Welcome to MedHelp Lyme --
Yes, indeed, there is a war raging between docs who think Lyme is all quackery and silliness vs docs who take it seriously and know it need particular diagnosis approaches and treatment.
In recent decades, we as a society have become conditioned to the medical world having everything tidy and ship-shape, with no disagreements or problems in the medical world. Welllll, Mother Nature doesn't play by those rules, and here comes Lyme and other infections that many docs simply are not aware of.
I had Lyme and babesiosis, and I was tested by IGeneX as well as other labs' tests, whichever ones my Lyme doc believed to be the most accurate and sensitive. I really don't know why there is so much hating going on about IGeneX, because it really has a novel idea: instead of measuring your immune system's reaction to a Lyme infection (as Western blot and ELISA tests do), the IGeneX test looks for Lyme DNA in your blood. Why does this matter? Because Lyme bacteria are ready and able to suppress your immune system and keep it from killing the Lyme bacteria ... and at the same time, making it look like you don't have Lyme because your immune system is not making antibodies against the Lyme.
Bottom line: The W.blot/ELISA tests are reliable if they are positive for Lyme, but if they are negative, they may be wrong because of Lyme's suppressive abilities. That's one big reason Lyme docs often use IGeneX testing: it's more reliable and not subject to alteration by the Lyme bacteria.
NonLLMDs have not accepted this view, because the old docs who first 'discovered' Lyme a few decades ago are stuck what their initial view of Lyme were: rare, hard to get, and easy to cure. It turns out that Lyme has a bag of tricks the old docs didn't discover, but the old docs (and their followers) are still around clinging to their now outmoded concepts. We as a society are used to people making new things (including new meds and treatments), but sometimes humans get in the way too, and that has happened big time with Lyme.
My Lyme doc used both PCR testing *and* W.blot and ELISA -- he liked to get a lot of data, and if one knows the limitations of a particular test, then it can be taken into account. They aren't bad tests: they are just not as good as they could be. So we bolster the options and get as many different views as possible, to keeping hunting down and killing the bacteria.
If your docs don't like PCR, then I'm sorry to say that they may not be very up to date on other aspects of Lyme etc. Think about getting a second opinion. You don't need to tell your current docs you are doing that, but it's what it would do -- it's your health, after all. Take care, let us know how you do, okay?
IgeneX is just a more specialized/sensitive test for Lyme. Not everyone tests positive on it.