In Fiscal Year 2001, the United States Department of Agriculture (USDA) was charged with implementing a monitoring program to collect information regarding the incidence, number, and species of important foodborne pathogens and indicator organisms on domestic and imported fresh fruit and vegetables. USDA's Agricultural Marketing Service (AMS) was appointed to undertake the creation and implementation of such a program, known as the Microbiological Data Program (MDP). MDP began collecting and analyzing samples in April 2001. MDP operations ended in December 2012 due to the elimination of program funding.

MDP was primarily designed to provide data on microbial presence in order to establish a microbial baseline to assess the risks of contamination, if any, in the domestic food supply. The data was used to establish "benchmarks" by which to evaluate the efficacy of procedures to reduce or eliminate harmful foodborne microorganisms. The data was provided to stakeholders for decision-making purposes (e.g., Federal and State public health agencies, growers, processors, retail stores, and food handlers).

Program authorization was based on the Agricultural Marketing Agreement Act of 1946. The Federal Agriculture Appropriations Bill for Fiscal Year 2001 provided AMS with funds to initiate MDP. The program was not regulatory in nature and was part of a broader Presidential Food Safety Initiative.

MDP coordinated its planning and policy requirements with the Centers for Disease Control and Prevention, the Food and Drug Administration, the Agricultural Research Service, and the National Agricultural Statistics Service (NASS). MDP and NASS statisticians designed appropriate sampling plans based on per capita consumption, marketplace availability, product origin, and time in transit and storage. Samples were obtained at terminal markets and chain store distribution centers.

Sample collection and testing activities were carried out with the support of 11 States –California, Colorado, Florida, Michigan, Minnesota, New York, North Carolina, Ohio, Texas, Washington, and Wisconsin - through cooperative agreements with their respective Departments of Agriculture. MDP provided quality assurance oversight and technical/administrative support to Program participants.

The State laboratories performed analytical testing of domestic and imported produce samples for specific foodborne pathogens. The sample history and laboratory results were sent to the Monitoring Programs Division office for review and compilation. Isolated organisms were sent to reference laboratories for genomic fingerprinting, antibiotic resistance examination, and serotyping. In addition, one State laboratory collected/maintained all MDP isolates and made them available to researchers.

The data generated from MDP are available to Federal and State Public Health agencies and industry for food safety decision-making purposes, risk modeling, and trend analyses. The information can also be used to establish benchmarks by which to evaluate the efficacy of good agricultural and manufacturing practices to reduce or eliminate harmful foodborne microorganisms and thus improve the quality and safety of the fresh produce supply.