jana, my feeling is that the fungi spreads by roots. It is known that leaky bowel syndrome occurs due to the roots of the fungi penetrating the intestinal wall. The roots then act as sponges allowing the larger food molecules through to the bloodstream. The body sees this as invaders and sends out antibodies. It is kind of like the immune system overreacting. In my case, it acts as though I am allergic to all foods. This causes my sinuses to swell; as well as other vile symptoms.
My best guess is that fungi is hard to destroy; because the roots are either hard to get to, or they are not acidic anaerobic pathogens.
Jim Humble says that Lyme disease takes a long time (maybe a year) to resolve as well.