Foodborne Illness and the Rise of Environmental Pathogen Analysis

September 9, 2014

By Ricardo Carvajal

FDA has made no secret of its increasing investment in, and reliance on, databases of genetic information to investigate outbreaks of foodborne illness.  In public presentations, compliance officials have lauded the utility of PFGE and PulseNet, the Whole Genome Sequencing (WGS) Program, the Genome Trakr network and database, and Global Microbial Identifier.  FDA has also been ramping up its environmental sampling, such that the agency is taking samples during multiple inspections to identify potential resident strains of pathogens in specific facilities.

The marriage of all of these resources is evident in the recent CDC announcement, "Multistate Outbreak of Salmonella Braenderup Infections Linked to Nut Butter Manufactured by nSpired Natural Foods, Inc."  According to the announcement, FDA isolated Salmonella Braenderup from environmental samples taken during routine inspections at an nSpired facility, and performed PFGE and WGS on those isolates.  PulseNet was then used to identify “ill persons with the same PFGE ‘fingerprint.’”  Via WGS performed on the clinical isolates, CDC “determined that the bacteria from the ill persons were related to the environmental isolates taken from the firm.”  In subsequent interviews, those persons reported eating a product produced by nSpire, thereby tightening the association.

As FDA continues to build its databases, chances are that we’ll see more investigations following the pattern outlined above.  That trend could get an additional boost from the implementation of FSMA, depending on the nature of any environmental monitoring requirements that are incorporated into the final rule on preventive controls.