A study in mBio today that was spurred by a 2014 outbreak of listeriosis in caramel apples found that the act of puncturing the apple with a dipping stick produces conditions favorable for growing Listeria monocytogenes, especially at room temperature.
University of Wisconsin researchers swabbed four outbreak L monocytogenes strains onto Granny Smith apples, inserted wooden dipping sticks through half the apples, then dipped them all in hot caramel and allowed them to cool. They then stored the apples at either 25°C (77°F) or 7°C (44.6°F) for up to 4 weeks.
The team found Listeria increased 1,000-fold on caramel apples with sticks stored at room 
temperature for 3 days, but Listeria growth was delayed on apples without sticks at the same temperature. Refrigeration substantially slowed the growth of the bacteria, but refrigerated apples with sticks had some growth after 1 week that continued for the next 3 weeks, while those without stick had no Listeria growth in the 4 weeks of cold storage.
Dipping the apples in hot caramel killed off much of the surface bacteria, said lead author Kathleen Glass, PhD, in a news release by the American 
Society for Microbiology (ASM), which publishes mBio. “But those that still survived were the ones that were able to grow. If someone ate those apples fresh, they probably would not get sick. But because caramel-dipped apples are typically set out at room temperature for multiple days, maybe up to 2 weeks, it is enough time for the bacteria to grow.”
The authors conclude that Listeria growth was likely accelerated by apple juice caused by the puncture to pool underneath the caramel, creating a favorable environment. Caramel and apples by themselves are not good substances for promoting bacterial growth. Possible solutions to the problem include disinfection of the apple, adding growth inhibitors, or employee temperature controls.