Dagwood quoted the Merck Manual regarding shipping fever. It, and enzootic pneumonia are two parts of the bovine respiratory disease complex. They share similarities in infectious agents, etc. Enzootic pneumonia applies more to calves less than 6 months of age, while shipping fever is in older calves of feedlot age.
Of course, for any infectious disease to occur, you need an inusufficient immune response, and infectious agents. In shipping fever, the broken immune system is mainly caused by fear (releasing cortisol, an immune suppressant, from the adrenal gland) during weaning, crowding, shipping, running them through a chute to give shots, etc. Putting them in a new pen, with new feeders, watering systems, new kinds of feed, etc. Having to work out new pecking orders. A lot to handle all at once for a young animal, a lot of things we don’t think about unless we put ourselves in their frame of mind.
Some try to spread out these stresses by separating the events, e.g. weaning well before shipping to feedlot, starting them on new feed, getting used to feed bunks, etc.
As my brother who worked in a feedlot said, “You’re not a real cattleman until you’ve got a dead pile.” I once read a vet say we shouldn’t ask why some feedlot cattle die from the stress and disease, but we should ask why any survive. One more reason to raise your own and give them a better life.
In enzootic pneumonia of young calves, the disease can be the same as in shipping fever, but the broken immune system often results because they received too little antibodies from mom (didn’t get sufficient or the right colostrum). This is called failure of passive transfer of antibodies. (Passive means they were given to you and will go away, active means you make your own antibodies continuously.)
Ideally you would vaccinate the cow who actively makes antibodies she dumps in the colostrum for the calf. Hopefully the vaccines are against the bugs the calf will run into when in a sale barn, or being mixed in a group.
Without the antibodies, treatment with antibiotics has much less chance of success. One problem with calves from sales are that you don’t know how much colostrum they got, or whether their moms were vaccinated.
Anyway, that's my interpretation of what you can read here from the Merck Manual. There are more factors to consider, like quality of milk replacer, etc.
http://www.merckvetmanual.com/mvm/in.../bc/121207.htm