First let me say I am a fan of genetic engineering. It offers a way to feed a growing planet and a way to get nutritious food to people who other wise might not have it. To learn how to best benefit from this technology we will have to experiment with this technology. That is how we learn about the risks and benefits. The question for all of us now is how to manage the risks involved.
It is difficult to tell whether the transfer of a few modified cells into a plant is successful. So genetic engineers early on used antibiotic resistant genes ( npt11 ) as markers. This gene gives antibiotic resistance to kanamycin and neomycin. The bla gene was also used which is resistant to ampicillin. These markers would be attached to the genes being inserted and used as a way to check to see if the insertion was successful. These markers should have no effect on the plant. The genes have been turned off. These genes can be found in most genetically engineered food today. It is not known if they are harmful.
Genes that are transfered to plants might be turned off and on in the plant and the plant’s future generations.
It is possible that eating these foods could reduce antibiotic effects in people. It is thought that eating these foods and taking your antibiotic with your meal may reduce the effectiveness of the antibiotic.
It is also possible that these genes could be transfered to pathogens making them resistant to the antibiotics. It is unlikely that this kind of transfer could take place. However, DNA is not fragmented in the intestine as had been previously thought. It can be excreted or passed into the blood of the person eating the food. The rise of antibiotic resistance coincides with the rise of this genetic marker being released into the food supply. But these tests were done in a lab, not a human and what happens in the labs does not always work the same way in the real world.
In Europe the use of npt11 in commercial products is being phased out. I could not find information on US phase out of these markers.
Union of Concerned Scientists, Risks of Genetic Engineering
US FDA Guidance for Industry: Use of Antibiotic Marker Genes in Transgenic Plants
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