Disease hunters are using genetic sequencing in their investigation of the ongoing food poisoning outbreak linked to romaine lettuce, a technique that is revolutionizing the detection of germs in food
The genetic analysis is being used to bolster investigations and—in some cases—connect the dots between what were once seemingly unrelated illnesses. It also is uncovering previously unfathomed sources of food poisoning, including one outbreak from apples dipped in caramel.
"There are a lot of outbreaks where they don't connect the dots. Now they're going to be connected," said Michael Doyle, a retired University of Georgia professor who is an expert on foodborne illness.
"It's turning around how outbreaks are figured out," said Bill Marler, a prominent Seattle lawyer who has made a business of suing companies whose products sicken people.
The CDC began using the technique in food poisoning investigations in 2013. Initially, state labs sent samples to a CDC lab in Atlanta for testing. Now, the CDC is working to get labs in all 50 states up and running.
Last year, the federal agency awarded about $32 million to state and city health departments to work on foodborne, waterborne and fungal disease outbreaks. That included $12 million to help them set up whole genome sequencing technology.
This 2002 electron microscope image made available by the Centers for Disease Control and Prevention shows the kind of listeria bacteria that is behind some food poisoning outbreaks. (Elizabeth White/CDC via AP)
Since whole genome sequencing began, the CDC says it's catching more listeria outbreaks with a food source identified. By that measure, the number rose from about two per year to an average of more than six per year from 2014 to 2016.
One of the first success stories came to a couple of weeks after Halloween in 2014, when listeria cases began popping up in Arizona, New Mexico, and the Midwest. Through whole-genome sequencing, investigators discovered about three dozen people had been sickened.
Scientists hadn't considered them a threat, because apples and caramel aren't hospitable to listeria individually. But it turns out that putting a stick in a caramel-covered apple gives germs a door into tiny spaces between caramel and the apple's skin.
In 2015, state officials in South Carolina and Texas found listeria in tests of Blue Bell-brand ice cream products. Investigators used pulsed-field gel electrophoresis to find 11 illnesses with a similar genetic pattern, but whole genome sequencing definitively linked 10 and caused one to be tossed out as unrelated. Some of the illnesses had happened as far back as 2010.
Whole genome sequencing is becoming increasingly important, but it's not yet the basis of outbreak solving. It was used in the current investigation of E. coli bacteria found in romaine lettuce grown in Arizona, which has sickened at least 84 people in 19 states, according to a CDC update released Wednesday. But "that's not how we first detected the outbreak," said Matthew Wise, a CDC food poisoning investigator.
It was more crucial in an investigation last year of a 21-state salmonella outbreak that ultimately was linked to ground beef. Whole genome sequencing allowed health officials to wade through a wave of cases to parse out the illnesses that were most closely matched and then look for a common origin, Wise said.