As JackieCalifornia notes, the ILADS site has a lot of information.
There is content there devoted to the 2009 hearing regarding the IDSA guidelines. Just skimming for the information you want, about Lyme being able to hide in the body even after treatment, see here:
http://www.ilads.org/lyme_disease/written_testimony/6%20Stricker-Challenge%20to%20Implausibility.pdf
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Lists of letters, presentations, and videos can be found at the below:
http://www.ilads.org/lyme_disease/lyme_testimony.html
http://www.ilads.org/lyme_disease/lyme_slides.html
http://www.ilads.org/lyme_disease/lyme_idsavideo2.html
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Based on my own personal experience, I believe that Lyme can be dormant, causing only minimal symptoms, until stress or other illness enables it to become active.
Good luck with your doctor & more good wishes.
Greetings, and welcome home. Sorry to hear your symptoms have returned. It's possible you picked up something in Iraq, not necessarily Lyme but some other bug, or exposure to an environmental toxin.
In my reading, CSF does not usually show evidence of Lyme, even if you have Lyme.
Which Lyme tests did you take recently? Which labs were they sent to? Igenex seems to be a favorite of the LLMDs these days. (LLMD = Lyme Literate MD, that is, one who takes a broader view of Lyme and its coinfections.)
Were you tested for co-infections? Babesiosis, bartonella, ehrlichiosis, etc.
I understand that taking a short course of antibiotics can cause negative Lyme tests to convert to positive, by stimulating your immune system to produce detectable antibodies and thus a positive Lyme test.
You might check ILADS [dot] org, website of the International Lyme and Associated Diseases Society, which is the best known LLMD organization. They have much good information on current trends in diagnosis and treatment posted on their website. That can bring you up to date on recent developments in diagnosis and treatment.
I am beginning to understand that Lyme can simply lie dormant, even after treatment, due to its habit of hiding in cysts in the body when the environment is adverse (e.g., when antibiotics are present.) There is a recent book which outlines some of this in the process of telling a good story, called 'Cure Unknown' by Pamela Weintraub, now in paperback. Even if you're not up for a lot of reading, it's a riveting tale of the diagnosis and treatment of Lyme and of real people dealing with it as we are too.
To answer your specific question, yes, the bacteria can lie dormant, and when your immune system is down, rise up again. I am not medically trained, so this information is simply what I have learned from reading here and there. I think you are wise to consider the possibility.
Thank you for your service to our country. Best wishes for your return to health -- let us know if we can help here.