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State Health Department using DNA sequencing to combat foodborne disease outbreaks

ALBANY – Pinpointing the source of a salmonella outbreak may soon take less time and be more accurate, thanks to next generation DNA sequencing techniques being used at the New York State Department of Health's Wadsworth Center Laboratories.

The introduction of small, affordable benchtop whole genome sequencing equipment has made it possible for clinical and public health labs to add the technology to their arsenal of tools to help combat foodborne pathogens.

The technology enables public health laboratories such as Wadsworth to rapidly identify strains of salmonella and in turn, quicken responses to potential outbreaks. Wadsworth is one of the first public health labs to have this technology, which places New York on the front lines of detecting foodborne pathogen outbreaks. Scientists at Wadsworth are now applying the technology to follow outbreaks in real time to further test its utility in a public health laboratory.

"Having this technology at our disposal will greatly enhance our capacity for protecting the public from foodborne illnesses, which sicken thousands of Americans every year," said Acting Commissioner Howard Zucker, M.D., J.D. "Knowing the exact source of an outbreak can prevent illness from spreading and prevent many people from getting sick."

Scientists at Wadsworth have been working with the Cornell University Food Safety Lab, who helped analyze the data, to demonstrate the effectiveness of this technology. Their proof of concept was published July 16 in the Centers for Disease Control and Prevention journal Emerging Infectious Diseases. The research uses a case study of an outbreak in a long-term care facility to demonstrate how the technique could benefit public health labs.

Traditional methods of assessing bacteria samples submitted to public health laboratories – based on pulsed-field gel electrophoresis (PFGE) – often do not deliver the level of precision needed to pinpoint specific strains of pathogens, their relationships to each other, and whether they share a common origin – vital information when trying to trace the source of illness outbreaks.

For Salmonella enterica serovar Enteritidis, for instance, 85 percent of isolates can be classified into just five PFGE types, and 40 percent belong to one subtype in particular.

"For most cases of Salmonella food poisoning, the lack of variation in the genome makes it almost impossible for scientists to differentiate one strain from another," said William J. Wolfgang, PhD, a scientist at Wadsworth who led the research. "Without the ability to differentiate, we cannot identify the precise source of an outbreak."

By sequencing all 4.5 million base pairs of the bacteria's DNA in a technique known as rapid whole-genome sequencing, scientists are able to get much more nuanced information.

"This kind of detailed information improves our ability to tell whether outbreaks are isolated, sporadic, or part of a cluster, which allows for more thorough epidemiologic investigations," Wolfgang said.

The salmonella samples used in the study came from an outbreak associated with a long-term care facility and were provided by the Connecticut Department of Public Health. The sequencing by Wadsworth and analysis by Cornell showed that the outbreak was larger than originally suspected. In addition to the seven facility residents who had been identified in 2010 as being sickened during the outbreak, the researchers discovered nine additional samples matching the strain from patients living in surrounding communities.

"This suggests a common contaminated source outside the long-term care facility," the researchers wrote in the paper. "Knowledge of these cases at the time of the outbreak might have improved the chances of finding the outbreak source, which was never identified."

It took eight days to sequence and analyze the samples for the case study, and the lab has since hastened the process. As the lab accumulates genome data and if technologies improve as expected, it may be possible to link sequenced samples to historical data and shorten the turnaround time to four days, Wolfgang said.

The study was partly funded by a grant from the USDA Agriculture and Food Research Initiative, the Center for Food Safety and Applied Nutrition at the FDA, and Wadsworth Center Public Health Genomics Center.

Whole genome sequencing is gaining traction in several other states through the GenomeTrakr initiative sponsored by the U.S. Food and Drug Administration (FDA). The FDA is providing equipment, reagents, funds for personnel, and training on the equipment to seven State Public Health Laboratories including New York. In return the public health labs upload raw sequence data to a centralized site for analysis. Any clusters that appear are reported back to local labs and epidemiologists, allowing for a quick, coordinated response.