Whole-Genome Sequencing: Opportunities and Challenges for Public Health, Food-borne Outbreak Investigations, and the Global Food Supply.

Food-borne disease is burdensome, affecting 1 in 6 persons or an estimated 48 million ill, 128 000 hospitalized, and 3000 deaths in the United States annually [1]. In addition, societal costs from lost lives, lost labor, lost wages, and even lost revenue in the food industry are substantial. Globally the burden is even higher, and multinational outbreaks due to the global movement of contaminated foods are being described increasingly. The global food supply links nations and economies, emphasizing the need to view food safety with an integrated farm-to-fork lens. As predicted, advances in molecular techniques and information management have been transformative for food-borne disease investigation [2]. Almost 2 decades have passed since the Centers for Disease Control and Prevention (CDC) launched a national molecular subtyping system known as PulseNet, and since that time it has become an indispensable laboratory surveillance system for detection of multijurisdictional foodborne outbreaks. With PulseNet, public health authorities developed a unique system able to link bacterial isolates that could identify food-borne outbreaks dispersed far and wide geographically with only a few cases. Notable examples of PulseNet’s impact include elucidation of the association of Escherichia coli O157 and ground beef [3], as well as numerous produce-associated outbreaks [4, 5]. Not only food-borne disease investigations have been enhanced; investigations related to direct animal contact have improved as well [6, 7]. Indeed, PulseNet has facilitated more cluster evaluations, faster outbreak investigations, and timelier regulatory interventions and has undoubtedly prevented many illnesses and deaths [8]. A national success story, PulseNet won the prestigious Innovations in American Government Award because of its substantial contribution to public health [9]. Its standardized methods of enzymatically restricting bacterial DNA into large fragments and then subjecting them to pulsed-field gel electrophoresis (PFGE) creates a unique molecular “fingerprint” suitable for real-time data transmission, computer analysis, and epidemiological investigation. With this history of success, it is with not without some nostalgic reluctance that the public health community is moving away from PulseNet as we currently know it. However, technological opportunities compel moving forward to build on the success of the past 2 decades. Advances in and increased availability of whole-genome sequencing (WGS) have arrived, as well as innovative ways to analyze the standard epidemiological data of person, place, and time. In this issue of The Journal of Infectious Diseases, Hoffmann et al [10] describe a retrospective analysis of a multistate US Salmonella Bareilly outbreak associated with tuna imported from India. They demonstrate the promise of combining WGS and analytical tools to trace foodborne pathogens through complex international distribution networks, leading to the source of the contaminated food. The context for the retrospective analysis is a 2012 food-borne outbreak with >400 reported cases in 28 states [11]. Hoffmann et al illustrate the power of WGS by analyzing a cross-section of environmental, regulatory, and human historical and outbreak-related Salmonella Bareilly isolates to differentiate clonal PFGE clusters into distinct genetic lineages associated with the contaminated tuna source. The phylogenetic analysis pointed to a common origin at a facility in India, while excluding Salmonella Bareilly lineages not associated with the outbreak. Geographic mapping and use of transmission networks are core epidemiological Received 11 May 2015; accepted 18 May 2015. Correspondence: John R. Dunn, DVM, PhD, Communicable and Environmental Diseases and Emergency Preparedness, Tennessee Department of Health, 710 James Robertson Pkwy, Nashville, TN 37243 ( [email protected]). The Journal of Infectious Diseases © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals. [email protected]. DOI: 10.1093/infdis/jiv298