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Lyme disease can sometimes be challenging to diagnose. If a person has removed a tick from his or her skin, had a known tick bite, and lives in or has visited an area of the country where Lyme disease is most prevalent, then the timing of the potential infection can be closely estimated.
However, the tick is about the size of the head of a pin and the bite may not be noticed. Not everyone will develop the characteristic rash,and the symptoms that a person does have may be nonspecific and flu-like in the early stages, with joint pain that develops into chronic arthritis and/or with neurological symptoms that appear months later.
A blood test for antibodies to the bacteria is the preferred test for the diagnosis of Lyme disease.
However, if a person has central nervous system symptoms, such as meningitis, then IgM, IgG, and western blot testing may sometimes be performed on cerebrospinal fluid (CSF).
In special cases, polymerase chain reaction (PCR) testing may be performed on a sample because it is a more sensitive way of detecting an infection with Borrelia. However, this is not an FDA cleared or approved test method and it is not widely available.
The CDC does not currently recommend PCR testing for the diagnosis of Lyme disease.
https://www.mayoclinic.org/diseases-conditions/lyme-disease/symptoms-causes/syc-20374651
There is no gold standard for testing Lyme disease but there are two laboratories who's specialty is immunology.