Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database

Abstract

The FDA has created a United States-based open-source whole-genome sequencing network of state, federal, international, and commercial partners. The GenomeTrakr network represents a first-of-its-kind distributed genomic food shield for characterizing and tracing foodborne outbreak pathogens back to their sources. The GenomeTrakr network is leading investigations of outbreaks of foodborne illnesses and compliance actions with more accurate and rapid recalls of contaminated foods as well as more effective monitoring of preventive controls for food manufacturing environments. An expanded network would serve to provide an international rapid surveillance system for pathogen traceback, which is critical to support an effective public health response to bacterial outbreaks. R ecent devastating outbreaks associated with the consumption of fresh-cut produce have reinforced the notion that foodborne disease remains a substantial global challenge to public health. In the United States alone, one in six or an estimated 48 million people fall prey to foodborne pathogens, yielding 128,000 hospitalizations and 3,000 deaths per year (http://www.cdc.gov /foodborneburden). Economic burdens are estimated cumulatively at $152 billion dollars annually, $39 billion of which is attributed directly to the contamination of fresh, canned, and processed produce (see the Produce Safety Project, http://www .pewtrusts.org/en/about/news-room/press-releases/0001/01/01 /foodborne-illness-costs-nation-$152-billion-annually-nearly -$39-billion-loss-attributed-to-produce). Mitigating foodborne illness, at times, seems to be an intractable challenge.One longstanding problem is the ability to rapidly identify the food source of the contamination. Despite the best efforts of food safety experts, the previous technology, pulsed-field gel electrophoresis (PFGE), often lacks the resolution to effectively pinpoint the source of an outbreak. The promise of whole-genome sequencing (WGS) came in 2012 when scientists with the U.S. Food and Drug Administration's Center for Food Safety and Applied Nutrition (FDA-CFSAN) performed a retrospective outbreak study on a 2012 Salmonella outbreak that was linked to spicy tuna sushi rolls by PFGE. The clinical isolates, food isolates, and historical isolates of the same PFGE pattern were all sequenced on the Illumina MiSeq. In contrast to the PFGE results, where isolates from the current outbreak looked exactly the same as unrelated historical isolates, WGS uncovered a surprising level of resolution distinguishing all of the isolates. Moreover, the isolates from the outbreak were most closely related to a 5-year-old historical isolate that was linked to a processing facility only 8 km away from the source of the outbreak (1). This isolate was collected at the port of entry from an earlier inspection of contaminated seafood and, like many others, was saved in the freezer collection of the FDA-CFSAN. The idea that the FDA's historical isolates could all be sequenced, providing investigators with geographic clues from a ...

A Primer on Infectious Disease Bacterial Genomics

“…The GenomeTrakr network in the United States mitigates this challenge by segregating the HTS data away from the sensitive metadata. In that system, only HTS data from microbial cultures and a minimal set of metadata are deposited in public archives to facilitate efficient monitoring of foodborne pathogens nationally and globally, while the more sensitive information is kept confidential (21). However, even in the absence of storing identifiable information within cloud services, plans should be made in advance related to data control, security, and accountability in the event of a cloud service failure (22).…”

“…The application of genomic epidemiology to other high-profile events, such as the 2011 German E. coli O104:H4 outbreak (212), has cemented the reputation of genomic epidemiology as a powerful new method for outbreak investigation, and it is currently positioned to replace the existing gold-standard methods as the main tool for both surveillance and outbreak response by public health laboratories around the world. Indeed, some early adopters, such as the CDC and the FDA, are already using HTS to assist in their real-time foodborne disease detection, surveillance, and outbreak response activities via the GenomeTrakr network (21). Bacterial pathogen genomics employs the methods described under "Phylogenomics."…”

TreeToReads - a pipeline for simulating raw reads from phylogenies

“…However, these estimates of shared ancestry may rely on only a handful of data points. When the resulting phylogenetic trees are used by public health agencies to make public health decisions, such as to define the scope of foodborne outbreaks [1], to identify the source of these outbreaks [2][3][4] and where appropriate to follow-up with *Correspondence: ejmctavish@ucmerced.edu 1 University of California, Merced, Merced, CA, USA Full list of author information is available at the end of the article regulatory or legal actions, it is particularly important to ensure that the WGS analysis methods used are validated.…”

Commentary: The Future of Whole-Genome Sequencing for Public Health and the Clinic

“…The last minireview, from the Genomics for Public Health Pathogen Surveillance session, outlines how the authors used WGS methods to create the GenomeTrakr network and databases for state, federal, and international laboratories to collaborate and share data during investigations of foodborne contaminants, to enhance food safety (5). The authors describe the development and growth of the FDA's efforts in using WGS methods from earlier case studies (6,7) to the regular use of WGS to support foodborne pathogen investigations.…”