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

Discussion in 'Diagnostic Guidelines and Laboratory Testing' started by Garz, Aug 28, 2018.

  1. Garz

    Garz

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    After a 4 year journey with CFS and many related health issues that have turned our life upside down, my fiancé and I have recently come round to the conclusion that what has made us both so ill is likely to be blastocystis hominis - or something very similar.

    Initially, not knowing any better, we followed the conventional medicine approach through our local GP who did all the basic blood tests and found nothing amiss despite us being at 20% of our prior capacity mentally and physically, after much prodding he eventually referred to infectious diseases specialists who also found nothing. So, we reverted to a paleo lifestyle and functional medicine approach - which improved our situation significantly. However, we were still v ill.

    On this functional health approach, we of course started with the gut and got ourselves tested 3x complete stool analysis with parasitology with both Drs Data and Biolab in parallel to give us what we thought would be the best chance of detecting a pathogen if present

    The test showed some overgrowths of normal flora and “some” or “many yeasts” in each sample so we embarked on a gut treatment protocol involving diet, an antimicrobial protocol including berberine, allicin, undecylenic acid, and other natural antimicrobials along with probiotics for 12 weeks. This was a very comprehensive program including a gut rebuilding phase and gentle reintroduction of foods afterwards. In general, this made us feel much worse for the entire time we were taking antimicrobials. Then much better for 2-3 weeks afterwards which then relapsed to as it was before.

    A follow-up stool test with parasitology found all overgrowths now in the green and yet we were still v ill. In functional medicine failure of this type is usually a sign that there is an underlying problem with infection, like a tick-borne disease, or some such deeper issue preventing recovery. So we went on another long journey looking into many rare diseases and treatments for CFS.

    One of these investigations was Ubiome gut explorer. Our gut microbiome was only slightly different from the average. No obvious pathogens and nothing way out of whack. But one of the interesting things we found were that the previous stool tests had clearly mis-identified several of the species it claimed were overgrown (the specificity of the PCR based microbiome testing is much higher)

    This, together with the pattern of our illness, has made me wonder if the stool tests by Drs Data and Biolab are in fact reliable for Blastocystis. After looking into it in some detail I found 6 or 7 studies on PubMed looking at the various methods of detecting it and found that direct microscopy (the method the stool tests use to detect ova or parasites) is typically only 20 to 60% accurate at detecting it, when it is in fact present. Test accuracy is also highly dependent on the training and experience of the microscope operator. This is a particular problem with Blastocystis as the organism takes several forms, depending on its life stage and its environment and each of these look very much like something else - the most common form looks like and is often mistaken for yeasts (which were found in our sample).

    So, the long and the short of it is that I am now looking for a lab that can provide PCR based testing for this organism in stool samples for patients in the UK.

    I know of at least 2 companies that make PCR test kits, and these are demonstrated to be highly specific and sensitive (around 100% for both)

    The two companies are Certest in Spain for Blastocystis and the RIDA®GENE Dientamoeba fragilis kit from Biopharm, but please do post if you know of others.

    I am in communication with the manufacturers to try to find labs that way but, this is proving very longwinded so

    I would be very grateful if anyone knows of a lab offering PCR based tests for these organisms.


    Many thanks

    Garz
     
    ljimbo423, Learner1 and Art Vandelay like this.
  2. Art Vandelay

    Art Vandelay Senior Member

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    Adelaide, Australia
    Hi @Garz I'm in Australia so unfortunately won't be much help. The standard government-approved test here for parasites does do a PCR test for blasto (although apparently it is harder to access in some jurisdictions unless the doctor specifically requests it).

    Have you seen the Badbugs website? There are a few testing options mentioned here including one in the UK (I don't think it offers PCR though) but I don't know how up to date the list is: http://www.badbugs.org/Blasto_diagnosing.htm

    Hope someone from the UK sees you post and can help you.
     
    Last edited: Aug 28, 2018
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  3. Garz

    Garz

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    Thanks Art,
    I will take a look at that site and report back in case it's of use to others here
     
  4. Garz

    Garz

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    OK the summary of the BadBugs site on PCR testing is there are two Australian pathology labs that they list as providing a Mutiplex PCR type test that includes Blastocystis along with several of the other common gut pathogens.
    ( a multiplex test is one that tests multiple pathogens in a single panel).
    these are:
    • Laverty Pathology (Sydney & ACT) has introduced a Faecal Multiplex PCR for the detection of ten major enteric pathogens' (from their website)
    • Douglas Hanly Moir Pathology in NSW, also perform Multiplex PCR testing for Blasto., D.fragilis and other pathogenic organisms.
    Unfortunately - no Blastocystis PCR test locations are listed on Badbugs in Europe/UK

    they suggest to just repeat the parasitology x3 tests to get 6 or 9 total - but this is v expensive.
    they mention
    London School of Hygiene & Tropical Medicine:
    http://www.parasite-referencelab.co.uk/
    Phone: 0207 927 2427
    but neither its website of handbook mention testing for Blastocystis and you need a health practitioner to refer you for a test.
     
  5. Hip

    Hip Senior Member

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    And also it does not tell you if any Blastocystis hominis they find is a pathogenic strain or not. Because of these testing difficulties, what I did was to try a Blasto treatment protocol without being tested, on the assumption that Blasto might be behind my gut and anxiety/depression symptoms. In my case the protocol did not help.

    See this post for a list of Blastocystis hominis treatment protocols proven effective in studies.
     
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  6. Garz

    Garz

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    @Hip. thanks for the link. - yes, I have come across the same treatments.
    Re. pathogenic strains. The thing about Blasto is there are so many unknowns. It was originally classified as a commensal yeast and, because many people who are infected with it show no obvious symptoms, it has been put in that "harmless" box and we all know how the medical fraternity hate to change stuff like that.
    This is despite the fact that something like 95% of the papers on it in the last 2 decades agree that it is pathogenic, at least for a portion of the population.
    Only with the advent of DNA/PCR technology was it possible to determine that it is, in fact, a single-celled parasite related to diatoms and algae.
    Because of the lack of knowledge we don't actually know what makes it make one person ill and another asymptomatic. It is not even classified into strains in the normal sense, historically there was no way to tell one variant from another so any form found in humans was deemed to be Blastocystis Hominis.
    The currently accepted naming protocol in use is Subtypes. eg B. Hominis Subtype 3.
    Molecular techniques have shown but up to 17 subtypes, of which 9 have so far been found in humans. One theory, as you mention, is that it is the specific subtype that determines pathogenicity, but studies on that have failed to prove a strong association or at least several studies showed differing results. There are other theories along the lines of symptomatic infections being more to do with the gut environment( which could be influenced by variables such as diet and lifestyle and genetics) but the work just hasn't been done.

    There are some interesting findings though relating to gut health.
    • Symptomatic persons tend to produce amoebic forms in stool cultures vs those with asymptomatic infections who typically do not.
    • Ameobic forms are known to get through the mucus layer in the gut lining and directly attach to epithelial cells.
    • here, like most other bugs that are able to do this, they trigger inflammatory reactions involving IL-8 and NF-kB
    • Persons with two or more subtypes tend to have more symptoms.
    • And infected persons tend to have disturbed microbiota - lacking, in particular, some of the beneficial bacteria.
    • Persons with symptoms often have significant carbohydrate intolerance. Carbs or sugars or anything containing them tends to make all symptoms much worse. This is atypical and only giardia infections are likened to it in this manner.
    Going back to testing, I understand a therapeutic trial is an option. But, I really would prefer to get clear before and after high specificity tests done so I can be confident I am not chasing ghosts and dragging my fiance through the trials of it unnecessarily. its a tough thing to get rid of so may take multiple tries so this could take a year of our lives.

    I would be surprised if PCR is not available somewhere accessible as these PCR based kits have been around for 5 or 6 years now, and I have found at least 6 manufacturers that make them and they seem to be widely used in some countries like Australia.

    If anyone knows of a lab in Europe doing PCR tests for this parasite please do post up.
     
    Last edited: Aug 30, 2018
  7. Hip

    Hip Senior Member

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    Apart from the ME/CFS symptoms, which other health issues are you suffering from? I take it that some gut symptoms are involved.

    Have you also explored the enterovirus link to ME/CFS and gut issues, Garz? As its name suggests, one of the main homes of enterovirus is the stomach and intestines.
     
    Last edited: Aug 30, 2018
  8. Garz

    Garz

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    Hi Hip, thanks for your contributions. I have read some of your posts.

    Yep, plenty of gut symptoms. A very good match for those described for Blastocystis, but of course the same symptoms are also a match for plenty of other things too. And therein lies the conundrum that so many people here seem to find themselves in.

    Yep, I am aware of enteroviruses, at least I have read much of what is known about them. They are also on my list of possible candidates and at a similar probability, I think. But, In our case, no one we know or have come into contact with since we became ill has gone on to develop the same symptoms. Whereas most enteroviruses are thought to be highly contagious as I think you describe in some of your posts. Blastocystis also attaches to and interacts directly with endothelial cells in the gut lining and by doing so initiates many immune system inflammatory pathways which we have evidence for in our case. It also modulates the gut microbiome in particular ways, which again we have evidence of in our case. That is of course not to say other things cannot do the same, its just that, in our case, the overall fit with blasto is high enough on the list to warrant pursuing a definitive test, at least in my view. In the end, we all just have to navigate this puzzle as best we can.

    This combined with the fact that getting a definitive test for enterovirus infections seems to be harder still than for Blastocystis makes me lean towards trying to eliminate blastocystis from the prospective candidate list first.

    I am also concerned about the current stage of infancy of knowledge on virus’s role in the gut and their impacts on health. I am just not fully comfortable that even if we were to find it in our case whether we could confidently say this is the root cause of our symptoms.

    I am therefore focussed at least for the moment on ruling out Blastocystis. Hence my posts here on finding a PCR based test I can access from the UK
     
  9. Hip

    Hip Senior Member

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    Fair enough. I've not come across any PCR tests from Blasto (I presume they would work with a stool sample).

    It might be worth investigating Aperiomics, which uses next generation sequencing to genetically identify the pathogens in your gut:
    But it would worth writing to them to ask how their test sensitivity for Blastocystis hominis compares to the standard stool microscopy test. Next generation sequencing (also called high throughput sequencing) sounds very advanced, but it may not necessarily be better than established methods of testing. I've no experience with Aperiomics, and I am not sure if any ME/CFS doctor uses this test.


    One gut parasite definitively linked to ME/CFS is Giardia lamblia, so that's something else to consider.



    They are contagious in the acute phase (which lasts a few days to a few weeks), but not very contagious after that once you enter into the chronic phase of the infection. In the case of my virus, which I think is an enterovirus (coxsackievirus B4), when it spread to a friend or relative, I noticed it would take up to a year to infect the rest of their household. So that's quite low contagiousness.

    By the way, I am in the UK, and got tested for enteroviruses in a lab in the Netherlands, by sending them a sample of my blood serum. This was a great lab, because it offered the same sensitive antibody neutralization test for coxsackievirus B used by Dr Chia in the US (the ARUP lab antibody neutralization test), but much cheaper (€110). That's how I discovered I had high titers (1:1024) for coxsackievirus B.

    Unfortunately that lab has now stopped doing the neutralization test, but there is also a lab in Greece called the Hellenic Pasteur Institute which offers a neutralization test even more cheaply. That's the only lab in Europe I know that offers a CVB antibody neutralization test.


    I don't know if you have seen the roadmap of ME/CFS testing and treatment document I compiled; it contains info on all the pathogens (and other causal factors) that have been linked to ME/CFS.
     
  10. Garz

    Garz

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    Thanks, Hip,
    I know of Arup - they seem to know their stuff on other infections. May even be worth contacting them on a test for Blasto as I believe they develop their own tests.

    Yes, I have seen your page on the roadmap etc and am sure it was helpful. I will add the testing info on enteroviruses to my process
     
  11. Garz

    Garz

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    also - yes I have come across Aperiomics. I think I had some correspondence with them but at the time I felt the cost was disproportionately high and the technology was not necessarily well proven at that point.

    I believe Ubiome may do something similar now to include all viruses and fungi in the gut - not sure if they cover the protozoans, Stramenopiles etc - will have to check - but again was a v expensive test.
     
  12. Hip

    Hip Senior Member

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    That's interesting. It looks like it's the uBiome ExplorerPlus that also tests for viruses and fungi, although they don't mention parasites. Whereas Aperiomics they explicitly say that they test for parasites.

    The trouble with such tests is that unless they are clinically validated through proper studies, the results may not be easy to interpret.
     
  13. Garz

    Garz

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    OK have written to Ubiome to ask the questions around this and other gut pathogens:
    • Blastocystis
    • other Amoebae
    • Protozoans
    • Enteroviruses
    since its a quantitative PCR type test it should give a "read count" for how many copies of that DNA signature it finds - which may be useful in determining how likely it is that the presence of such an organism is causing symptoms.

    if past experience with them is anything to go by, the answers will not be quick, but I will post up what I get back in case it's of help to others.

    I agree with Hip's comments about the interpretation of such new and leading-edge tests. However, Ubiome has published formal studies in the past around their bacterial DNA profiling technology, doing a decent job of demonstrating repeatability etc so they may also publish similar on this broader test in time. Their business model is based around selling the anonymised data from all samples and that only works if the technology is accepted.

    Price is reduced to $399 at the moment - approx half price. I suspect uptake is slow as there is, in general, less interest in viruses and other organisms in the gut than for bacteria at the moment.
    I do however think the development of these technologies with access to the public is a huge step forward and over time, as the technology and knowledge stabilises, it will benefit many people.
     
  14. Hip

    Hip Senior Member

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    I think the difficulty is that you would probably have to publish a study for each pathogen–disease connection.

    For example, if we look at Dr John Chia's work of detecting enterovirus in the stomach tissue biopsies of ME/CFS patients, through his published studies, he has correlated the amount of enterovirus present in the tissues with the clinical severity of ME/CFS. See the image below which shows various degrees of enterovirus infection (brown stain) in stomach tissue samples taken from different ME/CFS patients and controls.

    Various degrees (A = high, D = none) of enterovirus VP1
    protein (brown stain) in ME/CFS patients' stomach tissues

    Chia 2008. Fig 1. Grading immunoperoxidase staining copy.png

    So if you get a positive result for Blastocystis hominis via Aperiomics or uBiome tests, it may not necessarily answer the question of whether you have enough Blasto present to cause disease.
     
    Last edited: Sep 5, 2018
  15. Garz

    Garz

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    Yes, I follow you, and actually, I think it reasonable to assume the same goes for any organism living in the gut.

    Things in the human body and particularly in complex systems like the gut do not happen in isolation. They are instead part of complex cascades of events, like a pyramid, but with many loops or cycles also.

    Therefore just finding an organism in the gut, even in abundance, doesn't necessarily mean its the thing at the top of the pyramid, ie the root cause. It may be a downstream effect of something else higher up the chain.

    In my opinion, all we can do is digest everything we can find on pathogen/disease connection for each of our candidates.
    Then look at the test results in the light of that and make our decision on how to move forward.
    it is not a deterministic world, but a probabilistic one.

    The problems become unmanageable when both the pathogen/ disease connection data is ambiguous and the test accuracy is also ambiguous and you are pretty much in the dark.

    Which is what set me down the path of at least bottoming out the test variable.
     
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  16. Garz

    Garz

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    by the way - Ubiome say Explorer plus can detect

    ·Stramenopiles like Blastocystis hominis

    ·amoeba like Entamoeba histolytica

    ·enterovirus such as Coxsakie virus B4

    I am in communication to get a little more info on the sensitivity if they have it
     
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  17. Hip

    Hip Senior Member

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    That would be interesting to hear about.

    It would also be interesting to know if they are able to quantify how much virus, bacteria, fungus and parasite is present. Some PCR pathogen tests, for example, only give you a yes/no answer: they tell you if the pathogen is present or not, but they do not tell you how much pathogen is there.

    Given that that the severity of any illness produced by a pathogen is likely to be related to how much of it is present, a quantitative result will be more useful.


    It is a shame that uBiome do not sell just a single gut test: their pricing for the Explorer is $399 for 4 tests (the 4 tests to be taken within 1 year). It would be nice if you could pay $100 for one test.

    EDIT: I meant to say "their pricing for the Explorer Plus is $399".
     
    Last edited: Sep 8, 2018
  18. Hip

    Hip Senior Member

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    I am not really sure if uBiome will be able to detect chronic infections with enteroviruses such as coxsackievirus B4. I am sure uBiome would be able to detect enterovirus during acute infections (the first few weeks of infection), when there is a lot of viral particles (virions) to be found in the stool.

    However, in chronic infections, enterovirus actually morphs into a completely different pathogenic entity, called a non-cytolytic enterovirus, which lives inside human cells as an intracellular infection, and produces few viral particles.

    So this means the virus may not be present in the stool, even though it may be chronically infecting the cells in the gut and stomach lining. This is why Dr Chia tests stomach lining tissue samples for enterovirus, because chronic enterovirus infections are mainly just found in the tissues.
     
  19. Garz

    Garz

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    ref Ubiome

    Yes, it's a quantitative test, I have done their standard explorer test ( gut bacteria only - not virus, fungi, or protozoans - but my understanding is its the same process) and that is how it presents the data. There is little or no human intervention the process happens on a chip.
    The machine multiplies up all DNA material in a sample(via PCR) then looks for the genetic fingerprint of the known organisms and reads how many matches for each organism it finds.
    If the fingerprint of the organism is known this is well-proven technology and pretty reliable.

    PCR can also detect ridiculously small amounts of genetic material, from the papers I have read its something in the order of 1 or 2 fragments in the entire sample. So, for instance, even if 1 in a million virus-infected cells were shedding into the digestive tract I would expect it to easily detect it.

    If it's of interest, maybe write to them they will give you access to a sample report that will make it clearer than I can explain here.

    regarding pricing - there are different tests and they package the tests in different ways so it can be confusing.

    1. there is a single explorer test available - or at least there was when I did it earlier this year - it was $89link to that one here https://ubiome.com/consumer/explorer/ (I should be on commission!)
    2. you can do a 5 site explorer if you would like to see what lurks on your dangly bits :)
    3. you can do a 4 or 5 time gut time-lapse kit that allows you to see how things are changing over time $199
    4. then there is smartgut - which is supposed to have more useful information for clinicians - but I saw only limited value over explorer
    5. then there is this new Explorer plus test - I have been discussing above and they have just recently launched - which is not only bacteria - but fungi, viruses, etc etc

    OK
     
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  20. Hip

    Hip Senior Member

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    Sorry, I meant to say the Explorer Plus in my above post about pricing: that's the one I'd like to take, to test for viruses, but unfortunately it does not seem to be available as a single test, just 4 tests for $399.
     

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