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Gene markers that are resistant to antibiotics are used, providing the possibility for humans to have increased antibiotic resistance. That would be your best answer.
The biggest challenge is the unpredictability of genetically engineered organisms. They could pose an unforeseen hazard to the environment. An example is an engineered virus vaccines may have its DNA recombine with those of naturally occurring organisms. The progenies could have unpredictable characteristics and pose a risk of health hazard such as epidemics or antibiotic resistance.