Systems and methods for identifying pathogens in food using whole genome sequencing are provided. In some embodiments, gene sequence data derived from food pathogen samples are subject to bioinformatics processing in order to align the sequences and detect single-nucleotide polymorphisms (SNP's). In some embodiments, a SNP matrix is generated and a phylogenic tree is created, and it is determined whether the strain of pathogens detected in one food pathogen sample is the same strain of pathogen present in other previously-encountered food pathogen samples. If a match between samples is determined, then metadata associated with the matching samples is leveraged to trace the spread of the strain through a supply chain in space and time, and parties associated with the matching samples may be notified.