According to chronic Lyme disease treatment protocols, Doctors generally diagnosed the Lyme disease patient with certain antibiotics, including Doxycycline (Vibramycin), Amoxicillin (Amoxil) and Cefuroxime Axetil (Ceftin). These biotics effectively treat the patients. However, in many cases, it has been found that antibiotics are not capable of eliminating Lyme disease from the root.