Microbiologist Robert Brackett predicts that more precise gene-based tools will help pinpoint the source of outbreaks in record time.
Today, the risk is stark: Forty-eight million Americans—one out of every six people—suffer from a foodborne illness every year, according to the U.S. Centers for Disease Control and Prevention (CDC). Within that group 128,000 people are hospitalized, and 3,000 die. But Robert Brackett, vice president of the Illinois Institute of Technology (IIT) and director of the school’s Institute for Food Safety and Health, believes promising new technological advances like DNA “fingerprinting” are going to help turn the tide.
“Regulatory agencies and food companies have much better resolution and ability today to track specific strains of organisms than they did a decade ago,” says Brackett. Advances in genetic mapping and DNA sequencing will continue to make it easier, he says, to determine quickly whether people in different locations have been sickened by food from a single source.
Beyond simply showing that there’s salmonella in a food sample, one can show that it came from a certain factory in a specific place.”
The traditional method for detecting and identifying pathogens in food—culturing the agent from food samples in a laboratory—can require days to weeks for a result. In addition, regulators need evidence connecting multiple illnesses to a specific source before they can order a batch of food recalled or close a plant.
“When multiple people in multiple states get sick, it can take regulators and public health agencies weeks or months to find patterns and link cases into an outbreak,” says Brackett. “Sometimes experts think an outbreak is restricted to a particular lot number or region, but as they do more investigation they find that it’s happening in multiple states or multiple products. Until they are absolutely sure about the outbreak, they are reluctant to request a recall.”
Brackett has wrestled with this challenge from many perspectives: He directed the U.S. Food and Drug Administration’s Center for Food Safety and Applied Nutrition from 2004 through 2007, then served as senior vice president and chief science and regulatory officer for the Grocery Manufacturers Association. But he’s particularly optimistic about the impact of the new Food Safety Modernization Act (FSMA), signed into law in 2011, in helping to propel new technological advancements. Rules implementing the law are scheduled to take effect starting in August 2015.
“Food companies will have to analyze what risks exist in their plants and develop food safety plans, and will be accountable for following up,” says Brackett. “It’s a more predictive and proactive approach.”
Dominant gene-based tactics
Regulators and food manufacturers may also find it easier to comply with the new FSMA rules as rapid advances in genomics (the study of genes and their functions) give them better tools for identifying pathogens like E. coli, Listeria and salmonella, says Brackett.
For example, scientists can use a process called polymerase chain reaction (PCR) to make many copies of small segments of DNA quickly and inexpensively. Tests based on PCR have become valuable alternatives for detecting the presence of infectious agents in many types of food. Another process, pulsed-field gel electrophoresis (PFGE), can identify subtypes of many pathogenic bacteria. PulseNet, a national laboratory network headquartered at the CDC, is using PFGE to produce DNA fingerprints from reported foodborne illnesses nationwide, so states can compare bacteria from sick people in far-flung locations.
To identify suspect bacteria even more precisely, the FDA and a handful of laboratories nationwide have begun using whole genome sequencing—a process that determines an organism’s complete DNA sequence at once. This method performs the same function as PFGE, but it can distinguish between strains of an organism that are very closely related. (PFGE targets parts of an organism’s genome, not the entire sequence, so it may not detect minor variations between closely related strains.)
“Whole genome sequencing is helping regulatory agencies identify discrete problems much more precisely,” Brackett says. “Beyond simply showing that there’s salmonella in a food sample, one can show that it came from a certain factory in a specific place.”
In January 2015, IBM Research and Mars Inc. announced a two-year joint project called the Consortium for Sequencing the Food Supply Chain. This effort will sequence the genes of a wide range of organisms present in food industry supply chains, from ingredients to kitchens and packaging plants. The goal is to create a database of known organisms that includes information about how they develop in food industry settings. FDA’s whole genome sequencing and PFGE networks currently are reliant on live isolates of specific pathogens, but this initiative seeks to produce a broader baseline of pathogens that may not yet be recognized as potential food contaminants. IBM and Mars believe that companies will join the consortium so they can use the database to identify areas in their own plants where contamination could occur.
“The Food Safety Modernization Act stresses prevention, so companies are motivated to try to find pathogens and eliminate places that harbor them,” Brackett says. “They can take samples of a food or a surface [in a factory], evaluate the genetic makeup of everything they find there, and look for patterns instead of a particular pathogen. The focus is on understanding the microbial ecology that exists in their plants.”
Although these methods are promising, they are not silver bullets, stresses Brackett. And other trends, such as the globalization of food markets, make food safety regulation increasingly challenging.
“Regulatory agencies don’t always have methods for detecting contamination in foods that they have never seen before, or know that it should be handled in a certain way,” Brackett points out. “As we’re exposed to new types of foods from new locations, we need to learn about them from their host countries and do some public education.”
In the meantime, new smart technologies could also help consumers prepare food safely so that any existing pathogens are eradicated before the food is eaten. Manufacturers already are designing refrigerators with compartments to keep different types of food at optimum temperatures. Brackett says he would like to see more features like this, such as microwaveable food packages with codes that transmit cooking instructions, or packages that contain biosensors to detect contamination.
For now, he says, one of the best investments consumers can make is a set of color-coded cutting boards for preparing meat, seafood, poultry and produce. “They’re dishwasher-safe and inexpensive, and they make it easy to avoid cross-contaminating foods,” says Brackett. “The other thing everyone should do is get a good digital thermometer and use it to make sure that things are cooked. They’re affordable and reliable, and it’s a good habit.”