Illumina, Inc. have announced it was awarded a contract from the U.S. Food and Drug Administration (FDA) to provide the agency with MiSeq sequencing systems and reagents for conducting whole genome analysis on produce and produce-related environmental Salmonella and shigatoxigenic E. coli isolates. The contract is worth up to $17 million over a period of five years.The FDA currently has several MiSeq systems already deployed and is building its existing capacity to provide resources and training to enhance whole genome sequencing capabilities as part of a proof-of-concept initiative. More immediately, the agency is looking to collect data that is crucial to source tracking Salmonella that may be involved in future produce-related outbreaks.

Using MiSeq, the FDA's national and state laboratories, where numerous and diverse enteric pathogens are detected, isolated and processed, will be able to generate high-quality whole genome sequences from historical pathogen collections and from bacteria collected from produce sources across the country. Sequencing data will be uploaded real-time to the National Center for Biotechnology Information (NCBI) curated database, thereby enhancing the database's power for source tracking queries. This data will serve as early proof-of-concept for rapid networking of resources using a whole genome sequencing based approach to pathogen detection, identification and traceback.

'Illumina applauds the FDA's commitment to improving the public's safety from foodborne illness outbreaks, as demonstrated by its decision to further integrate whole genome sequencing into its efforts,' said Christian Henry, SVP and General Manager of Illumina's Genomic Solutions business. 'We are extremely pleased MiSeq was selected as the technology platform for this large-scale initiative. We are well-positioned to deliver on the program's requirements, based on MiSeq's rapid turnaround time, unmatched accuracy, and ease-of-use, as well as our proven track record.'

Sequencing provides accurate subtyping and cluster analysis for investigating food-borne outbreaks and traceback to the food or environmental source. However, conventional molecular typing tools lack the resolution for differentiating tightly linked bacterial isolates and provide limited genetic differentiation of certain strains such as Salmonella. MiSeq is ideally suited for screening bacterial pathogens due in part to its speed, simple workflow, high resolution, and accuracy, which enhance the ability to identify close related bacterial isolates.

This project supports FDA's mission of protecting public health by generating baseline data to identify and remove contaminated produce from the nation's food supply. Currently Salmonella is the leading cause of food-borne illness in the United States.