ST. LOUIS — As with so many sessions at this year’s conference of the International Association for Food Protection, whole genome sequencing was in the spotlight during a discussion of Salmonella problems on the Delmarva peninsula.

Tourism and agriculture are the top activities on the 170-mile stretch of land that takes its name from the states of Delaware, Maryland and Virginia but in recent years the area has been plagued by Salmonella on its tomatoes and cucumbers. Progress is being made, though as scientists from state and federal agencies working with local growers have confirmed that Salmonella Newport is in the environment and can be mitigated. Before that work began, though, the problem had to be noticed, and some working on the problem credit the immediate past deputy commissioner of the Food and Drug Administration, Mike Taylor, with getting the ball rolling. “Mike Taylor saw the data and told us to go there and talk to people, set up some research and find out what’s going on,” said Eric Brown, FDA’s director of the division of microbiology in the office of regulatory science. People like Brown and Ian Williams, chief of the Outbreak Response and Prevention Branch at the Centers for Disease Control and Prevention, have been aware of the Salmonella situation in the Delmarva area for years. Williams said Tuesday seasonal spikes in Salmonella that coincide with fresh tomato and cucumber season have been on the radar with about 60 to 200 cases recorded. Advances in laboratory technology such as whole genome sequencing (WGS) have allowed public health agencies to detect and confirm Salmonella outbreaks linked to fresh produce from Delmarva with increasing accuracy. Williams described the differences between WGS and Pulsed Field Gel Electrophoresis (PFGE) typing in terms of reading a book. “With PFGE you might test about 30 slices (of a bacterium) but with whole genome sequencing you look at 3 million,” Williams said. “It’s like comparing the words of one chapter of a book to the whole book. You get a lot more information.” That information has shown the Delmarva region is home to Salmonella and helped confirm five outbreaks liked to Delmarva produce and shown definite links between the produce and four other outbreaks from 2002-2011. Scientists are unsure if there is a link for three other outbreaks in 2004, 2008 and 2013. One thing the research has shown is that the region is a Salmonella hotspot. In 2014 there were a dozen subclusters of infections that provided investigators with an opportunity to review 58 different isolates of Salmonella. Eleven of the 12 subclusters matched and the source was traced to cucumbers from one farm. The other subcluster was shown through WGS to be completely different and was not linked to the cucumber farm. FDA investigators went to the farm, but not until months after harvest, which made it impossible to collect relevant samples. One fact they discovered, though, was that poultry litter had been used as a fertilizer on the cucumbers about 120 days before harvest. FDA’s “Team Tomato” did not give up, though. They knew Salmonella Newport was in the environment, but they had not identified the so-called reservoirs of the pathogen in Delmarva. It can persist in water and soil for years, so the team put on their boots and went to work. Brown said Team Tomato tested everything including tomatoes, cucumbers, weeds, insects, soil, water, animal and bird droppings. They found Salmonella Newport most prevalent in creeks and streams and their sediment. Brown said one compelling bit of data discovered was that compared to soil from tomato fields on the West coast, the Delmarva soil has much less lactic acid. Considering Salmonella Newport is much less common — almost unknown — as a problem for the West coast growers, there is some discussion now about whether it would be helpful to introduce lactic acid to the operations in the East. Although the research is ongoing, growers in the Delmarva region are already making changes and they are apparently having an impact because the expected seasonal outbreaks in 2015 and so far this year are below previous normals.

Laura Strawn of the Virginia Polytechnic Institute and State University said growers are using good agricultural practices, worker training and continuing education and refresher training to combat the pathogen problem. The training is now available in multiple languages because of the high numbers of immigrant workers, which Strawn said has made a big difference. The growers are switching from surface water sources to wells and moving existing wells away from poultry operations. In Maryland alone, 900 growers have been trained in good agricultural practices and good handling practices. Strawn said one important factor in the training programs is that they have been tailored for the size of the operations. Farms in the Delmarva region range from one-half acre to 2,000 acres, which Strawn said requires very different approaches. (To sign up for a free subscription to Food Safety News, click here.)