there are multiple mechanism that can determine encephalitis, or autism or other severe reaction. this is a part of imunology.
start to think simply: if a person eats something and has side effects, it can manifest from mild urticaria to angioedema with severe dyspne and death. This occurs in an abnormal discharge of substances.
so is the vaccin it can occur in some people side effect of various forms. basically vaccine causes an immune response from the body. in this process the inflamation affects the brain- encephalitis, or the Ac resulting can attak some cells.
I need to explain a whole book process.

On the other hand the biggest problem facing doctors is now resistance to anibiotics that will generate more deaths than cancer.