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FDA Spends $17 Million to Go After Pathogens Faster

The U.S. Food and Drug Administration (FDA) is spending $17 million on technology it hopes will be fast enough to catch fresh produce with pathogen contamination.

FDA has awarded a five-year contract to Illumina Inc, a San Diego-based technology company involved in accelerating genetic research. Illumina will provide FDA with its MiSeq sequencing systems and reagents for conducting whole genome analysis on produce and produce-related environmental Salmonella and shigatoxigenic E. coli.

FDA wants to collect data said to be crucial to tracking Salmonella that will likely be involved in future produce-related outbreaks. The agency already uses Illumina’s MiSeq systems, but needs to improve its whole genome sequencing game.

The new contract will give FDA more resources and training capacity.

Numerous and diverse enteric pathogens are detected, isolated and processed at FDA’s network of state and national laboratories. With MiSeq, the labs will be able to generate high-quality whole genome sequences from historical pathogen collection and from bacteria collected from produce sources throughout the country.

Sequencing provides accurate subtyping and cluster analysis for investigating foodborne outbreaks and trackback to the food or environmental source. Conventional molecular typing tools are said to lack resolution for differentiating certain strains such as Salmonella.

By comparison, MiSeq is known for its high resolution and accuracy in identifying closely related bacterial isolates.

In announcing the contract award, neither FDA nor the company said anything about whether the technology investments will be stepped up produce inspections by the agency.

USDA’s Microbiological Data Program (MDP) has been doing more produce inspections than FDA in recent years, but Congress will cut off funding for those inspections when the new federal fiscal year begins on Oct. 1.

The Obama Administration wanted the $5 million program, carried out by state labs, cut from USDA’s $149 billion budget.

MDP labs this summer have found pathogen contamination in several fresh fruits and vegetables, leading to recalls of the products.

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