Even cancer mutates

Viruses and even cancer mutate and become resistant to drugs. Basically everytime they reproduce there are errors in the reproduction so that the progeny are not identical. If there are thousands (or millions) of versions, some small portion of them are resistant to your treatment. The only way to eventually treat these situations is to have custom cures. You take a sample of the offending organism that has infected you (i.e. HIV) . The device scans it and produces a version of the cure that the organism is not resistant to. The organism may keep mutating, but as long as you can keep creating custom cures, you will eventually kill all instances.

By the way, your immune system kind of works this way. You have antibodies for billions of combinations of foreign bodies. The cells that produce them lay dormant. When you are exposed, the particular cells that react to the foreign body become stimulated and reproduce. They then produce more of the antibody and eventually the foreign body is destroyed (or maybe you have an allergic reaction). As viruses mutate, different immune cells in your body are stimulated and reproduce.