Long term antibiotics are and have been used to treat a wide range of medical disorders. It seems the use of long term antibiotic therapy is acceptable for other conditions, except Lyme disease.
Rheumatoid arthritis: Doxycyline and Minocycline have been shown to be effective and used as maintenance drugs. Plaquenil, an anti-malarial antimicrobial drug which is frequently used for the treatment of Lyme disease, is also used long term in the treatment of rheumatoid arthritis and systemic lupus erythematosis.
Periodontal disease: Periostat- a formulation of Doxyclyine has been approved for long term use.
Acne: Doxycycline and Minocycline are frequently used for months and years. Acne, unlike Lyme disease, is a cosmetic disease, not a disabling or life threatening disease. Other antibiotics like Bactrim have also been used.
Chronic prostatitis: Cipro and similar antibiotics are frequently prescribed for 90 days and longer.
Urinary tract prophylaxis: Women with recurrent urinary tract infections have been treated with long term antibiotics to prevent recurrences.
Chronic otitis media- ear infections: Long term antibiotics have frequently been prescribed in children to prevent recurrent ear infections. Although this practice has been discouraged in recent years, current peer reviewed studies have again supported the benefits of this therapy.
Chrohn's disease: Antibiotic therapy, at times long term with Cipro and at time Flagyl, have proved to be beneficial, and safer than other recommended therapies.
Rheumatic fever: For patient with recurrent Rheumatic fever related to Steptoccocal infection, the use of Penicillin orally or by injection, on an indefinite basis has been recommended.
PANDAS: Pediatric Autoimmune Neurological Disorder: This disorder associated with OCD disorder and tics, especially in children, has been treated with long term antibiotics such as Penicillin. Although there may be controversy regarding this therapy, no psychiatrist has had medical board sanctions for prescribing this therapy.
Chronic osteomyelitis- bone infection and diabetic ulcers: Frequently treated with long term or indefinite antibiotic therapy.
Chronic constipation: Gastroenterologists frequently prescribe indefinite Erythromycin for the management of refractory constipation.
Herpes simplex: Valtrex, an anti-viral medicine is frequently prescribed indefinitely for this benign condition.
Toe nail fungus: Lamisil, a potent and potentially toxic antifungal, is routinely prescribed for 90 days for this cosmetic condition.
Q fever: May be a chronic bacterial infection requiring 4 years of antibiotic therapy.
Whipple's disease: Another chronic bacterial infection which routinely requires years of antibiotics and may be fatal.
TB: 6 months of a potent antibiotic, toxic to the liver, is frequently prescribed to prevent TB after exposure.
Active TB: 6 to 9 months of triple antibiotic therapy is required. In the recent past therapy was frequently extended for 2 years.
Coronary heart disease: Associated with elevated C-reactive protein. This is a circulating protein associated with activation of the complement cascade. This is an effector mechanism of the innate and acquired immune system responses. Chlamydia pneumonia, a chronic intracellular bacteria has been found in blood vessel plaques. Long term antibiotics have been studied for this disease.
Malaria: For persons in endemic areas long term antimalarials is frequently employed.
MS and other autoimmune neurodegerative disoders: The use of long term Minocycline and other antibiotics is an area of active research.
This list is by no means comprehensive. But is sure demonstrates the existence of a double standard.