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Why is the CDC Trying to Block an Accurate Lyme Disease Test

Posted: Tue 18 Nov 2014 0:41
by phyfe
http://www.nakedcapitalism.com/2014/01/ ... -test.html
Why is the CDC Trying to Block an Accurate Lyme Disease Test?
Posted on January 16, 2014 by Yves Smith

Yves here. While this article may seem a bit far afield for this website, it illustrates how political considerations influence science and medicine, two fields we have been indoctrinated to view as relatively free of corporate and ideological influences.

By Bob Goodwin, an investor and medical device entrepreneur who lives in Mercer Island, Washington

A recent article in Medscape is titled New Lyme Culture Test Failed CDC Analysis. At first I took the article and paper at face value, and tried to dig into the errors of a chronic-Lyme disease researcher. The only errors I could discover were by the CDC, and they seem blatant. In the same article about the CDC paper was the explanation that they did not want tests that might lead to unnecessary antibiotic treatment. While it is understandable that the CDC would not want a bad test, why would they block a good test? Because it will cause people to get treated? The CDC is on record taking the position of the Infectious Disease Society of America on treatment of Lyme disease, but it seems odd for the CDC to be taking a position to kill this test, especially considering that two different university hospitals are currently doing independent reviews of the same test.

I wrote here last week that I was getting blocked on Wikipedia from providing details about the Lyme Wars because Wikipedia only wanted to present the mainstream view.

The two camps in the war have only one scientific disagreement that I can detect. The mainstream medicine’s view is that the Lyme bacteria is non-persistent if treated with a few weeks of antibiotics, and even if untreated, the infection should be considered cleared when the immune system is no longer fighting the bacteria. People can still be sick later, but this sickness is likely due an auto-immune reaction. The minority position is that the bacteria hides and burrows, changes forms and builds biofilm colonies that both make the bacteria resistant to antibiotics, but also invisible to the immune system.

For 20 years there has been no meaningful change in the treatment For Lyme disease or the scientific consensus due to the war. Contrast that with the HIV epidemic, and the pace of innovation by the exact same set of researchers and doctors, and yet the CDC estimates that 4 million people in the US may have been infected, and only 10% of those diagnosed.

A good Lyme test would go a large way to ending the wars, because at some point in the debate one side is right and the other is wrong. Eva Sapi is a researcher in at University of New Haven and has been treated with long term antibiotics for Lyme disease. She is firmly in the minority camp. She has done work in both the culturing of Lyme bacteria and the ability of Lyme bacteria to form biofilms.

Culturing bacteria is the gold standard, and has been in use for 100 years. A culture is a medium that allows a bacteria to reproduce. Given enough time, a small amount of bacteria can turn into a measurable amount of bacteria. And unlike PCR (DNA identification of the bacteria), culturing cannot detect dead bacteria that are lurking from a long extinguished infection.

Culturing Lyme bacteria has not worked in the past, and that part of the story is outside the scope of this post. There has been an attempt made about every decade, but they have proven faulty. What is different today is that there are microscopes now that can see the details of bacteria and microbiology is flourishing with new insights. And testing a test is very easy. Unless there is a war.

This is how a test of a test should work: Start with N known infected samples, and N known uninfected samples and send them blind to the lab. It is a commercial lab in Pennsylvania. The CDC does not have to use its own address to send samples to the lab. 10 days later the lab will return whether the sample of each blood was infected or not. Pretty simple?

There is even a gold standard on how to find known infected blood. If someone has a bulls-eye rash, they have Lyme disease. Extract blood and send to lab.

So two years after Eva’s paper comes out we hear the CDC say the test failed? The details are interesting.
First, the CDC never actually tested the test. They merely reviewed Eva Sapi’s paper and said that it must have failed, they even concluded “(the data) indicate that laboratory contamination was the probable source of the borrelial DNA found in the patient samples.”

Note that the paper is about a culture, and the criticism was about DNA. In fact the laboratory in question does provide a second DNA service on any successful culture, primarily to detect which of the three types of Lyme bacteria were found. The CDC made no statement about the accuracy of the cultures. But notice the tricky Medscape article title “New Lyme Culture Test Failed CDC Analysis.” Is it just my imagination, or did the CDC just broadcast to the scientific and medical community the impression that the test failed?

The DNA piece gets a little technical, and I might have gotten in over my head. Sapi’s test only sequenced 603 base pairs of the pyrG gene. That gene was selected because it is an “essential gene” which therefore is useful for identifying a genus, and useless for identifying an individual. And for testing, that is the properties you want. Another property of essential genes (I think this is right) is that mutation survival is poor. A genus tends to keep this gene intact.

The CDC paper first claimed that 44% of the positive results came from a European genus, and none of the tested people had recently traveled to Europe. The Sapi paper had produced the same result. But the CDC presumption was that the European genus did not exist in the US. The primary difference between the US and Europe in regard to Lyme disease is the tick population, and not the bacteria population. If you look at the geography of reported Lyme infection in the US it is similar to region of our main tick vector. But California also has confirmed Lyme cases, but different tick species. It seems more likely to me that the European genus was never isolated to Europe. Without a reliable culture test this cannot be known.

The second claim was that 80% of the DNA had exact matches with the DNA that Sapi used in her lab, and thus the CDC assumed cross contamination. There was no mention in the CDC article of what number of mutations should be expected in an essential gene, and I also didn’t see any mention that the verification tests were done at a medical testing company, not the lab that Eva used for her research, so I am not sure how the precise form of cross-contamination that was cited in the CDC paper was even possible.

With 2 universities already testing the culture, and the ability to independently test so simple, why is the CDC wading into research wars? In the words of Professor Durland Fish of Yale University, “This battle cannot be won on a scientific front. We need to mount a socio-political offensive; but we are out-numbered and out-gunned. We need reinforcements.”

Re: Why is the CDC Trying to Block an Accurate Lyme Disease

Posted: Wed 19 Nov 2014 18:28
by Henry
Might one assume that the test indeed was examined by 2 universities and was not found to be valid? Otherwise, ALS would have publicized the fact that their test was validated -- I assume. Might that have been the objective in the first place? Or, could it just be that they have something to hide? Under the circumstances do you think it is ethical for them to charge patients $500-$1,000 for a test that has not been validated ? How can any one with more than 3 functional brain cells defend such individuals?

And why do you assume that the ALS is an ACCURATE test when there is no independent evidence to indicate that is the case? Isn't that the main problem?

Re: Why is the CDC Trying to Block an Accurate Lyme Disease

Posted: Wed 19 Nov 2014 20:12
by phyfe
Henry wrote:Might one assume that the test indeed was examined by 2 universities and was not found to be valid? Otherwise, ALS would have publicized the fact that their test was validated -- I assume. Might that have been the objective in the first place? Or, could it just be that they have something to hide? Under the circumstances do you think it is ethical for them to charge patients $500-$1,000 for a test that has not been validated ? How can any one with more than 3 functional brain cells defend such individuals?

And why do you assume that the ALS is an ACCURATE test when there is no independent evidence to indicate that is the case? Isn't that the main problem?
Might one assume that Henry doesn't realize that the author of this piece is Bob Goodwin not Phyfe? :bonk:

Re: Why is the CDC Trying to Block an Accurate Lyme Disease

Posted: Wed 19 Nov 2014 21:25
by Henry
Yes, but you posted it. I assume you think it has some relevance? Why did you post it?

Re: Why is the CDC Trying to Block an Accurate Lyme Disease

Posted: Wed 19 Nov 2014 21:36
by phyfe
Because it oozes relevance! That's obvious. Oh! Was your question rhetorical?

Re: Why is the CDC Trying to Block an Accurate Lyme Disease

Posted: Wed 19 Nov 2014 21:47
by Henry
Then the questions that I asked are relevant as well. Do YOU think the CDC is trying to block an accurate Lyme disease test?

Re: Why is the CDC Trying to Block an Accurate Lyme Disease

Posted: Wed 19 Nov 2014 22:05
by duncan
What is relevant is whether there is merit to the author writing to the possibility, wouldn't you agree Henry?

There are certainly a few conceivable considerations swirling around such a possibility that might make for an interesting article, and may have factored into his decision. For instance, do any current or former CDC members have diagnostic patents in the works? Isn't it true that the lion's share of diagnostics being funded by the NIH/CDC reflect indirect testing, as in antibody testing? Would an effective culture test undermine the entire Lyme diagnostic industry as we know it today? Certainly none of these questions would mean necessarily the CDC would actually try to block an accurate test. But some may consider these to be fair questions, and who knows where such questions may lead one person vs another? And who knows what was in the author's mind?

It's not what we think Henry, it's what motivated the author, so maybe you may wish to reach out to him

Re: Why is the CDC Trying to Block an Accurate Lyme Disease

Posted: Thu 20 Nov 2014 0:33
by Henry
You live in a fantasy world, Duncan. By this date, any patents for the antibody based test used for the diagnosis of Lyme disease (ELISA and Western blot) have expired. So, there is little threat that the development of a new test based on culture will have an economic impact. Secondly, if any of the work related to the development of the ELISA and Western blot tests was funded by the NIH, all patent right belong to the institution -- not the principal investigator-- awarded the grant. The principal investigator is allowed to receive a small royalty (usually about 5-8%), but the bulk of the royalties go to the institution (the university of small business) where the work was done. Few people realize that NIH grants are -- by law-- awarded to institutions, not individuals. Congress in its "wisdom" devised these rules, decades ago when they thought this would be a good way to make research institutions self sufficient and cut down on the expense of funding so many research grants. However, things did not turn out that way. Marketing expenses are the major limiting factor in how much is to be realized in royalty income and universities are not very good at marketing. In all of my years as a scientific investigator, I have yet to see anyone "strike it rich" from any patent rights associated with their research. They would have a far better chance of getting rich by putting their money on a horse or buying a lottery ticket. So, don't waste your time spinning such a fantasy. It's just not going to happen.

As far as I can tell, none of the work done by Sapi et al on their new culture method was supported by an NIH grant. So, they don't have to play by the aforementioned rules. Once they get enough suckers to buy into their bogus method, they can really make a bundle and charge what the market will bear. Their biggest threat is that the method has not been validated or independently confirmed. Consequently, it is not likely to get wide spread use in the clinic -- nor should it.

ELISA and Western blots are generic type tests that can be used for a variety of purposes, not just for the diagnosis of Lyme disease. So, if a new culture test proves to be ideal for the diagnosis of Lyme disease, ELISAs and Western blots will continue to be used as a platform for other diagnostic tests. No threat from that point of view.

Re: Why is the CDC Trying to Block an Accurate Lyme Disease

Posted: Thu 20 Nov 2014 1:18
by duncan
Henry, how large would you estimate the Lyme diagnostic market to be, as of year-end 2013? And I'm not speaking to monies directly pertaining to patents alone, anymore than I am speaking solely to ELISA and Western Blots. I'm speaking running the gamut from B31 kit manufacturers, to C6 Peptide tests, to CSF exams, and everything in between. How much do companies like Imugen and Immunetics and IgeneX and SB pull in each year? WHAT'S THE TOTAL MARKET SIZE IN TERMS OF GROSS REVENUES GENERATED IN 2013 FOR ALL LYME DIAGNOSTICS?

How much do you imagine the Payphone industry realized annually before the advent of the cell phone? You recall payphones, don't you? Because the parallel is fairly evident to me. The cell phone was a paradigm shift and eclipsed a long-standing market for Payphone services. An affordable Lyme culture test, one that could apply equally to acute and late stage cases, could represent a similar dramatic recasting of the TBD diagnostic world.

We are talking about a potential game changer.

Moreover, we are not just speaking to old patents, but to recent ones. Patents whose dividends might never be realized with an effective Lyme culture alternative.

Henry, there is a lot at stake here, and to pretend otherwise is, um, well, if not fantasy, it's imo certainly not embracing economic realities.

Re: Why is the CDC Trying to Block an Accurate Lyme Disease

Posted: Thu 20 Nov 2014 14:06
by Henry
Sorry, I don't "buy" your argument. New technologies are always evolving and will continue to evolve, some of them developed by those who use currently available diagnostic procedures. I prefer numbers, rather than the use of blots and dots and spots, since they permit one to measure changes that may be significant in response to antibiotic therapy . Quantitative ELISAs have been developed, but they are too expensive, complex, and time consuming for ordinary lab tech to use for routine diagnosis.

I repeat -- you live in a fantasy world, filled with all sorts of imagined conspiracies and devious plots. As I said previously, the actions of Sapi et al. precipitated the difficulties that they now face. All this could have been avoided had they sought independent confirmation of their work and published the results thereof BEFORE putting their test on the market as though it were a proven and validated entity. Had they done so, their incompetency would have been discovered and handled in a quiet manner. Clearly, they were not interested in doing this and appear to be more interested in making money. I don't feel sorry for them in the least. Nothing they do can restore their credibility.

Case dismissed.............