Is there any risk of illness from eating an apple?

Yes. Fresh apples may harbor the food-borne pathogens E. coli  and salmonella as a result of  the way they are grown, harvested, processed, or distributed. The human hand can spread these bacteria from apple to apple at any juncture in the food chain, including the supermarket and home. Before apples are harvested, birds and other wildlife can cause contamination. Therefore proper handling is essential when storing and preparing apples.
 
Apples are also subject to spoilage bacteria (the kind that don’t cause illness but alter taste, smell, and texture for the worse). Spoilage can occur in just a few days if apples are stored at room temperature. They will last considerably longer in the refrigerator,  but not forever.  Apples are also subject to mold growth after an extended period of time. Fortunately, proper storage and  handling of fresh apples eliminates most risk of illness.
 
Source(s):
FDA "Guide to Minimize Microbial Food Safety Hazards for Fresh Fruits and Vegetables"