Design and methodology for monitoring the occurrence of foodborne pathogens in meat and poultry in United States: Case study of Campylobacter on chicken

In the United States, the Food Safety and Inspection Service (FSIS), which is part of the U.S. Department of Agriculture, oversees multiple sampling programs that focus on detecting microbial contamination of meat and poultry in slaughter and processing establishments. There have been efforts across scientific disciplines to describe data collection methods and estimation strategies for large scale surveys to allow for the integration of data from multiple sources. The FSIS sample selection methods can be described as a close approximation of either a stratified or two-stage cluster sampling design. These surveys therefore support estimates of pathogen occurrence that are derived under both design- and model-based inferential paradigms. This retrospective study will describe population-level estimation strategies and how changes in pathogen contamination can be monitored across time using a trend analysis. An example based on Campylobacter on broiler chicken carcasses is provided. The example demonstrates that changes in the apparent prevalence during the study period are predominantly the result of changes in laboratory methods.