Issue link: https://read.dmtmag.com/i/696150
26 JULY 2016 Good Fruit Grower www.goodfruit.com O ver the past year or so, whole genome sequencing has gotten a lot of attention as a means of pinpointing where an illness outbreak started, but what exactly is it and how does it work? Whole genome sequencing is a tool to determine an organism's full complement of genetic material, or the entire DNA sequence, in one fell swoop. An organism's DNA sequence is made up of building blocks, called nucleotides, that serve as the blueprint for that particular organism, whether it is a bacterium like Listeria or a human being. The more closely two organisms are related to one another, the more similar their DNA. Therefore, whole genome sequencing can be used to provide evidence in paternity suits, or to determine whether the bacteria causing a person's foodborne illness is possibly the descendent of the bacteria found on machinery involved in making that food, or on the fresh fruit from an orchard. Before whole genome sequencing was developed, scientists used other methods to tell organisms apart, but whole genome sequencing provides a much more What is whole genome sequencing? Cracking cold cases Besides using whole genome sequencing to track current illness, the U.S. Food and Drug Administration (FDA) has begun using the technique to revisit long-past instances of illness so it can find their source, much as police cold-case squads reinvestigate old crimes to find the culprit. "A lot of what's going on in triggering what seems like the weekly product recalls nowadays is the FDA's, or state public health labs, conducting market-basket surveillance testing," said Trevor Suslow, extension research specialist in the Department of Plant Sciences at the University of California. In other words, he explained, regulators are collecting bacterial samples from various foods and food-related locations during their standard or commodity- targeted inspections, and subjecting those positive samples to whole genome sequencing. When the FDA finds pathogens from those routine inspections or assignments, it is comparing them against the database of illnesses kept by the Centers for Disease Control and Prevention (CDC), and looking for connections between the two. "We're talking about going back and looking at past cases, finding indistinguishable isolates associated with your apples or cherries or whatever, and then holding you responsible for those illnesses," he said. "That's really how the FDA is using whole genome sequencing — as both a current and as a retrospective assessment of food-safety risks to determine responsibility." Although Suslow said the FDA seems confident that whole genome sequencing is an accurate tool for tracing illnesses, he is not so sure. "We're starting in my lab to develop data based on environmental testing, and it's suggesting that such results may not be as ironclad as some might think," he said, noting that his research group has been conducting this study specifically in tree fruit orchards for about two years. "We're now getting the first wave of isolates characterized by whole genome sequencing, in addition to other techniques, FARM THE SUN ON APPLES Bitter Pit Photosynthesis Color & Fruit Finish ON CHERRIES Size & Firmness Shelf Life Harvest Timing Fruit Maturity Rain Cracking ON PEARS Photosynthesis Cork Spot & Greening BioGro.com / Cal-8 W W W . B I O G R O . C O M L E A R N M O R E A T A G R O N O M I S T S RANDALL MONTGOMERY (509) 439-3018 MIKE HULBERT (360) 770-2374 PGR FRIENDLY! JUST ADD NUE CAL-8 WITH YOUR PGRS! CAL-8 NUE PGR FRIENDLY! QUALITY CA PRODUCT + 35% ORG ACIDS MARCHANT LADDERS, INC. Quality Ladders Since 1978 509-882-1912 Grandview, Washington Heavy Duty Top Bracket Heavy Duty Bottom Step Extra support on longer steps, all steps 3" wide • Buy factory direct • BEST ladder at the BEST price • Available 6 to 16 foot Built of sturdy, lightweight ALUMINUM— Specifically for agriculture "The Standard for the Serious Orchardist"