These protocols apply to Mycoplasmas, C. pneumonia, Borrelia (Lyme), Streptococcus pneumonia L-forms, and persistent CWD L-form bacteria of many other species. Physicians may be reluctant to use the as advocated by Dr. Brown for any of several psychological or economic reasons:
• The Herxheimer reaction may be mistaken for an allergic reaction to the antibiotic and the patient is ordered to stop using the protocol, which is not restarted with antioxidant vitamins and anti-inflammatory complement drugs; or the patient loses confidence in the doctor and stops the treatment during the first microbe die off.
• Appropriate non-pill forms of the antibiotic are not convenient to administer and pill forms are likely to result gut dysbiosis if probiotics are not ordered as part of the treatment; really severe cases require IV over weeks.
• Antibiotics in the gut promote the evolution of drug-resistant microbes by exchange of plasmids; shots are a better alternative, but patient must visit doctor’s office many times for these.
• Physicians are not familiar with the appropriate complex combined/sequential antibiotic administration protocols for long-term treatment; some practitioner resistance to Trevor Marshall’s protocol due to learning curve.
• Many costly tests needed along the way to measure microbe and immune response to gauge progress in long-term polymicrobial reduction.
• Many physicians have not had the training to interpret the test results correctly and authoritatively; many tests have high false negative results or are equivocal in their results, especially Lyme disease tests.
• Specific diagnostic tests for mycoplasma infection and complex immune assays are not on approved labs’ authorized lists for HMOs and insurance coverage. They are costly, and administrators have no way for patients to pay for or share the cost. Patients may be unwilling to pay for them.
• Many patients are not disciplined enough to stay the course of a sustained treatment lasting months or years, even if it is clearly explained to be beneficial; but some are highly motivated and succeed.
• Tetracycline-type antibiotics are not promoted by the drug companies compared to high-profit NSAIDs and DMARDs, but they should be used together for maximum benefit; Along with antioxidant vitamins especially A, C, E, coconut oil, red palm oil, palm kernel oil, and omega 3 oils.
• Doctors may be reluctant to use antibiotics because they have been indiscriminately over-prescribed in the past; doctrine calls for minimal use of antibiotics instead of combinations with maximum microbe sensitivities.
• When combined antibiotics are necessary, the treatment may be hard to understand in a time-varying protocol; see: Marshall protocol.
• Some rheumatologists cling steadfastly to an approved list of drugs and treatments, to the exclusion of any alternatives; they do not like it when antibiotics reveal latent lupus or other infections that are bad news and hard to treat.
• Laws still say doctors must use CDC (Lyme) study criteria; these minimize false positives by maximizing false negatives, but these criteria fail to work at all as clinical tests. Borrelia burgdorferi are hard to kill.
• The patient may get worse initially before getting better because the Herxheimer reaction is not understood or anticipated, or not explained to the patient, who just might use the reaction as an excuse to bring legal action.
• Managed care works adversely against doctors who prescribe long-term treatment. Cost controllers try to find reasons to deny any treatment or specialist referral that does not bring short-term results; (Long time = higher cost)
• Clinicians may prefer the actual success in the short term with anti inflammatory prescription drugs. Even if a relapse may occur. Diagnosis of polyinfections and treatment is harder than just treating the symptoms. A long-term treatment that eventually succeeds has short-term immune flares that need special treatments. Once the symptoms stop, the patient loses interest in further treatment.
• Medical boards and insurance companies have punished doctors who have prescribed long-term antibiotic protocols for Lyme, RA, and other diseases. Only a few States have passed doctors’ protection acts; 
• Doctors are unable to provide the nutritional advice required to restore the patient’s immune system to proper balance in addition to the antibiotic therapy.
 RA patients should show their doctors Appendix II of the book, Rheumatoid Arthritis: The Infection Connection, written by a medical doctor explaining the details of Dr. Brown’s antibiotic treatment. Alternatively see the more detailed protocol description on the Road Back Foundation website