Recently, significant changes have been made to how the US Food and Drug Administration (FDA) conducts investigations of food manufacturing facilities. For starters, note that I did not say FDA inspections; they are now investigations. This change in semantics indicates a shift from a superficial “look around” a facility to diving into records and sometimes taking hundreds of environmental pathogen samples. The Food Safety Modernization Act (FSMA) has prompted many of these changes, and has given the FDA increased power and access to records. The FDA is also now much more likely than in the past to involve the Department of Justice if there is any possibility of criminal intent. Along with this significant new regulatory authority, the industry has seen major leaps forward in microbial strain tracking technology, the most important being Next Generation Sequencing and its use for Whole Genome Sequencing (WGS).