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Preventing the development of pathogen resistance to processing and preservation techniques will require an understanding of the genetic mechanisms that pathogens use in situ to adapt and develop tolerance to stresses they encounter in the food environment. RNA isolation and reverse-transcription (RT)-PCR protocols were developed as tools to detect gene expression in bacteria on beef carcass surfaces. The utility of these procedures was demonstrated by detecting the expression of a selectively-inducible green fluorescent protein (GFP) gene in a plasmid-transformed strain of Escherichia coli O157:H7 inoculated onto beef carcass surface tissue. These procedures should serve as useful tools for studying the genetic responses of bacteria when exposed to antimicrobial interventions applied to food animal carcasses.