the proper functional tests. If I had been working with a quality practitioner then I’m sure that it would have happened within 2 weeks! So much for trying to save money.

The amount of cash that I have blown on supplements is astounding! I don’t even want to think about it.

As I’ve written about before, the recommended tests to run when you are suffering from any GI distress symptoms include


  1. CDSA – comprehensive digestive stool analysis
  2. PCR – Polymerase chain reaction


And here is the EXACT reason why!

My CDSA test, even though it still provided very valuable information, completely and utterly missed both of the parasites living in my intestinal tract! 


CDSA stool testing GI infection


Fortunately the PCR test caught both of them. This is the exact reason why it is highly recommended to run both the CDSA and the PCR. If I had only run the CDSA (saving a bit of cash) then it would have sent me down the wrong track in terms of treatment plan and I would still be suffering from GI issues indefinitely.


PCR stool testing GI infection


As you can see both tests aren’t really enough on their own. The most important information that you get from both the tests is the screening for the parasites. In the case of the Nutripath lab (a highly recommended lab in Australia) this is the only thing that the PCR delivers.


Test Results

The CDSA picked up an insufficiency of beneficial bacteria – Lactobacilli spp.

It also picked up TWO different Klebsiella spp. These are nasty little bacterial infections that are commonly contracted in hospital settings – nosocomial infections are actually quite common. One reason I like to avoid hospital trips unless necessary!

The last bacterial infection the CDSA stool test picked up was a Citrobacter spp. infection.

The PCR testing only screened for a handful of common parasites. My testing resulted in two fairly nasty and recalcitrant protozoan infections. It screened positive for Blastocystis homminisextremely common here in the Byron Bay region, and a somewhat less known parasite Dientamoeba fragilis. The reason I say less known is possible because the average and limited stool test recommended by your local GP will have a hard time detecting Dientamoeba fragilis due to it’s fragile nature outside of their host species. I would make a prediction that Dientamoeba fragilis is actually quite common in the Byron Bay Hinterlands and many other warm subtropical locations.


Common Questions

If the CDSA screens for the pathogens why run the PCR as well?

The PCR test is a fine tuned machine. It works by amplifying any DNA that is present in the sample. Compared to the CDSA it is much more reliable at finding the pathogenic microorganisms if they are present. It only provides a small amount of information but is considered essential for proper screening.

If the PCR is so reliable why run the CDSA?

The CDSA provides more information that simply the presence of a pathogen. Many times it depends on the CDSA level that you have ordered (Nutripath has 5+ options for a CDSA) but even the more basic packages screen for beneficial microbes, other microbes and pathogenic microbes as well as yeasts and your quality of digestion. More on what the CDSA provides here.


Recommendations For Gut Testing

If you are suffering any symptoms of GI distress it is highly recommended to run both a CDSA and a PCR test together. The standard of care stool testing that is on offer from your doctor is incredibly basic and doesn’t give you the whole picture. Many times it misses the pathogen and even if there isn’t a pathogen present that doesn’t mean that you are free and clear. In the case below both a yeast colony (Candida) and an opportunistic bacteria are present plus the CDSA picked up the fact that this individual was lacking in beneficial organisms.

This could be the reason why the opportunistic bacteria had overgrown. Without a healthy population of beneficial microbes, the gut is an open door for the more opportunistic (and less beneficial) microbes to take hold.

The next step is finding a practitioner that can guide you in the process of bringing your disrupted (and possibly infected) gut microbiome back into balance. This is someone that I am still struggling to find and don’t have any recommendations yet. When I do I will update this article to include them.  

Please remember to RETEST a few months after your antimicrobial treatment protocol has finished. Even though you may be feeling better, you need to be 100% sure that you have completely eliminated the pathogenic microorganisms!

Now over to you. Do you have any experiences running GI testing? If so what was your experience? Comment below.


References and Resources

  3. Nutripath labs
Legal and Affiliate Disclosures: This post may contain affiliate links. That means if you decide to make a purchase through one of these links, I may earn a small commission at no extra cost to you. Learn more here

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1 comment

  1. Just got my comprehensive stool analysis +4 citrobacter freundi complex +4 Kiebsiella pneumonia given choice
    of three antibiotics with history of c-diff don’t want to take
    very low lactobacillus & bifidobacterium as well. How did
    you get rid of these bad bugs? & what probiotics did you use.

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