I absolutely agree with Beekissed about adding dirt from the hen's pen when chicks are put into a brooder, and also about fermented feed. Don't think sterile if setting up a brooder, think 'gotta get that exposure happening right away'. Baby chicks can't eat a whole heap so how much cocci can...
I'm sorry I'm answering this so late -- and I may not be speaking with any great authority. However in 'Natural Goat Care', Pat Coleby (well renowned down here in Aus) talks about a herd that became Johnes-free (after being diagnosed earlier) after mineral supplementation and changing pasture...