There are literally hundreds of articles in the medical literature published in respected journals which demonstrate the persistent of Borrelia burdorferi in various tissues after antibiotic therapy. Here I will only summarize some interesting current scientific information.
In the Journal, Molecular Medicine an article was published December 13, 2007. The article was published by the Departments of neurology and Microbiology by the Ludwig-Maximilian University in Munich Germany. The piece is called "The Pathogenesis of Lyme Neuroborreliosis: From Infection to Inflammation." The piece is a well researched eloquent summary with a detailed bibliography which covers the basic science of the infection in incredible and well documented detail. The clinical manifestations of these disease are presented. A detailed explanation is given as to how the organism hides from the immune system. Its ability to thwart the complement system is described. Its ability to upregulate and down regulate its surface proteins to evade immune destruction is detailed. The spirochete is able to use complement neutralizing substances found in tick saliva to aid its escape from immne destruction, as described in detail. It states that "Bb appears to possess a complex arsenal for an active immune suppression by both downregulationt he immune responses and neurtralizing its effector mechanisms." The article describes how Borrelia hides in less accessible compartments or protected niches. These include the extracellular matrix. It binds to plasminogen which permits invasion of the organism. It can attach to several proteins of the extracellular matrix such as decorin which allows the spirochetes to remain hidden from circulation white blood cells. Methods by which Borrelia enters the nervous system are discussed. The complexities of the inflammatory response in the nervous system are reviewed. The mechanisms of neural dysfunction, including direct cytotoxicity, neurotoxic mediators and autoimmune reactions are discussed. The basic science presented here can be dovetailed with serious clinical trials.
In October, 2007 Columbia University released the findings of the first placebo controlled study of cognitive impairment due to chronic Lyme disease. The study was lead by Dr. Fallon. Patients with a history of previously treated Lyme disease who had cognitive impairments (neuroborreliosis) were prescribed intravenous Rocephin. It was shown that there was significant cognitive improvement in patients treated with 12 weeks of Rocephin. Patients had complete relapses after 3 months without treatment. Patients improved when the treatment was repeated.
A study by Krupp in 2003, published in Neurlogy showed that patients treated with IV Rocephin experienced a substancial improvement in fatigue. This was also a placebo controlled study.
There are insufficient clinical studies at this time, but there is a large body of scientific support for the chronic Lyme paradigm.