"Approximately 10 to 20% of patients treated for Lyme disease with a recommended 2–4 week course of antibiotics will have lingering symptoms of fatigue, pain, or joint and muscle aches. In some cases, these can last for more than 6 months. Although often called 'chronic Lyme disease,' this condition is properly known as 'Post-treatment Lyme Disease Syndrome' (PTLDS).
The exact cause of PTLDS is not yet known. Most medical experts believe that the lingering symptoms are the result of residual damage to tissues and the immune system that occurred during the infection. Similar complications and 'auto–immune' responses are known to occur following other infections . . .
Regardless of the cause of PTLDS, studies have not shown that patients who received prolonged courses of antibiotics do better in the long run than patients treated with placebo."
That's fair, but keep in mind that the CDC this year revised their estimates of people with Lyme 10x. This suggests that they've had a strained understanding of the problem.
"Approximately 10 to 20% of patients treated for Lyme disease with a recommended 2–4 week course of antibiotics will have lingering symptoms of fatigue, pain, or joint and muscle aches. In some cases, these can last for more than 6 months. Although often called 'chronic Lyme disease,' this condition is properly known as 'Post-treatment Lyme Disease Syndrome' (PTLDS).
The exact cause of PTLDS is not yet known. Most medical experts believe that the lingering symptoms are the result of residual damage to tissues and the immune system that occurred during the infection. Similar complications and 'auto–immune' responses are known to occur following other infections . . .
Regardless of the cause of PTLDS, studies have not shown that patients who received prolonged courses of antibiotics do better in the long run than patients treated with placebo."
http://www.cdc.gov/lyme/postLDS/index.html