I was reading Dr Chamberlains Q&A, and he mentions the herxheimer reaction.Regarding rifabutin, there may have been some confusion early on about rifabutin vs. rifampin dosage. I clarified with Dr. Chamberlin recently, and he said it was generally 300 mg daily rifabutin, 600 mg daily of rifampin. Patients take one or the other. However, he also mentioned RedHill would sometimes use 450mg rifabutin, and they have done a lot of research on dosages. So definitely not 600mg rifabutin!
Typically, it's low level sepsis.
That's fever, tachycardia, etc. It's the same "side effect" you get from vaccines (some people). Even non-vaccines will do it (obviously, since AMAT does it).
Crohn was trying to vaccinate people with anti-dysentery serum, and he found it only reduced symptoms, induced remission in people who had a reaction, much like the herxheimer. Other GIs of the time (Hurst, for example) then tried the same thing using silver/mercury/even horse serum. Same results. Only a response following the "serum shock"...
There is also the possibility that the antibiotic is efficiently killing alot of microbes, thus rendering the resulting broken up bacteria to be exposed and taken up through the intestinal wall and into the blood stream, and inducing "serum shock/herxheimer etc", which "resets" the immune system much in the same way Dr Chamberlain says.
It is more than possible that, in addition to hypothesising AMAT therapy works by targeting MAP, it also is equally possible, I suppose, that it is the mass wave of antibiotics killing any and all microbes and thus exposing the body to such a wave of antigenic diversity induces the herxheimer reaction which itself is the "culprit" for the clinical response. Whilst at this point all cards are on the table and each horse has a shot at winning, I lean towards this idea simply because it ties in across a spectrum of diseases (even cancer). But in the end, it's only the scientist in me that cares about that, the patient in me just wants something to work!