If by chance there are a small number of strands that are not degraded the chance of the antibiotic resistant gene being adapted by the digestive tract are again very low. Further, if this does happen the few strands have a very small chance of counteracting the orally ingested antibiotic. .
If by chance counteraction did happen the person could just be given a higher dose of the antibiotic. However low the risk of antibiotics not working, health care regulatory agencies still have antibiotics that are not clinically significant to animals and humans. These antibiotics come from outside the realm of genetically modified foods. The likely-hood of antibiotic resistant bacteria being ingested and becoming a significant health threat, are next to null. .
Another concern is that of toxins contained in plants. Many plants naturally contain toxic material for a defense against predators such as animals, insects and other plants in their environment. When a plant is genetically modified there stands a chance of an increase in the toxicity level of the food. According to regulations of the FDA, GM plants that are known to have even small levels of toxicity are tested. The chances of plants with deadly levels of toxins making it to the consumer are not likely. .
The next concern is one that I personally have. I am allergic to walnuts. If I eat anything with even a small trace of walnuts I will become very ill. I"m not alone. In the United States a quarter of all people report they have an adverse reaction to one or more foods, most commonly dairy products, eggs, wheat and nuts.(Sloan). The basic building block for a cell is protein, all foods contain them. For my self and others who cannot tolerate certain proteins, eating even trace amounts can cause allergic reactions which range from minor discomfort to serious illness and even death. In the new technology genes are transferred from one organism into another.