Wikipedia has an article on Lyme disease controversy now, expanded from the small section in the main Lyme disease article. In the section of the controversy article called Two standards of care, they compare various points of differentiation in the way the Infectious Diseases Society of America (IDSA) and the International Lyme and Associated Diseases Society (ILADS) view the diagnosis and treatment of Lyme disease. I think the following comparison on its own helps demonstrate why some people have issues with this:

Primary concern regarding misdiagnosis:

(ILADS): The under-diagnosis of Lyme may lead to untreated chronic, persistent infection resulting in severe disability and possibly even death (see Lyme disease#Prognosis).

(IDSA): The over-diagnosis of Lyme may lead to the unnecessary use of antibiotics resulting in side effects (most commonly nausea). Where intravenous therapy is used, there are more serious risks including central line infection, which has resulted in the death of one patient being treated for chronic Lyme disease. There are also concerns about the cost of antibiotic treatment.

Nausea is apparently the primary concern for "over-diagnosis?" I'll take an upset tummy over lifelong, crippling illness, thanks. IV therapy is extremely rare in treatment of Lyme disease, and typically only used when verified that the subject has had Lyme disease infection for years. (An old friend of mmsword's family was an early case in the 1980s; it took them around four years to finally diagnose him, at which point he was given IV antibiotics and has been on full disability ever since.) Note that the one patient reported to have died from IV antibiotic treatment (and no other deaths due to Lyme disease related antibiotics treatment reported) was on a 27 month course of IV antibiotics. This is extremely atypical.

One interesting thing is that it seems the IDSA has redefined Lyme disease to be infection by Borrelia burgdorferi. This is certainly the primary concern Lyme disease, but Lyme disease was named for the epidemic which arose in Lyme, Connecticut in the 1970s. At the time, Lyme disease was found to be transmitted by ticks and was related to a complex variety of symptoms. Ticks which carry the burgdorferi spirochete are known to carry a number of co-infections, and Lyme disease itself very clearly can have long-term or even permanent effects on the body, whether or not the Bb bacteria is still present -- a fact which because of the very nature of spirochetes, is not always empirically verifiable.

There is a very interesting quote in the IDSA's FAQ About Lyme Disease:

In more than 20 years there has not been one scientifically valid study published in the peer-reviewed medical literature that proves that the benefit of long-term antibiotic treatment outweighs the risk.

Interesting that they word it this way, since as far as I can find, there has also not been one scientifically valid study published in peer-reviewed medical literature that proves that the risk of long-term antibiotic treatment outweighs the benefit.

More later..