I just did a quick search on LS50, and one of the things people use it for is necrotic enteritis, so maybe while on it they were fine, but once off clostridium perfringens moved in, and LA 200 won't treat that. Call your vet and talk about clostridium perfringens, E. coli, etc, and ask them to do a gram stain. Funny your vet did don suggest doing that to rule out bacterial and/or fungal infections.
-Kathy
-Kathy