E coli is always present in a rabbit's GI tract. Something (perhaps cocci, a virus, plain old stress, a food issue) could have caused his immune system to not be able to keep the population of E coli low, and its overgrowth led to the disease. It's too bad that it was highly resistant to antibiotics--that means there was little you could have done for him, and little you can do to prevent it in the rest of your bunnies (if it were penicillin sensitive, you could preventatively treat them with penicillin,etc).