Untreated
strep throat can lead to
Rheumatic Fever caused by antibody cross-reactivity to your own tissues, flaring up an autoimmune disorder.
I would imagine getting a cocktail of vaccines can cause a similar response and I bet the cross-reactivity is to proteins responsible for brain
development. Hence why the vaccines are safer when you are older.
That would be a potential mechanism for higher rates of autism along with higher rates of vaccination. Developed countries in general that use alot of vaccines and have higher rates of autoimmune disorders. No one knows if its because of a lack of common contact with harmless bacteria (which could be an entirely different yet equally probable mechanism) but I'm thinking it could hypothetically be exposing people to like 100 antigens of some pretty nasty bugs and your body settling on an antibody that is cross-reactive with a protein used in brain development.
https://www.niaid.nih.gov/topics/autoimmune/Documents/adccfinal.pdf
All you really need to read is the first paragraph and the rest boils down to "we don't know."
Read the bottom of page 31 and the beginning of page 32. It could very well be that the immune system isn't meant to be immune to every possible pathogenic microbe the world over. There seems to be a risk with every antigen that you are exposed to that you develop an autoimmune disorder. So injecting 100's of them into newborns.... eh.
Hygiene hypothesis and autoimmune diseases.
http://www.ncbi.nlm.nih.gov/pubmed/22090147
If you were to go along with that theory by itself, then its pretty dumb to be giving out Streptococcus pneumoniae vaccines with Streptococcus pneumoniae lives in just about everyones nose, anyway.