True illnesses might mutate by magic, but it would not look like a template because there would be no need for it.
For instance this is what a pathfinder disease looks like:
Bog Rot
Type disease, contact;
Save Fortitude DC 16
Onset 1 day;
Frequency 1/day
Effect 1d6
Str,
Dex,
Con, or
Cha (determine randomly using 1d4)
damage;
Cure –
Creatures afflicted with bog rot do not heal naturally and gain only one-half benefit from magical healing until the disease is cured. Unlike normal diseases, bog rot continues until the victim reaches Constitution 0 (and dies) or receives a
remove disease spell or similar magic. The save DC is Charisma-based.
If it suddenly starts causing twice as much damage that is a mutation, maybe caused by magic, but it's not a template for the germs