I know that when my horse gets his intranasal strangles we have to keep him sperate from the other horses for like 30 mins, and wash our hands really well. My vet does our horses last. Mine gets so sore from the shot he can't move his neck to eat for like 4 days.
I've heard it's like us getting the flu shot, that some people get a mild case after they get their shot. My horse has been getting it for 4 years now and he has been fine, knock on wood.
If all else fails talk to your vet about what to do for you paticular horse.