Blastocystis - does anyone know of a PCR based test that is available

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ah, yes, correct, maybe they have been rejigging their offering, i think it used to be $799 for a single test but i must admit I had not looked closely while it was $800 and I was focussed on other directions of research.

still, at $399 its pretty good value and you could always give the 3 spare to your friends or partner

thinking laterally - 4 tests would allow a before and after treatment view for 2 people - if you didn't mind using the same account.

The business model is interesting - they sell the tests at below cost - as their main business is selling anonymized data to research institutions. Once they have paid off their initial investment in technology they may reduce prices to encourage volume.
 

Hip

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you could always give the 3 spare to your friends or partner
That's a good point: it would also be possible to team up with 3 other members of this forum, sharing the price, and each sending a sample to uBiome.

Though if you say that uBiome sells its anonymized data to research institutions, they probably won't like you doing that (at it may be against their regulations), as I imagine they will assume all the 4 samples are from the same patient. But I guess I could write to them and ask.



I may also write to Dr John Chia, and ask what he thinks of these uBiome and Aperiomics tests, for the purpose of enterovirus testing.

The main pathogens linked to ME/CFS are enteroviruses (coxsackievirus B and echovirus), herpesviruses (EBV, HHV-6 and CMV), parvovirus B19 and Chlamydia pneumoniae. This are the primary pathogens tested for by ME/CFS specialists.

Most of these pathogens can be easily tested for by any lab that offers viral antibody testing, so testing is straightforward (except parvo which I believe requires PCR).

But the problem is enterovirus, which is not straightforward to test for, because most antibody tests are not sensitive enough to detect chronic enterovirus (in the US its only ARUP lab that has a sensitive enough enterovirus test); and even when you use a sensitive antibody test like ARUP, it does not cover all the enteroviruses linked to ME/CFS (there are 6 coxsackievirus B and 26 echoviruses).

Thus the only way to get a reliable test for chronic enterovirus in ME/CFS is by stomach tissue biopsy, which involves a gastroenterologist sticking an endoscope down your throat, and snipping off some small samples of stomach tissue. Dr Chia's lab then tests these stomach tissues for the presence of enterovirus.

But that's a bit awkward, because it requires finding a willing gastroenterologist to take the stomach tissue samples.

So if uBiome and Aperiomics could serve as a substitute for the stomach biopsy enterovirus test, it would make testing for enterovirus more straightforward.



I wonder, out of uBiome and Aperiomics, which have the more sensitive test for viruses. I am not sure of the Aperiomics cost, but I read on a forum it is $750 to $1,000 per sample.
 
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I wonder, out of uBiome and Aperiomics, which have the more sensitive test for viruses. I am not sure of the Aperiomics cost, but I read on a forum it is $750 to $1,000 per sample.
Once you are using qPCR I don't think sensitivity is an issue anymore - I think its more a case of how deep into the taxonomy can you get. For instance, with many bacteria the 16S fingerprint is good enough to get you to genus level reliably - beyond that, it may only be 60% accurate. This should be no surprise as taxonomy is a human construct, a product of our need to categorize, whereas these little things simply are how they evolved. They even pass DNA around amongst themselves in a kind of genetic swapsies when they feel like it, so beyond certain point names don't help much. This is partly why so much work is being done on the "metabolome" so instead of asking "what do we call it?" - we ask "what genes are active?".

I am not sure what this means in terms of viruses. Perhaps a sample report would help.
 
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OK - so an update on this.

I have been researching available tests that do test for Blastocystis in stool via PCR or Next Generation Sequencing technology and have found some interesting products that are out there that fit the bill.

Some are quantitative - which gives another factor to help determine if the presence of teh organism is likely to be linked to any pathogenic symptoms - which is not a feature of most PCR based tests.

Many are available as multiplex tests (a test that detects more than one pathogen in a single assay) or "all eukaryote" or even "all pathogen" type tests - which are of interest as most symptoms associated with Blastocystis are non-specific and could equally well be due to a number of other intestinal pathogens. Of these, I am most interested in Entamoeba Hystolitica and Dientamoeba Fragilis - but there are other common ones that are well worth ruling out such as Giardia, and Cryptosporidium.

it's also worth noting that while Ubiomes new Explorer Plus test claims to detect all eukaryotes - they tell me that they can only reliably do so to genus level. This is a very broad test and certainly helpful, but in the case of the Entamoeba genus - several of the species are non-pathogenic and so whilst very broad and useful for an overview, a test that does not differentiate below genus level would not give the depth required to give a definitive diagnosis.

Several of the tests are only available via a registered healthcare practitioner, the definition of which can vary between providers. Others are available direct to consumer, or via a non-charging practitioner scheme. Costs of course also vary by the practitioner.
If I had to, I think I could find a practitioner or herbalist that would accommodate, but so far I have not found one I consider knowledgeable enough or trust well enough with my health to justify the fees. Since I have educated myself to a significant degree over the last 4 years I would so would tend to save my money and opt to go direct. Others should choose an approach that suits them best.

Based on my needs and preferences after a bit more digging I think I will opt for testing via DSL's GI-MAP product as the first course of action. Possibly following up later with one of the more comprehensive ( but much more expensive tests) if it is needed. its an interesting mix of quantitative tests for Bacteria, Eukaryotes, Genes and inflammatory markers that seems to tick the boxes I am most interested in. I will add a link to a sample report in a follow-up post.

I am also sensitive to cost as I need to budget for test, treatment, retest to confirm the outcome, and potentially further tests and treatment depending on what is found or what else may need treating after parasite is confirmed gone.

I have tabulated the information below and hope it is of help to others here:

Blasto PCR based tests.JPG
 
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a link to a sample report of the GI-MAP product below
https://www.diagnosticsolutionslab.com/sites/default/files/gi-map-sample-report-2018-2_0.pdf

also a white paper from them on their technology
https://www.diagnosticsolutionslab.com/sites/default/files/gi-map-white-paper-01-2018.pdf

An interesting paper from Fry labs also - who have entered this space more recently. I suspect many more will follow.
summary here - https://www.sciencedirect.com/science/article/pii/S2452231718300083

I say interesting because it discusses finding organisms not previously associated with human disease in the blood and other sample materials in the bodies of ill patients with chronic CFS like disease.

It should be noted that none of the organizations I have contacted have offered what I would consider to be high-quality validation studies of their products. This is initially surprising to me, but I think its driven by two main factors:
  • 1, the difficulty, and therefore cost, of proving their technology "does what it says on the tin"
  • 2, the preponderance of people in a similar position with an undiagnosed illness and desperate to find a way forward resulting in no absolute need to prove the product to have a business proposition.
They appear to be of the mind that much is written already in the literature about most of the technology they use and so they don't need to prove their product.
However, I am of the view that whilst I could build a car in my garage based on the technology originally developed by Ford or Toyota, but that does not mean it would meet the latest crash test, emissions, or performance standards of a properly validated product and I certainly couldn't prove that it would.

I would, therefore, conclude that none of these tests are fully proven, but they are one of the few options available, assuming you can afford them, and thus may still be worth pursuing
 
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Thanks for the interest.

The results of the GI-Map test from DSL were negative for all the protozoans it looked for including blastocystis.

However, the story doesn't quite end there as the other results in the panel raised some cause for concern.

Both my partner and I also had an alternate stool quantitative PCR test performed only a couple of months ago by another industry-leading testing company (Ubiome).

Where the same taxa are tested in both tests the comparison of results raises some concerns.


Specifically –

1. Even at Phyla level (where the testing companies tell us their results are most accurate and reliable), the results are radically different

a. DSL result dsl phyla.png

b. uBiome result
ub phyla.jpg

Summary

i. DSL firmicutes / Bacteroidetes ratio 0.30

ii. Ubiome firmicutes / Bacteroidetes ratio 1.28

Ie The results of the two tests are radically inconsistent


2. at the genus level, which all manufacturers and testing companies tell us can be reliably detected using this wonderful molecular technology, there are even more radical differences....

a. DSL result
dsl genus.png

b. Ubiome result
ubio genus.png

Summary -

i. All of the DSL detected bacteria are entirely absent from the Ubiome result -
(with the exception of organisms from the enterococcus genus which appears at a count 36 times higher than the normal healthy maximum in the dsl result. Whereas this entire genus is detected at around 100 times lower than the average in the ubiome result. So this is also an opposite conclusion)

Now, gut flora in humans is known to be quite stable over time, largely from childhood onwards, and especially so in the shorter term and particularly if diet has remained the same between samples, which in our case has definitely been the case.
In fact, we have done none of the things that are known to impact the gut microbiome the most:
  • Neither of us has had antibiotics in the intervening time ( nor any other pharmaceuticals for that matter)
  • Nor undertaken any other gut treatments of any kind in that time
  • Nor have we changed our diet in any way ( in fact we are strictly observing the same diet from well before the first test).
  • Nor has our lifestyle changed ( again we have stuck to the same protocol for the last 18months)

It is therefore extremely unlikely that both our bacterial communities have changed so radically in this time.

If they did change, then the chances of both mine and my partners changing in the same direction at the same time are even smaller and the chance that multiple( many)genera detected only a few months ago in both of us in high numbers are no longer present at all in either of us is smaller still.

I think it fair to say we would be talking of vanishingly small probabilities of this hypothetical scenario having actually taken place. And since we are talking of more than one individual sample tested in both labs, this is clearly not a one-off anomaly.

We must, therefore, assume the largest variable is the tests themselves.

Put simply one (or both) tests are a long way from correctly identifying and counting the organisms present.

For those of you who are familiar with stool PCR testing methodologies. There are two methods in use. Some simply put the sample in an airtight tube and ship it to be processed, others choose to preserve the sample in a preservative solution at the point of sample taking to prevent further microbial growth.
In this case, both of the above companies test methodologies involve stabilizing the sample at source such that no further microbial growth occurs, which removes this variable as a potential explanation in this case.
This also indicates that the difference in the tests lies downstream in the process.

Every company will, I am sure, insist that theirs is the reliable and more accurate test, but, given the above, this simply cannot be the case.

As a patient people need to know the tests offered are reliable and consistent with each other to a significant degree and this is clearly not the case yet.
Simply put, if there is no standardized way of knowing which test has value and which test does not, then they are all equally suspect to the consumer.

I raised these concerns to both companies involved and asked for their comment on the above, however despite promises of responses, after chasing them for many weeks no such reply has been forthcoming.

Sorry it's not a more positive result for anyone interested in similar illness/testing path

My advice (as many of the better practitioners also recommend) when using independent test labs, and especially if it's using any of the newer (less than around 30 years of clinical use) bear in mind its an industry and its first objective is to make money. Therefore it's wise to do more than one test for the same thing at a time to put yourself in a better position to verify the results you get.
 
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@Garz that’s pretty insightful and concerning at the same time.

I hope both companies get back to you with a response.
I wrote to Ubiome many many times over around 8 weeks from early September to November 2018 and received no useful response to my question. Their VP of Customer Communications is Jennifer Gerstenberger. She initially replied and said she would help get it answered but that was the only communication she ever made and there was radio silence from that point onward. I am not holding out any hope for an answer. As others have experienced, their customer service is appalling at the best of times.

DSL - Generally do reply promptly to most questions and the quality of the answers are generally better than those of Ubiome. But when sent the above data and asked for comment, they initially said they would send it to their experts for comment and then, when no response came and I followed up, their experts had all become too busy to answer questions or they do not answer questions from patients (despite being happy to do so up to that point) or both.
that was sometime in November 2018. I chased again for a response in December and received no reply at all.

As you may gather, neither inspired confidence.

Personally, I think the silence speaks volumes.