Wild animals whether small, such as rodents or birds, or large such as deer, can often gain access to a farm or orchard during the growing season and can contaminated produce with their feces and even other animals' feces with which they've come into contact. Lastly, the application of manure from cattle or poultry can easily introduce pathogens. There are no federal rules or regulations regarding the use of fresh manure as a fertilizer for produce. The location of the farm or orchard or processing facilities near other farm animals can also result in contamination. It is believed that some bacteria can form spores and be blown in dust onto nearby produce or into water used for rinsing.
Harvesting introduces the human element.
Unclean hands can contaminate fresh produce with human pathogens such as hepatitis A. Workers can walk through contaminated dirt and climb up ladders placing their hands on rungs they have just soiled. Often, workers sit on their picking bags while taking a break. Baskets are placed on the ground and can easily get contaminated soil in them. Thus, previously pristine produce can be subsequently contaminated during harvest. The processing facility itself can be left open to contamination from dust or animals.