ATLANTA (AP) – In the investigation of the ongoing food poisoning outburst associated with romaine lettuce, the disease hunters use genetic sequencing, a technique that revolutionizes the detection of germs in food.
The genetic analysis is used to strengthen investigations and in some cases connect the dots between seemingly unrelated diseases. It also uncovers previously unfathomable sources of food poisoning, including an outbreak of caramel-dipped apples.
So far, most of the work has focused mainly on one germ, Listeria. But it is expanding. By the end of this year, laboratories in all 50 states are also expected to use gene sequencing for much more common causes of food poisoning outbreaks, including Salmonella and the E. coli bacteria associated with the recent salmon outbreak
The identifiable outbreaks will probably explode even if the number of diseases does not.
"There are many outbreaks where the dots are unconnected and now they will be connected," said Michael Doyle, a retired professor at the University of Georgia who is a food poisoning expert.
Not only that, the new DNA tests enable detectives to detect food contamination before anyone becomes aware of a resulting human disease ̵
"It's about how outbreaks are found out" said Bill Marler, a prominent lawyer from Seattle, who has set himself the task of knocking out companies whose products make people sick.
Marler added that the program is at an early stage and it is too early to call it a success. But he said the new approach has the potential to transform how and when outbreaks occur.
The Center for Disease Control and Prevention is driving the program forward. It estimates that 48 million Americans suffer from food poisoning every year – and 3,000 die.
The new technique relies on the sequencing of the entire genome, which has been used in biology for more than two decades. The laboratory process determines almost the entire DNA of an organism, the genetic material needed to build and maintain an organism. And scientists use software to compare the DNA of samples to see if they are the same strains and how resistant they are to current drugs.
The technique allows for faster, cheaper, and automated analysis, Dr. Robert Tauxe. one of the leading experts of the CDC for food poisoning.
It is planned to use the technology against several germs that cause food poisoning, but so far all the work has been focused on Listeria. The bacteria cause about 1,600 diseases a year, a tiny fraction of the diagnosis of foodborne diseases in the US. But it is a particularly deadly infection that kills almost every fifth person who gets it.
Historically, listeria-induced epidemics were known as "the cemetery of epidemiology". It could take weeks for people to develop symptoms, meaning that food evidence was discarded – and some of the patients were dead – when officials began to clarify things.
From 1983 to 1997, only five Listeria in the region were identified United States. They were obvious and large – with a median of 54 cases per outbreak.
It was the same with other food poisoning outbreaks.
"Most food-borne outbreaks were discovered because it happened in one place," as in a city where the customers of a popular restaurant got sick, Tauxe said.
Outbreaks were investigated by asking people what they ate before they got sick, and then comparing comments to see what patients had in common.
The field made a big move in the 1990s, after a frightening eruption erupted in the Seattle area. Four deaths and more than 700 diseases in four states were eventually attributed to poorly cooked, E. coli-contaminated hamburgers at the restaurant "Jack in the Box".
The outbreak prompted the CDC to develop a program based on pulsed gel electrophoresis, in which researchers could view the DNA of a seed in lumps. It helped health officials to link diseases more easily, but it was imperfect: it could not match exactly and sometimes missed when cases were linked.
Then came the entire genome sequencing.
The CDC began using this technique in food poisoning investigations in 2013. Initially, state laboratories sent samples to a CDC lab in Atlanta for testing. Now, the CDC is working to get labs running in all 50 states.
Last year, the federal agency awarded about $ 32 million to state and city health departments working on food, water and fungal diseases. This included $ 12 million to help them build genome sequencing technology.
Since the entire genome sequencing began, the CDC says it detects more Listeria outbreaks with an identified food source. By this measure, the number increased 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 a few weeks after Halloween in 2014, when Listeria cases hit Arizona, New Mexico and the United States Midwest. Through full genome sequencing, the researchers found that about three dozen people were ill.
In interviews, patients and their families did not mention foods commonly associated with Listeria. But most said they had eaten packaged caramel apples.
The scientists had not considered them a threat, since apples and caramel are not individually suitable for Listeria. But it turns out that inserting a stick into a caramel-coated apple gives germs a door into tiny spaces between caramel and apple skin.
In addition to staining food that was previously considered non-threatening, genome sequencing has the potential to redirect research: in recent outbreaks of recent spills found at food inspections, product recalls have led to product recalls before any of knew an outbreak. Then sequencing the entire genome helped find and confirm diseases.
In 2015, state officials in South Carolina and Texas found listeria in tests on Blue Bell ice cream products. The researchers used pulsed-field gel electrophoresis to find 11 diseases with a similar genetic pattern, but complete genome sequencing was definitely linked to 10, which made them look unrelated. Some of the diseases had already occurred in 2010.
"They take up cases that are five years old, that's revolutionary," said Doyle.
Sequencing the entire genome is becoming increasingly important, but it is not the basis for the solution to the outbreak. It was used in the current investigation of E. coli bacteria in romaine lettuce in Arizona, which used to cause at least 84 people in 19 states to become ill, according to a CDC update released Wednesday. But "this was the first time we discovered the outbreak," said Matthew Wise, a CDC food poisoning investigator.
It was more important last year to investigate a 21-stage salmonella outbreak that was ultimately associated with ground beef. Sequencing the entire genome allowed health authorities to go through a wave of cases to analyze the most closely matched diseases and then search for a common origin, Wise said.
"With our previous technology," said Wise, "we would have had a really difficult time solving it."
AP video journalist Robert Ray in Atlanta has contributed to this report.
This Associated Press series was produced in collaboration with Howard Hughes Medical Institute of Science Education. All content is the sole responsibility of the AP