Salmonella research is the top priority for the pig industry especially related to pre-harvest reduction of pathogens with potential public health significance. The pre-harvest food safety research for Salmonella proposed here falls under the category of control strategy. The research proposed here is highly relevant and applied in nature. Without the groundwork, foundation and benefit of comprehensive genetic bioinformatics based analyses; many shotgun approaches based upon methods that are applicable to other microorganisms for instance, will ultimately fail when used for Salmonella spp. This project makes available to the industry and food safety scientists a powerful comparative sequence and genome comparison databases that can be used to develop epidemiological methods that are specific to Salmonella spp. rather than attempting to adapt methods that have proven to be of use with other organisms. Salmonella spp. because of how closely related the serovars tend to be presents a significant challenge to the development and applicability of molecular epidemiological methods. This project represents the primary and quite simply the only logical foundation step that will ever result in the development of a method that fulfills all the requirements of a superior molecular epidemiological method for Salmonella spp.