It's all about the dogs' immune systems. E. coli naturally resides in the intestines of dogs, only when it's highly concentrated that it poses a threat. Mostly, a puppy gets E. coli infection when he does not receive his mother's milk, which contains antibodies and supplement a puppy's immune system. Risk factors are poor nutrition of birthing mother, unsanitary or crowded birthing environment, mammary gland infection of a nursing mother who has E. coli infection herself and prolonged birth. Causes also include contact with an infected animal or objects, such as bedding, that has been contaminated by an infected animal.