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Basic definitions: antibiotic vs antibiotic resistance gene.
How do bacteria acquire antibiotic resistance?
Why do GE plants have antibiotic resistance genes?
How might antibiotic resistance genes in GE plants affect antibiotic resistance in bacteria?

In order to get a handle on this complex issue, its important to understand the distinction between these two terms and how they are related:

Antibiotic--

technically, any chemical that kills something, but it usually refers more specifically to a compound that kills bacteria.

Antibiotic resistance gene--

a gene encoding an enzyme that degrades a specific antibiotic to harmless byproducts, protecting its possessor from the lethal effects of the chemical.

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The evolution of antibiotic resistant bacteria is a critical issue for human health. When bacteria become resistant to an antibiotic, the antibiotic will no longer kill the bacteria, and thus no longer able to prevent the human disease caused by the bacteria. Many scientists have become increasingly alarmed by the growing number of bacterial strains that are resistant to multiple antibiotics, making the treatment of some diseases very difficult. Widespread antibiotic resistance is caused by the overuse (and misuse) of antibiotics.

Bacteria become resistant to a specific antibiotic when they acquire the corresponding antibiotic resistance gene. There are two ways bacteria can acquire an antibiotic resistance gene:

• A new antibiotic resistance gene could evolve in a bacterium from "scratch" (through mutation of another gene useful for something else) because of selection pressure caused by exposure to antibiotics. All antibiotic resistance genes got their start this way. This process is thought to take place very slowly-- despite the presence of trillions and trillions of bacteria on the planet, there are relatively few different antibiotic resistance genes.
• A bacterium could receive an antibiotic resistance gene from another bacterium. Bacteria have a tendency to put useful genes on little, portable loops of DNA called plasmids, and bacteria can pass these to other bacteria relatively easily-- a process called bacterial conjugation. Once a new resistance gene evolves and is present on a plasmid, the gene can be spread to other bacteria (even unrelated ones) very quickly, especially when selection pressure from antibiotic use is high. This process can take place almost anywhere bacteria are in contact with each other: in the guts of humans and animals, in the soil, etc. For most antibiotics we have, there are probably several resistance plasmids out there either already widespread in nature or waiting to spread. Bacterial strains which are referred to as multiple-drug-resistant (MDR) have collected plasmids that make them immune to many different antibiotics.
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Antibiotic resistance genes are used in the creation of genetically engineered plants as "selectable markers." Because it is often difficult to determine in the early stages of the process whether a plant has received the desired genetic modification or not, scientists engineer plants to carry both the desired gene plus an antibiotic resistance gene. Plants (while still tiny seedlings) that have been successfully genetically engineered will not die on a petri-plate full of the antibiotic-- and thus also must contain a copy of the other "useful" gene. Of the GE plants currently marketed in the US, two antibiotic resistance genes are used: bla, which confers resistance to ampicillin, and NptII (also referred to as kanr or APHII), which confers resistance to kanamycin.
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A bacterium in the gut of a human or animal (or maybe in the soil or munching on a plant) might happen to pick up a resistance gene from the DNA spilling out of the digested plant before the DNA is totally degraded. This seems even more plausible if the human or animal is also consuming the corresponding antibiotic at the same time, because selection pressure would be much higher for the bacteria to acquire the gene.

There are several factors that suggest this risk may be very low:

• No one has ever observed bacteria taking up plant DNA in someone's stomach, even in controlled lab conditions that would make the event much more likely.
• The resistance genes used in plants are taken from bacterial plasmids already in nature and were not synthesized in the lab. For example, the most commonly used antibiotic resistance gene, NptII, was isolated in 1979 from a strain of E. coli.
• The process of bacterial conjugation is very rapid (especially compared to a never-observed plant-bacteria transfer) and has already widely spread resistance to the same antibiotics used in GE throughout the world.
  

Nonetheless, given a very large scale (GE plants all over the world, trillions of bacteria in every animal's gut, many of them eating antibiotics at the same time), the odds are in favor of a bacteria eventually picking up a resistance gene from a plant. But would that contribute significantly the already widespread antibiotic resistance? Probably not. But just to be safe, the FDA has suggested developers use antibiotic resistance genes for which resistance is already widespread (as resistance to ampicillin and kanamycin is), and has encouraged the eventual phaseout of resistance genes as markers (as other markers now exist).
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