The Integrity of Advanced Lab Services

The Integrity of Advanced Lab Services

Until early 2012 there was no reliable diagnostic test beyond what is mentioned above. However as of 8/1/2012, a blood culture boasting 99% accuracy (later adjusted to 94% based on comparison testing ) was developed with the assistance of Dr. Burrascano which is accurate in all cases unless there is contamination. The test is a blood culture produced and run by Advanced Lab Services (http://www.advanced-lab.com ) .

After 3 decades of a 2-tier testing system that fails to catch a minimum of 50% of those infected. Wouldn’t you think that the CDC and IDSA would enthusiastically support such a test?

Apparently that is too threatening for the people who would like to be seen as the “Gods of Lyme Disease”

So instead of support, last year CDC’s Dr Barbara Johnson has published a paper accusing Dr Sapi (consulting for Advanced Lab Services at the time) of having contaminated the cultures she wrote about in her published research with Borrelia strains from her own lab.

In fact the strains in question were not with Dr. Sapi, who works at the University of New Haven – they were over 200 miles away in Philadelphia, PA in a clean and high quality lab.

Since that time there have been many articles condemning  Advances Lab Services for the contamination in their lab in spite of the fact that there have been several scientific studies to prove that there is in fact no contamination at Advanced Lab Services, and actual tests to verify the integrity of the blood cultures.

On April 21, 2014, The following letter was published by Philip M. Tierno, Jr., PhD, Director of Clinical Microbiology and Immunology New York University School of Medicine (Outside Consultant to Advanced Labs).  Even as an outside consultant, Dr. Tierno has no reason to risk his reputation by lying about such an important test, not just for the US but for the world.

He writes,

“I have read with great disappointment several reports by the CDC, Fort Collins Group, spearheaded by Barbara Johnson, criticizing Advanced Laboratory’s culture technique results reported by Dr. Eva Sapi last year, as being “probably contaminated”.

 Worse than that are the numerous lay reporters and professional medical news media all jumping on this bandwagon without just cause.

On top of that, these journalists erroneously reported that contamination of cultures did occur when the CDC, in fact, did not say or prove that. None of these reporters have had the decency to investigate before casting stones.

I have personally become involved reviewing the great accomplishment of Advanced Laboratory’s development of a culture technique reported to have a high sensitivity (94%) which is more than double the CDCs supported assay techniques sensitivities.

In light of the high reported sensitivity of the culture assay one would think that the CDC should be involved in aiding and supplementing such procedures helping to perfect same (if they feel it lacking) for the public good instead of discarding it outright. That does not seem to ring right to me. Interestingly the CDC did not criticize the culture technique itself (which by the way is excellent in my review) instead they assert that they “cannot rule out” contamination of the reported results. Yet interestingly, if contamination was so rampant not one of the controls was so contaminated and yet they ignore this.

And in one report I saw that will be soon published, a supercomputer Blast genome of GenBank analysis disputes Johnson’s contamination speculation.

I have firsthand knowledge of Advanced Labs facilities, their personnel, and their analytic techniques, which in my professional opinion are excellent.

 

 

 

His first-hand knowledge is listed here in an interview published at http://examiner.com  by  Allentown Family Health Examiner, Theresa O’Brien, and spoke with Dr. Philip M. Tierno, Jr., clinical professor of pathology and microbiology at NYU Langone Medical Center

The pertinent part of the conversation is presented here:

 

 Q: Your opinion of the likelihood of laboratory contamination in the case of the Advanced Laboratory test for Lyme disease?

A: The CDC never said or showed that there was in fact contamination.

They just said they could not rule it out.

To even use the word as they did in another area of the paper “probable” — those are the strongest words that they used.

They never said in fact contaminated. This is not the first time that Sanjay Gupta will have to retract his words when he looks more carefully into this.

He’s done that with marijuana. Then he saw some of the patients, and did further investigation — that’s what made him turn around. I want him to do the same thing here: come to his own conclusion by visiting the lab.

I have visited the Advanced Laboratory Services lab, so I can speak first-hand. I wrote a paper back in 1996, “Methods comparison for diagnosis of Lyme disease” (Lab Med. 1996; 27:542-546).

I was contacted by a faculty associate of mine who said, “Hey, there’s a lab in Philadelphia that could use your help in a new technique in Lyme disease.” He gave them my name and we discussed things.

I was amazed that they had a culture. Culturing is very tough. You can take some body fluids or use tissue from the erythema migrans and try to culture Borrelia, but with very low frequency. I was curious what they did that I didn’t do.

I went down there to visit and speak with the lab administration. I went through their whole facility, and if I tell you their clean rooms are clean … I also saw firsthand the spirochetes in their cultures.

They have a very intricate culture setup.

It uses collagen, a whole host of things, that even though I used a similar medium, they modified this Kelly medium, and cultured for extended periods — one month, two months, three months, four months — and did complex subcultures.

I don’t think anybody really did that to the degree that these people have done, and they have perfected it.

[The first reason to believe there is no contamination in the Advanced Laboratory Services lab:]

I have seen their cultures, and they verify the presence of Borrelia in the specimen. Of the 2000 they have done, they have a 38 percent positivity rate. By the way, if there were contamination, it would be across the board, and should be evidenced even here.

 [They use something] called an immunostain. They have an antibody stain that glows under fluorescent microscopy.

Once that’s positive, they then take the material and do a PCR on it, to look at a certain segment (16S assay) of the of the genome of the bacteria, so that they can identify it as being a member of B. burgdorferi species.

Now all Borrelia, by the way — it doesn’t matter what the species is, have certain conserved signature inserts and deletions (CSIs) and conserved signature proteins (CSPs) that are indigenous to all Borrelia species, and are unique in all Borrelia species.

Some scientists have identified seven CSIs and 21 CSPs that are uniquely found in Lyme disease Borrelia.

Then there are areas where there may be some slight differences. So you look at some of these base pairs, you amplify it so you can see it better, and it’s positive or negative.

So you confirm the fact that this spirochete is indeed Borrelia. And that’s the process of identification.

Now the CDC comes out with a report using some methodology which shows according to their report that these might be contaminants — that all positive cultures, or most of them, might be contaminants.

If that’s the case, then therefore it’s an invalid test, according to them. Of course they’re just going to suggest that you have the B31 control reference strain present in all of the cultures.

If one wanted to be disingenuous, one could take segments that all Borrelia share — to show complete 100% identities — with a species of organism — and that’s basically what they did.

I read those reports from the CDC group in Fort Collins, Colorado, saying that Eve Sapi, that her work was probably contaminated.

What hurt me more was these lay reporters that don’t know diddly squat what they’re reading, and professional medical news media that are involved, saying that it’s in fact contaminated, when it was not in fact contaminated.

They suggested that the PCR they did cannot rule out contamination, and I will tell you how that was ruled out, by these reports that are going to be published, one has already been accepted in the Journal of Clinical Microbiology for May, and there is a second that may come out in June. And there are others.

[The second reason to believe there is no contamination in the Advanced Laboratory Services lab:]

What bothered me is these journalists reporting as a fait accompli that contamination did occur, when the CDC did not say that or prove it.

None of these reporters tried to investigate further. They just took the word of CDC.

I was amazed at that, and yet if contamination did occur — and it was rampant according to them — but not one control was positive whatsoever, that is totally not expected (by Occam’s razor alone).

If you’re running the system and you’ve got — controls that go with every specimen, so that is one thing that should send up a red flag — no controls were positive for what they call contamination.

Another thing — it’s just a colloquial thing that we have in the field if you’ve done enough cases — simple observations.

When you take a reference strain like B41 (from American Type Culture & Collection, the company that sells reference strains), that reference strain will grow in about two days in your control bin.

Yet the culture from the patient will grow in a week if you’re lucky, but it could be up to 16 weeks.

If you had contamination, that contamination would also grow quickly — in about two days, the time it takes the reference strain to grow. It’s a frame of reference that you have for the organism.

All the controls came out in two days — I think the longest was three. Microbiologists can buy any culture for reference and controls. That’s the second thing. The growth of the controls was rapid, two to three days, compared to weeks or months depending upon the individual test person.

 

 

[The third reason to believe there is no contamination in the Advanced Laboratory Services lab:]

Number three. If you were to do something where, of course the specimens are gone, but you do have some 16S — some genetic markers, some PCR — we have these in a bank called the GeneBank.

In other words, there is a genome center where you can compare things, it’s gene sequences in a gene bank. It’s in their computer, the data on the genetics. They were sequenced. You can do something called a BLAST [Basic Local Alignment Search Tool].

It’s something that you use to compare your current findings with something stored in the GeneBank. You’re taking certain gene sequences.

If you do a blast comparison with the GeneBank, for this B31 strain — this is an ATC&C strain, you have that in the GeneBank — if I run a sequence and I want to compare it to the GeneBank, I can do that.

Let’s say my sequence is ABFK — of course, it’s more than that — and the sequences I get are ABFO, then that’s not identical. Or ABGHI, that’s not identical. So you can take your control and see what the homology is. The CDC reported 100% homology. But they did a method where they’re taking a certain number of base pairs.

Remember what I said about the Borrelia species have in common 82 different signature proteins, and other inserts and deletions? Well, that occurs in all Borrelia.

If I look at that subset, I get 100% homology, not only with the control, but if I ran any Borrelia, I would get that same set. The CDC says this shows 100% homology, but the BLAST analyses did not show that. It did not support 100% homology.

Johnson alleges that 48 of the 51 Sapi isolates with a sequencing match perfectly the CDC GeneBank haplotypes, but when you ran a BLAST taking the actual GeneBank sequences and comparing them to see what the degree of likeness is, they did not get (on this and a second analysis) 100% likeness.

They got 93%, 96% [which is what you’d expect from similar, but not identical, strains].

My point is, if there’s a genetic difference in the sequences you’re looking at, then it’s not identical.

Then there was a second BLAST study done. Same results: non-identity. When you fact-check the assertions of contamination of patient specimen, they were not substantiated.
[The fourth reason to believe there is no contamination in the Advanced Laboratory Services lab:]

The fourth thing was that the CDC claimed that one of the strains that the Advanced Labs were using was a B. garinii — it an ATC&C strain that’s also used as a control.

They claimed that Advanced Labs detected a B. garinii in some of the sequences, and then they said it shows that there’s contamination, because B. garinii is never found in North America — but it turns out that CDC gave in on that point.

They decided that some of the reports that came out against their comment are correct.

That species has been found even in birds in the US and Mexico, so they concede that yes, there is that organism here. There is a commonality.

Bottom line, all of the ATC&C strains that were tested and matched with a BLAST, showed that not one was 100% matches to 51 patient samples tested.

All these people did with the BLAST was to show the difference — they’re not identifying with their technique, as it is not meant to do that — they’re only showing that the strains are different.

If you say 100%, that’s a pretty strong statement. I can do a sequence where I do any Borrelia and get 100% positive, if I look at a certain segment (high conserved) that is common to all of them.

Many laboratories and physicians are intimidated by pressure from the CDC regarding the types of tests they perform for patients.

Many laboratories and physicians

from the CDC regarding the types of tests they perform for patients.

Many laboratories and physicians are intimidated by pressure from the CDC regarding the types of tests they perform for patients. Photo by Photo by Getty Images/Getty Images

 

Q: S iCDC, until recently headed by Kathleen Sebelius, advocates a two-tier test for Lyme disease that may produce false negatives for as many as half of Lyme patients.

The CDC, until recently headed by Kathleen Sebelius, advocates a two-tier test for Lyme disease that may produce false negatives for as many as half of Lyme patients.

 

Q: Your view of the appropriate type of testing for Lyme disease (enzyme immunoassays, immunoblots, serum sample cultivation, etc.)?

A: Now the sensitivity of the Advanced Labs test is 94%. The sensitivity of the two-tier testing recommended by CDC is 50%. So you’re missing half or maybe more of the cases. Look at the agony of these people. People send me letters and say,

“My daughter is dying.” I make recommendations that physicians check out that lab — but now they’ve stopped doing cultures.

It’s such a huge ramification that this one paper by the CDC is having. I don’t know how it actually got past review.

Well, I guess everybody’s afraid of this Fort Collins group, headed by Barbara Johnson. We used to think that if you treat with two weeks, maybe a month of therapy, that should be enough.

One of the things that came out of this work by Advanced Labs is that you have to treat for longer periods, even months. We used to think two or four weeks was long enough.

I think unfortunately when you hurt these people who are looking for help, and you prevent them from getting the proper therapy, because the tools they’re using do not show any active disease.

It’s shocking to me what’s going on. Another thing the CDC has been in print with — they used to quote statistics of 30,000 reported cases of Lyme each year.

The Advanced Labs spoke with some of the CDC people other than the Fort Collins group, and they said it’s likely ten times higher. Advanced Labs said it’s 300,000 cases per year, minimum. Now the CDC decided yes, it’s true: the figure should be 300,000. They reversed without an apology, just as they did with the B. garinii statement.

Even if they want to allow a change in diagnostic policy — there is another company, it’s a genetic company — that suggests two or three of the ten bands, bring down the number you need for the IgG test from five of ten to two or three of five — they should do that immediately.

But the Advanced Labs test is excellent to confirm active or chronic infection. In microbiology, there is one gold standard: the smoking gun is a live organism that is isolated from a patient. Serology is usually a retrospective look. It means at some point you were exposed. You don’t know if you have the disease currently, or whether you’re in the end phase of it, or whether it was in the past.

You would think that the CDC would develop their own culture system, or work to improve the Advanced Labs culture method, rather than throwing stones at it. This is an agency that has the task of protecting the health of America.

They shouldn’t knock a system that can help toward that goal — and even if they felt it was in need of fixing, then they should help fix it. When I see things like the current situation, it is just frustrating, and that bothers me.

During [the] toxic shock [controversy], the manufacturers called the dean of NYU — tampon manufacturers got an NYU alumnus who worked at the company to call NYU — and said that NYU had a researcher who was causing trouble.

I was checked out by numerous administrators. They tried to apply pressure to stop my toxic shock research. That’s the length that people go to. They didn’t pursue that area — nothing happened — because my three superiors said, “He’s an upstanding faculty member,” but believe me, boards of trustees of universities can be affected.

This research has been tightly controlled by the same lead IDSA Lyme guidelines authors for the last two decades. Collectively, their university labs have received over $130 million dollars in government grants since 1990.

Over half of these grants have gone to only two universities, New York Medical College and Yale, and a disproportionate amount of the grants have been used to support these researchers’ personal interests in tick-borne disease vaccines and tests. For example, New York Medical College researchers alone have founded 5 test/vaccine companies in the last few years.

For further reading go to http://www.advanced-lab.com/resources.php, and look at the Publications listed there.

Also of interest is: http://beforeitsnews.com/health/2014/04/more-on-cdc-testing-and-advanced-laboratory-lyme-disease-culture-test-2532212.html?currentSplittedPage=0

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4 Responses to The Integrity of Advanced Lab Services

  1. Pingback: Best Test for Diagnosing Lyme | Jenna's Lyme Blog

  2. sou do brasil gostaria de fazer o teste p lyme em minha filha como fazer

    • Jenna Seaver says:

      Translation: “I’m from Brazil would like to take the test p lyme my daughter how to make”

      Response: Advanced Lab Services in only available in the US so for your daughter to take the test, she needs a US doctor (preferably not from NY) to order the test, draw the blood and send the blood to the lab according to explicit instructions.

      Translation to Spanish: “Laboratorio de Servicios Avanzados en sólo está disponible en los EE.UU. por lo que para su hija a tomar la prueba, ella necesita un médico estadounidense (preferiblemente no de NY) para ordenar la prueba, extraerá sangre y envía la sangre al laboratorio de acuerdo con las instrucciones explícitas.”

  3. Pingback: Borrelia Miyamotoi Is Here -- We Call It Lyme | Jenna's Lyme Blog

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