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One of the articles from PubMed through the above links suggests spinal taps, checking the CSF - for studies to be set up. They should know, though that CFS does not always yield spirochetes and that the spinal taps are very hard on some folks.
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An excellent article about MS/Lyme misdiagnoses and co-diagnoses by a LLMD/neurologist.
CONTROVERSIES IN NEUROBORRELIOSIS Audrey Stein Goldings, M.D.
Updated October, 2002 =====================
Includes details of the life cycle of spirochete and she suggests minimum of 4-month treatment at the earliest sign of lyme. Different forms of the spirochete are discussed, too.