Reprinted with the kind permission of Naked Capitalism.
By Bob Goodwin
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.” (here)