“The genetics does not help in determining the source, or which field it came from, or when it happened. That requires old-fashioned traceability and epidemiology,” says David Acheson, MD, former FDA associate commissioner for foods. “If you don’t have the bacteria on the commodity, the genetics doesn’t help you,” he tells Food Quality & Safety.
Also mystifying is that the contamination went totally undetected. “Given the amount of testing that occurs in the industry, both pre-harvest and throughout the supply chain, how could something have such a wide public health impact but not have been detected through testing?” asks Jennifer McEntire, PhD, vice president for food safety and technology at the United Fresh Produce Association.
“In the quest for more rapid tests that often have shorter enrichment times, are we limiting our ability to detect microorganisms? I don’t know, but I feel like the question needs to be asked,” Dr. McEntire tells Food Quality & Safety.
WGS Going Global
The World Health Organization and other international groups have been encouraging wide adoption of WGS technology to help manage infectious diseases, including foodborne ailments. While industrialized countries are using WGS for food safety management, its application in developing and transitional countries has been limited. According to a 2016 report by the United Nations Food and Agriculture Organization, barriers include cost, data storage, infrastructure requirements (such as high-speed Internet), legal issues, data ownership, sharing, and intellectual property rights, and sustainability.
Several of these issues are not unique to developing countries, and present challenges to the U.S. and other developed nations. “Food producers, researchers, and regulators are each affected by the current absence in standards around laboratory preparation and bioinformatics methods,” explains Kristen Beck, PhD, technical lead for the Consortium for Sequencing the Food Supply Chain and a research staff member at IBM Research-Almaden. “This makes standardization and comparative analysis very challenging,” she tells Food Quality & Safety.
An additional limiting factor is the cost of culturing microbial samples. “This will need to be orders of magnitude less than today’s per-sample cost to be usable at the scale of current routine testing,” Dr. Beck says. But as costs decline, this will become less of an issue and “will further enable technologies, such as culture-free sequencing of food microbiomes for hazard detection.”
Another challenge to adoption lies in data sharing—who can access potentially sensitive information derived from WGS, including information on virulence factors and antibiotic resistance. “How will these data be used and interpreted, and who will have access?” asks Claudia Narvaez, PhD, professor of food safety at the University of Manitoba. “And how will regulatory agencies interpret the findings, and how could this affect current regulations?”
While policymakers and regulators wrestle with these issues, researchers and equipment manufacturers continue to make advancements in genomics instrumentation. For example, researchers at the University of Georgia Center for Food Safety have developed a portable device that can shorten pathogen sequencing time from one or two days to one or two hours. Instead of culturing the sample, which can take 24-48 hours, the USB drive-sized device uses tiny magnetic beads coated with antibodies to separate pathogen DNA from the sample. It then amplifies the DNA and sequences it in real time.
In another example, researchers at Pittsburgh State University have created hybrid nanosensors composed of special iron oxide particles blended with optical dye, plus antibodies that specifically latch onto E. coli O157:H7 cells. By combining magnetic resonance imaging technology with fluorescence emission, they can quickly detect the pathogen in fluids, such as milk or lake water.
Even PCR technology, long a mainstay of food industry testing, is being upgraded. Bio-Rad Laboratories’ Droplet Digital PCR (ddPCR) technology allows for sample partitioning. “In traditional PCR, a single measurement is performed on a single sample. In ddPCR, a single sample is partitioned into thousands of nanosized droplets, allowing thousands of independent, single amplification events within that sample,” explains Mike Clark, the company’s international PCR group manager. This can help determine whether a single E. coli cell contains the virulence genes making it pathogenic or if those genes are just present in different cells within a food sample.