Prevailing methods to track bacteria in food, the environment, and animals are not meeting the need for modern food security demanded in a global food chain. Microbiology professionals have embraced high-throughput genome sequencing because many longstanding questions can be quickly and directly addressed with individual organisms or entire microbial communities, including the gut, which is the source of many foodborne bacteria, at a precision level that has never been seen in public health or food safety. Genetic signatures can be examined quickly to produce millions of individual pieces of information that become a detailed fingerprint of bacterial uniqueness. Existing methods use a handful of individual information pieces to define bacterial identification after many weeks. Genomics is a platform technology that delivers new opportunities to quickly detect and identify bacteria in the food supply to shorten outbreaks and track microbes directly in food to immediately replace outdated methods that hinder food security.
While genomics is revolutionary for microbiology and food security, there are still challenges to be addressed that bring about widespread application of these methods. Use of bioinformatics is needed to facilitate this process. A continued need for broad application will be addressing informatic analysis to present the complex data in ways that are useful to food safety professionals along the food chain. The data are completely new to most food safety professionals, which presents a challenge to distilling the vast amount of genomic information to actionable knowledge. In spite of this set of challenges, progress is underway so that the epidemiological information
are tied to the genome sequence so that the diagnostic and forensic analysis can be done on the genome sequence to produce actionable information to reduce outbreaks, control the bacteria in food, and find new risk factors for animals to act as reservoirs. The 100K genome project is the largest of its kind – scaled at 10 to 100 times that of any other genome project in the world and will produce ~50 times more genetic information than available since genomics began, and is estimated to require five-years to complete.