The dead byproducts of bacteria are called “pyrogens” because they cause (among other things, such as death) fevers. While they aren’t a problem in our day-to-day life (even consuming them wouldn’t affect your health), they are a crucial issue in the medical and surgical fields.
Depyrogenation is the process of cleaning up the germ corpses and the death juices they spit out in their hate. For things like heart surgery scalpels, there will usually be a second step of “Depyrogenation.” This is the process, not of killing bacteria, but of removing the bits left behind so that they don't trigger an immune reaction.
Problems occur when a scalpel with dead bacteria is used in surgery. The immune system works by identifying certain chemical triggers in bacteria, and it has no way of knowing if the lipopolysaccharide hanging around in someone's heart is not part of a living bacteria, but the floating corpses of dead bacteria.