Chronic" Lyme diseaseThe term "chronic" (Lyme disease) or "post-Lyme disease syndrome" is not recognized by mainstream medicine, and most medical authorities advise against long-term antibiotic treatment for chronic Lyme disease. The term is often applied to several different sets of patients. One usage refers to people suffering from the symptoms of untreated and disseminated late-stage Lyme disease: arthritis, peripheral neuropathy and/or encephalomyelitis. The term is also applied to people who have had the disease in the past and some symptoms remain after antibiotic treatment, which is also called post-Lyme disease syndrome. A third and controversial use of the term applies to patients with nonspecific symptoms, such as fatigue, who show no objective evidence they have been infected with Lyme disease in the past, since the standard diagnostic tests for infection are negative.
Up to one third of Lyme disease patients who have completed a course of antibiotic treatment continue to have symptoms, such as severe fatigue, sleep disturbance, unconsciousness, and cognitive difficulties, with these symptoms being severe in about 2% of cases. While it is undisputed these patients can have severe symptoms, the cause and appropriate treatment is controversial. The symptoms may represent "for all intents and purposes" fibromyalgia or chronic fatigue syndrome. A few doctors attribute these symptoms to persistent infection with Borrelia, or coinfections with other tick-borne infections, such as Ehrlichia and Babesia. Other doctors believe that the initial infection may cause an autoimmune reaction that continues to cause serious symptoms even after the bacteria have been eliminated by antibiotics.
A review looked at several animal studies that found persistence of live but disabled spirochetes following treatment of B. burgdorferi infection with antibiotics. The authors noted that none of the lingering spirochetes were associated with inflamed tissues and criticized the studies for not considering adequately the different pharmacodynamics and pharmacokinetics of the antibiotics used to treat the animals in the trials versus what would be expected to be used to treat humans. The authors concluded, "There is no scientific evidence to support the hypothesis that such spirochetes, should they exist in humans, are the cause of post-Lyme disease syndrome." 
An advocacy group called the International Lyme And Associated Diseases Society (ILADS) argues the persistence of B. burgdorferi may be responsible for manifestations of late Lyme disease symptoms. It has questioned the generalizability and reliability of some of the above trials and the reliability of the current diagnostic tests. Major US medical authorities, including the Infectious Diseases Society of America, the American Academy of Neurology, and the National Institutes of Health, have stated there is no convincing evidence that Borrelia is involved in the various symptoms classed as chronic Lyme disease, and advise against long-term antibiotic treatment as ineffective and possibly harmful. Prolonged antibiotic therapy presents significant risks and can have dangerous side effects. One death has been reported from complications of a 27-month course of intravenous antibiotics for an unsubstantiated diagnosis of chronic Lyme disease.
Antibiotic treatment is the central pillar in the management of Lyme disease. However, in the late stages of borreliosis, symptoms may persist despite extensive and repeated antibiotic treatment. Although these chronic symptoms are possibly due to either autoimmunity or residual bacteria (see immunological studies below), no Borrelia DNA can usually be detected in the joints after antibiotic treatment, which suggests the arthritis may continue, even after the bacteria have been killed. Lyme arthritis that persists after antibiotic treatment may be treated with hydroxychloroquine or methotrexate. Corticosteroid injections into the affected joint are not recommended for any stage of Lyme arthritis.
Patients with chronic neuropathic pain responded well to gabapentin monotherapy with residual pain after intravenous ceftriaxone treatment in a pilot study. Some antibiotics may have a dual effect on Lyme disease, since minocycline and doxycycline have anti-inflammatory effects in addition to their antibiotic actions, including anti-inflammatory effects specific to the inflammation caused by Lyme disease. Indeed, minocycline has been suggested for other neurodegenerative and inflammatory disorders, such as multiple sclerosis, Parkinson's disease, Huntington's disease, rheumatoid arthritis and ALS.