Just ran across this info in humans:
"Chronic Babesia infects only about 1% of RBCs so it isn't all that easy to find."
From here:
http://lymemd.blogspot.com/2008/09/babesia-i-hope.html
That means that a PCR test, that looks for fragments of DNA and such, sounds like it is looking like a needle in the haystack. NCSU may have better information.