The NY Times has an interesting series of articles on Lyme diesease called "Deconstructing Lyme disease" which you can read here.

I only just started reading but I've already learned new things. The first article, "Focus on the co-infections" opened my eyes to the fact that ticks carry multiple pathogens, including Lyme disease, which can infect someone at the same time and be hard to detect and diagnose. So treatment for Lyme can seem ineffective and cause confusion because it is actually these other pathogens that are continuing to cause symptoms, some of which cause symptoms which mimic those of Lyme disease. Antibiotics work on bacteria like the one responsible for Lyme disease, but do nothing about other pathogens like viruses or parasites which can also infect you from a tick bite.