FDA’s tracking and analysis of surveillance sampling isolates for outbreak detection
Authors: Blessington Tyann , Beal Jennifer , Clemmons Roblyn , Clendenin Alyssa , Curry Phillip , Elliot Elisa , Kuntz Thomas , Melka David , Rotstein David , Strain Errol , Wynens Christopher 
Published: May 2017

ObjectiveTo create a forum and database for FDA and CDC epidemiologists,laboratorians, and outbreak scientists for tracking recent food andenvironmental surveillance sampling isolates identified throughReportable Food Registries reports and regulatory inspectionalfindings, and analyzing them for matches to clinical isolates for earlyoutbreak detection.IntroductionIdentifying, solving, and stopping foodborne outbreaks in theU.S. requires the collaboration and coordination of multiple federalagencies and centers as well as state and local authorities. FDA’sCoordinated Outbreak Response and Evaluation (CORE) Networkis responsible for outbreak surveillance, response, and post-responseactivities related to incidents involving multiple illnesses linked toFDA-regulated food. CORE collaborates with CDC to obtain data onfoodborne illnesses and illness clusters and with FDA Centers andfield staff to obtain laboratory and inspectional information relatedto contaminated foods and foodborne illness outbreaks. CORE’sSignals and Surveillance team coordinates isolate tracking activitiesamong several organizations within FDA and CDC and the isolatedatabase was developed for timely information sharing and earlysignal detection.MethodsThe isolate tracking database combines information fromestablished laboratory, inspectional, and regulatory programs;investigators across FDA and CDC evaluate the information forearly outbreak signals. PulseNet is a national laboratory network thatcompares the Pulsed-field Gel Electrophoresis (PFGE) patterns ofclinical and non-clinical bacterial isolates and identifies increases innumbers of isolates with matching PFGE patterns as outbreak clusters.Foodborne outbreak investigational partners, including the CDC andFDA, utilize the CDC/Palantir Technologies-developed platform, theSystem for Enteric Disease Response, Investigation, and Coordination(SEDRIC), to evaluate clinical, food, and environmental isolates.CORE provides additional firm-identifying metadata for new foodand environmental isolates from FDA, contract lab, and ReportableFood Registry (RFR)-reported samples and analyzes them for PFGEpatterns matching those of recent clinical isolates. FDA laboratoriansprovide early information about food and environmental isolatesthat are in queue for PFGE and whole genome sequence analyses,trend analysis for recently completed isolates, and genetic clusteringwith clinical and other isolates. The RFR is a FDA-hosted platformfor industries and public health officials to report when there is areasonable probability that a human or animal food that is regulatedby FDA will cause serious adverse health consequences. The RFRcoordinator tracks patterns of adulteration in food, and gathersinformation from FDA district investigators on the availability ofpathogen isolates for FDA analysis, from FDA inspections of firms,and from investigations into the root-cause of contamination. Eachpathogen detection is evaluated for associations to current outbreakclusters.ResultsThe isolate tracking activities have provided investigatorswith information for hypothesis development, identified trends inlaboratory and inspectional findings, aided in the identification ofcausal food sources in illness clusters, and provided early laboratoryand inspectional information to outbreak investigations. Within thepast year, isolate tracking activities identified early indicators of thepresence ofListeria monocytogenesin frozen foods before a multistateoutbreak of listeriosis was linked to frozen vegetables; identifiedearly indicators of the presence ofSalmonellain pistachios beforeidentification of a multistate outbreak ofSalmonellaMontevideo andSalmonellaSenftenberg; further characterized the microbial hazardsof cucumber and pepper contamination through FDA’s enhancedsurveillance sampling program; and expanded the forum’s scope toinclude animal foods and their link to human and animal illnesses.ConclusionsThe database and forum provides a platform for informationsharing, and collaboration between agencies, offices, and centersby informing the participating groups about early signals ofcontamination and emerging food risk trends.