PCR or Western Blot?
Comments from an experienced Lyme treating doctor...
When testing, a very basic and helpful start is to measure serum immunoglobulins (IgM, IgA and IgG) as well as IgG subclasses.
Frequently in late Lyme there is a subclass or total deficiency of IgG and if this is found, then seronegativity, or at least weak serological responses will be expected.
It turns out that that there is a reciprocal relationship between serology results and PCR results, meaning that when the antibody response is weak, the PCR is more likely to be positive.
This holds true not only with IgG deficiencies, but also in very early Lyme when spirochetemia is relatively high and antibody response has not fully developed yet.
The flip side is that in those with depressed IgG, borderline serologies or indeterminate WB bands might need to be given greater weight- more likely to get a false negative than a false positive.
T-cell testing can also be positive when someone is seronegative, but may not be as sensitive as expected because if someone is sick enough to have a low B-cell response, they are more likely to have a low T-cell response as well, meaning false negatives.