Like you said, the standard Lyme test is not very reliable. Even if laboratory tests
are ordered, labs are still using immunoassays for confirmation of Lyme (ELISA, then a Western Blot), which have relatively poor sensitivity (~70% or lower[1]) due to low serum concentration of
Borrelia or possible absence of antibodies—so they can miss one in four true-positive cases. The newer PCR-based assays have much better sensitivity (>70%, maybe closer to 90%[2]), but the assays are not yet in widespread use, are still being proven, and thus are seen only as adjuncts to immunoassays that can provide further evidence of Lyme. It can also take a couple weeks from when the bullseye rash appears (or when the tick bite occurs) for serology to test positive, again due to the
Borrelia/antibody concentration being below the limit of detection. Samples tested are also usually blood, which may not be as good as CSF. It's a tricky bug to diagnose in the laboratory, which is why it comes down to the discretion of the clinician and the doctor's knowledge of the patient and his or her history.
1. http://www.igenex.com/files/should_know.pdf
2. Laboratory Diagnostic Testing for
Borrelia burgdorferi Infection, Lyme Disease: An Evidence-based Approach: http://www.cdc.gov/lyme/resources/Halperin_2012_Chap4_Johnso...