Review: 'Through the Shadowlands’ describes Julie Rehmeyer's ME/CFS Odyssey
I should note at the outset that this review is based on an audio version of the galleys and the epilogue from the finished work. Julie Rehmeyer sent me the final version as a PDF, but for some reason my text to voice software (Kurzweil) had issues with it. I understand that it is...
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New Test can detect Among a Vast Range of Infections

Discussion in 'Other Health News and Research' started by SK2018, Jul 5, 2018.

  1. SK2018

    SK2018 SK

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    "2 people I know have already had this done last week still awaiting results"

    ARTICLE
    A genome sequencing test developed at UC San Francisco that can rapidly pinpoint the cause of a bacterial, viral, fungal or parasitic infection from among a huge range of possibilities is now available to help physicians nationwide diagnose mysterious cases of neurological infection in acutely ill patients.

    Scientists at UCSF have already used the test on a trial basis to diagnose a number of patients, including the well-known case of a 14-year-old boy who was near death with swelling in his brain. The boy had undergone months of unsuccessful attempts to identify the cause of his illness with conventional lab tests, expensive imaging technologies and invasive procedures, including a brain biopsy. By sequencing his cerebrospinal fluid (CSF), UCSF scientists found that he had a bacterial infection called leptospirosis, and he rapidly recovered after receiving targeted treatment with penicillin.

    The test has now been validated in UCSF’s Clinical Laboratory Improvement Amendments (CLIA)-licensed clinical microbiology laboratory and is approved for clinical use.

    Pinpointing Genomic Signatures of Pathogens
    Over the last year, UCSF physicians and researchers have examined the utility of the test using CSF collected from more than 200 patients enrolled in a nationwide study of eight hospitals, including three University of California medical centers. All of these patients suffered from acute neurological illnesses, including meningitis (inflammation of the coverings around the brain and spinal cord), encephalitis (inflammation of the brain), and myelitis (inflammation of the spinal cord).

    Doctors often have trouble figuring out why these tissues become inflamed, as these conditions can have many causes, including infection, cancer and autoimmune disease. This can lead to inappropriate treatment. For example, steroids and immunosuppressive agents that are commonly used to treat autoimmune diseases make it harder for the body to fight infection.

    The new sequencing test can help overcome this uncertainty by pinpointing the genomic signatures of a wide range of pathogens – including fungi, bacteria, viruses and parasites – all at once. If no pathogen is detected using this comprehensive test, doctors can also be more confident in pursuing other non-infectious causes of the illness. While the test does not always establish the cause of inflammation, it has the potential to speed up the diagnostic process significantly, and to spare patients from having to undergo a large number of diagnostic tests and invasive procedures.

    Starting with Neurological Illnesses
    The technique, known as metagenomic next-generation sequencing, or mNGS, is a “shotgun” approach in which all of the DNA and RNA in a clinical sample are sequenced at very high depth, with the generation of 10 to 20 million reads per sample. Currently, only testing of CSF for patients with neurological illnesses is available in the clinical lab. UCSF is actively working on making clinical mNGS testing available for other sample types including blood for patients with sepsis and lung fluid for patients with pneumonia. The testing process in the diagnostic laboratory takes about 72 hours, and results are generally available within one or two weeks.

    More information on the test and how to order it is available at the Center for Next-Gen Precision Diagnostics. The center serves as a reference lab to help doctors make diagnoses, but it does not provide consulting services directly to patients. The mNGS test must be ordered by a licensed provider authorized to order clinical laboratory tests and results are reported to the provider’s referring laboratory.

    FULL LINK
    https://www.ucsf.edu/news/2017/07/407736/next-gen-precision-diagnostics-now-available-ucsf
     
    Last edited: Jul 5, 2018
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  2. perrier

    perrier Senior Member

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    What did they send in? Blood, stool? urine?
     
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  3. SK2018

    SK2018 SK

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    CSF , but I think serum can be used also ,both are most comprehensive though.
     
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  4. Ema

    Ema Senior Member

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    It says CSF, with other specimen types coming soon.
     
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  5. overtheedge

    overtheedge Senior Member

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    Good stuff, the more gigantic tests the better since there are so many places CFS could be coming from, I'd be interested to hear how it works out for your friends, keep us posted
     
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  6. SK2018

    SK2018 SK

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    Agreed
     
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  7. Markus83

    Markus83

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    I think one should distinguish between acute and chronic conditions. In chronic conditions there is typically a much lower pathogen load and therefore you need much more sensitive methods (for example borrelia are normally not found in CSF, even in acute cases). I'm skeptic if this tests are of benefit for chronically ill people. But let's see what it will bring up in the future.
     
  8. junkcrap50

    junkcrap50 Senior Member

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    2 people with CFS/ME?

    Does Ron Davis know of this test?
     
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  9. SK2018

    SK2018 SK

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    one has a CFS diagnosis , other had undiagnosed neuro symptoms
     
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  10. junkcrap50

    junkcrap50 Senior Member

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    I hope you report back their test results if you can. I'm quite interested in this test.
     
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  11. Hip

    Hip Senior Member

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    It's great that this single test is able to cover all classes of pathogen — viral, bacteria, fungal and protozoan; I wonder what the cost is. Doctors can order the test for their patients here.

    However, I suspect this test will still not be able to detect the enteroviruses found in ME/CFS patients, unless an actual stomach or muscle tissue sample is provided (or brain tissue, but that's only usually possible in deceased patients).

    You do not find much enterovirus in the blood of ME/CFS patients, as in chronic form, this infection exists as an intracellular infection, mostly in the tissues.

    And Dr John Chia points out that in enterovirus infections, the cerebrospinal fluid is often negative for enterovirus. In this video presentation (at timecode 9:33), Dr Chia says that:
     
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  12. Sidny

    Sidny

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    If enterovirus is so difficult to detect in an acute setting and even less so in a chronic presentation I wonder how many other pathogens are equally difficult to detect in CSF.

    @SK2018 thanks for sharing this. Would you happen to have an idea on what the test costs?
     
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  13. Sidny

    Sidny

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    In the case multiple pathogens are detected in either acute or chronic infections does the test determine the levels of those microbes in the CSF as well or just identifies there presence?
     
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  14. Hip

    Hip Senior Member

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    Enterovirus is actually quite easy to detect in acute infections, because the bloodstream at the acute stage is full of virus (although you have to be quick, because the acute phase may be over in a week or so). It's only the chronic infections which are hard to detect, and the reason is because in chronic infections, enterovirus goes off and hides inside cells, in the body tissues.

    So unless you chop a bit of the patient's tissues out and check that tissues for infection (ie, perform a tissue biopsy), it's hard to get direct evidence of the infection in ME/CFS.

    In the past, enterovirus researchers used to take muscle tissue samples from ME/CFS patients, and these were found to contain enterovirus RNA, indicating a chronic enterovirus infection in the muscles.

    But such muscle biopsies are painful and leave a scar, and so are not ideal for routine clinical use. Dr John Chia's great innovation is that he realized that in ME/CFS, enterovirus also infects stomach tissues, and that it is much easier to take a stomach tissue biopsy than a muscle biopsy. So this stomach tissue biopsy is what Dr Chia uses in routine clinical use for enterovirus testing.


    Dr Chia is at pains to point out that unless researchers start testing the tissues for infection in ME/CFS, we are never going to make much progress in ME/CFS viral research.
     
    Last edited: Jul 9, 2018 at 6:05 AM
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  15. GlassHouse

    GlassHouse

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    I’m a CFS/ME patient with significant brain inflammation and an altered state of consciousness (delta (slowest) brain waves even while awake, which makes me very sleepy and confused all the time) and Dr Peterson sent my spinal fluid to UCSF to have this done.

    It came back positive for HHV-7 DNA in my spinal fluid.

    I don’t know if I’m allowed to upload the test results here since I think it’s pretty new. It was done by the DeRisi Lab.

    I’d originally asked for VirCapSeq-VERT, which is a very similar test but only for viruses, developed by Dr. Lipkin. My CSF is being sent there too and we’ll see if the HHV7 is confirmed.

    I’m not sure what to think. I don’t want to place too much hope on having a virus to chase and treat. The spinal fluid was also drawn a year ago and I’ve just been in limbo treatment wise (I see Dr Peterson and Dr Kaufman). I have small fiber neuropathy, sjogrens early antibodies, antibodies against my liver and against multiple receptors in my brain. So there’s autoimmune issues but I have many infections and there has always been concern about an active brain virus. So no one wants to suppress my immune system if there’s a brain virus. I understand this but I’m also frustrated because I’ve been sick 7 years (POTS for 12 years) and haven’t been on antivirals or IVIG yet.

    It’s going to be tricky if the UCSF test is positive and the Lipkin test is negative. And my blood has always been negative for HHV7. I’d love for this to be the answer to my brain inflammation, I just don’t know what to think right now.
     
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  16. Gingergrrl

    Gingergrrl Senior Member

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    I am always so happy when I see a post from you @GlassHouse and I know that you are fighting for your life. I agree completely with what you said above that you should not suppress your immune system, in spite of all the autoimmunity, because of the active infections and potential brain virus. I was confused though why something like low-dose IVIG (for immune deficiency) to strengthen your immune system to fight the viruses is not an option?
     
  17. Sidny

    Sidny

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    @GlassHouse Was HHV-7 the only pathogen detected in your CSF? And x2 on the question about IVIG. You're seeing two specialists and neither have recommended that as a treatment? It seems to really work miracles for many with chronic infections and/or autoimmunity.
     
  18. crypt0cu1t

    crypt0cu1t Twitter: @skagginwagon

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    @GlassHouse I'm with everyone else here, if you have all of those autoantibodies, I would definitely pursue IVIG. Especially since you have other chronic infections.
     
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