Eric- I think your questions and observations are very thoughtfully made, but I also think you haven't delved deeply into the Cpn literature yet. )Other Chlamydia's also have persistence due to EB's and cryptic conversion for example.
Dr A (interview on www.CPn Help.org
) mentions the efflux pump issue in his interview:
Dr. A- Not only the tissue penetration, but also both the organism and your cells have active efflux pumping mechanisms to pump out the antibiotic. You have to work against these natural mechanisms to keep adequate concentrations in the cells. Rifamcin tends to inhibit these efflux pumps. I also use another drug, Quercetin, a bioflavonoid that also acts as a cell efflux inhibiter. It works on a different efflux pump than Rifamcin. It’s, also active against Chlamydia on it’s own.
In other words, there is quite specific knowledge about some of these things for Cpn, and also some very careful, full, research on what makes for sucsessful treatment. The protocols are general, but Stratton, et al have ways of subjecting infections to much more sophisticated testing than is yet available, which can not only measure the multiple phases of a Cpn infection, but also suceptibility testing for the most sensitive agent, which can vary from person to person. The patent materials are particularly detailed on this.
Also see (again on the www.CPn Help.org
site) the interview with Dr. Powell who has used INH in recalcitrant infections with great sucsess, based on the findings in the original Vanderbilt work that this agent cleared infections from macrophages more effectively than other combinations.
I'm emphasizing this because I think there is much more known, especially about Cpn, that doesn't require a lot of speculation. The science that's actually out there has not been listened to much. Only a few clinicians have enough hands-on experience to even look at adapting the protocol to different patient needs, or what to are reasonable next-step dosage or med changes with challenging cases (although, aren't we all!).