“As the size of the (GenomeTrakr Database) grows, so will its strength as a tool to help focus and speed investigations into the root causes of illnesses.”

– Dr. Marc W. Allard, senior biomedical research services officer,
Food and Drug Administration

Introduction

DNASimilar to how authorities use DNA evidence to investigate crime, Food and Drug Administration (FDA) officials use the same technology to investigate food outbreaks. This technology is called whole genome sequencing (WGS)—the latest, most advanced tool currently being used to support investigations of foodborne illness. WGS technology is the motivation behind implementing a worldwide network that reports pathogenic origin in aims of expediting foodborne illness outbreaks.

Using WGS technology, the FDA is attempting to build a network in which federal, state, and international food safety laboratories can share information. Laboratories upload a pathogen’s genetic sequence, which can be publicly accessed via the database. The FDA states that its main focus is to expand the scope of outreach efforts while making foodborne illness investigations quicker and more effective.

What Is Whole Genome Sequencing?

WGS is the rapid process of solving how DNA nucleotides are ordered in organisms. All living things are made up of these DNA bases, and are characterized by the letters A, C, G, and T. Human beings have a very complex genomic pattern that is made up of close to 4 billion of these genetic letters.

Bacteria, in comparison to humans, have far fewer genes and letters that comprise their makeup. Scientists study the disease-causing genetic material within bacteria, in an attempt to correlate which are pathogens, to find the cause of an outbreak.

How does this work? Eric Brown, director of the Division of Microbiology at the FDA’s Center for Food Safety and Applied Nutrition, states, “Think of Salmonella, for instance, as a tribe of many thousands of subtly different pathogens.” The DNA makeup of each pathogen has a “signature,” similar to how each human being has their own fingerprint.

Brown continues: “Whole genome sequencing helps us to crack the genetic code. A pathogen can evolve very quickly, and begin to acquire unique genetic signatures that identify it as coming from a particular geographic region.”

This process of narrowing down the source using geographic data is essential to the investigation. Brown states, “By pairing genomic information with geographic information, we can narrow the search for the source of a contaminated food ingredient, even if it is located halfway around the world.”

Foodborne outbreak investigations are very time-sensitive—the more time that elapses directly correlates with the number of people who become ill. Using genome sequencing expedites investigatory processes, which makes it possible for health officials to: (a) remove the food product from market, and (b) alert consumers regarding food safety hazards related to the product.

Recent Cases of Genomic Sequencing

bacteriaWGS technology was recently used while investigating a multi-state outbreak of Listeria monocytogenes. DNA sequencing via WGS resulted in the FDA identifying the likely source, including the specific company, location, and product. In this case, frozen food products by CRF Frozen Foods in Pasco, Washington.

In the CRF Frozen Foods case, the FDA, in cohort with the Centers for Disease Control and Prevention (CDC) and state health and agriculture departments, WGS helped to match frozen food samples collected by investigators to bacterial DNA found in people who’d fallen ill with listeriosis. CRF Frozen Foods was then contacted with the investigation’s findings. The company voluntarily recalled hundreds of frozen fruit and vegetable products across 42 brand names.

Shortly after the CRF investigation, investigators were able to identify and match a strain of listeria from another production facility located in Pasco. Samples taken from the production facility were the same as those obtained from people who had become sick. Using the process of elimination, the FDA pinpointed the source as the Oregon Potato Company, which subsequently issued a recall of onion-based products, followed by a secondary recall of related products.

Role of the Database

Collaboration efforts play an important role in foodborne outbreak investigations. The FDA now implements an international database, the International Nucleotide Sequence Database Collaboration (INSDC) to aid in such efforts. Laboratories that are part of INSDC electronically upload the genetic code of pathogens—a code that is supplemented with various information about the pathogen, including the location(s) where the pathogen was initially found.

This valuable information is entered into a publicly accessible database appropriately named GenomeTrakr. Created in late 2012, the GenomeTrakr network is shared and accessed by laboratories on the federal, state, and international level. In essence, the FDA is directing outbreak efforts on a global scale.

Currently, the database contains genome sequencing information on over 50,000 strains of bacteria, called isolates. The database is also growing exponentially, as researchers are entering new sequencing data on over 1,000 isolates each month. As one prominent researcher states, “We’re on a growth curve, and there’s no evidence that it’s going to stop.”

 

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