These pathogens create very toxic by products that accumulate in the brain and body it is these toxins that make one sick- plus the immune response (cytokines) are uptaken in the brain which cause many brain disorders http://ajp.psychiatryonline.org/article.aspx?articleID=174101
Furthermore, these infections require a lot of nutritional aspects for the immune system to fight - these are lost rapidly which further hamper the brain - a couple of nutrients such as b12, magnesium, proteins, fatty acids etc. This leaves the brain without the vital nutrients it needs. http://pptu.lefora.com/2012/06/20/neutrophils-protozoa-and-nutrition/#post0
Also these infections evoke an adrenal response, adrenochrome is a byproduct of adrenaline (adrenal hormone) = adrenochrome gets up into the brain and cause schizo type of reactions - niacin in high enough amounts reduces the adrenochrome thus lessening the schizo reactions. http://www.ncbi.nlm.nih.gov/pubmed/12829415
Adrenochrome
Adrenochrome, chemical formula C9H9NO3, is a compound produced by the oxidation of adrenaline. The derivative carbazochrome is a hemostatic medication. Wikipedia