The use of natamycin is an exception to the prohibition on the use of antibiotics in the food industry, as it has no bacterial action.
Natamycin binds to the cytoplasmic membrane ergosterol present in fungi. This is absent in bacteria, and as such ingestion of natamycin does not cause resistance in normal bacterial flora. The number of fungi detected as normal flora in the human intestine is extremely low. This means that the probability of a fungus in the intestine being exposed to natamycin and developing a resistance would be infinitely small.