Food-Illness Outbreak Investigations Will Be Transformed By Rapid Whole-Genome Testing

By Laurel Maloy, contributing writer, Food Online

Pulsed-Field Gel Electrophoresis may become a thing of the past. Rapid Whole-Genome Testing is expected to replace it with lab-friendly, bench-top equipment and the unsurpassed ability to identify specific pathogenic DNA

What DNA evidence has done for conviction rates for law enforcement authorities, whole-genome DNA sequencing is expected to do for food safety. As the global population steadily increases and the global food supply chain becomes more complex, the incidents of foodborne illnesses will also rise. Some studies suggest even though we are getting better at tracing back the infection to the source, in some years approximately 70 percent of outbreaks go unsolved. The average of unsolved cases over the last 10 years is between 34 and 44 percent. There is definitely room for improvement.

Introducing Rapid Whole-Genome DNA Testing

The FDA, the New York State Department of Health’s Wadsworth Center Laboratories, and researchers at the Cornell University Food Safety Lab may have made it possible for even the smallest labs to present great results. Desktop-sized genome sequencing equipment has arrived. Currently, while this new technology is being fully developed, the cost may still be prohibitive for smaller public health and clinical labs. However, technological advances tend to come down in price relatively quickly. Look at flat screen TVs and computer hard drives, for instance. The same is expected to hold true for this latest weapon in the war against foodborne illnesses. What remains to be seen is the cost associated with the number of qualified people available to analyze the DNA data.

Further evidence of the advantage of using Rapid Whole-Genome Testing, as opposed to Pulsed-Field Gel Electrophoresis (PFGE), was presented in the CDC’s Emerging Infectious Diseases, Volume 20, Number 8 — August 2014. The study utilizes 58 isolates of Salmonella enterica serovar Enteritidis obtained from a single, 2012 outbreak. Both PFGE and whole-genome testing results were analyzed in real time. The whole-genome sequencing tests were able to identify additional isolates that were not apparent with PFGE testing (page 1306 of the report/page 40 in the PDF).

The isolates were attributed to the outbreak, but differed from the isolates associated with PFGE typing. To sum it up, whole-genome testing was able to attribute more cases to the outbreak than what PFGE did, or ever could. According to the study, this “demonstrates the practicality of implementing this approach for outbreak surveillance in a state public health laboratory.”  Being able to analyze pathogens down to the DNA not only improves the detection of cases, but provides invaluable detail for outbreak investigators.

The Centers for Disease Control and Prevention (CDC) considers an outbreak to be evidence of two or more people getting the same illness from the same contaminated food. The keyword here is evidence, which is the reason the number of unsolved outbreaks is so high. Speaking of evidence, the Center for Science in the Public Interest (CSPI) says the missing key to unsolved cases is either the specific food item or the specific pathogen involved. CSPI’s study gave a letter grade to states considered to have the best, and the worst, reporting and systems of detection.

In giving grades, two things clearly stand out. First, the states with an A-grade had the best funding available and the most outbreaks — though the reason they have the most outbreaks is because they are more readily reported, investigated, and identified — because they have adequate funding. Secondly, the states with an F-rating are mostly southern states. These states have climates most conducive to pathogen growth, though they have the least amount of funding. Ironically, though NY seems to be leading the field in research, it received a D-grade.

• States with an A grade: FL, HI, MD, MN, OR, WA, and WY
• States with an F grade: AZ, AR, IN, KY, LA, MO, MS, NE, NM, OK, SC, TX and WV

It’s obvious, based upon this comprehensive report, the emphasis on food safety does not seem to be as much of a priority in some states, as in others. It is also evident that the newer, more accurate, and less expensive rapid whole-genome technology may help to even the odds in all states and around the world. When combined with European research on DNA Barcoding, perhaps the consumer can quit worrying so much about food safety.