Experts decode germs' DNA to fight food poisoning

April 6, 2014 by Lauran Neergaard
This photo taken Nov. 25, 2013 shows microbiologist Dr. Molly Freeman pulling Listeria bacteria from a tube to be tested for its DNA fingerprinting in a foodborne disease outbreak lab at the federal Centers for Disease Control and Prevention in Atlanta. The nation's disease detectives are beginning a program to try to outsmart outbreaks by routinely decoding the DNA of deadly bacteria and viruses. The initial target: Listeria, a kind of bacteria that's the third-leading cause of death from food poisoning, and one that's especially dangerous to pregnant women. Already, the technology has helped to solve a small listeria outbreak that killed one person in California and sickened seven others in Maryland.(AP Photo/David Goldman)

Chances are you've heard of mapping genes to diagnose rare diseases, predict your risk of cancer and tell your ancestry. But to uncover food poisonings?

U.S. disease detectives are beginning a program to try to outsmart outbreaks by routinely decoding the DNA of potentially deadly bacteria and viruses.

The initial target is listeria, the third-leading cause of death from food poisoning and bacteria that are especially dangerous to pregnant women. Already, the government credits the technology with helping to solve a that killed one person in California and sickened seven others in Maryland.

"This really is a new way to find and fight infections," said Dr. Tom Frieden, director of the U.S. Centers for Disease Control and Prevention. "One way to think of it is, is it identifying a suspect by a lineup or by a fingerprint?"

Whole genome sequencing, or mapping all of an organism's DNA, has become a staple of medical research. But in , it has been used more selectively, to investigate particularly vexing outbreaks or emerging pathogens, such as a worrisome new strain of bird flu.

For day-to-day outbreak detection, officials rely instead on decades-old tests that use pieces of DNA and aren't as precise.

Now, with becoming faster and cheaper, the CDC is armed with $30 million from Congress to broaden its use with a program called advanced molecular detection. The hope is to solve outbreaks faster, foodborne and other types, and maybe prevent infections, too, by better understanding how they spread.

"Frankly, in public health, we have some catching up to do," said the CDC's Dr. Christopher Braden, who is helping to lead the work.

This photo taken Nov. 25, 2013 shows microbiologist Heather Carleton pulling up results of Listeria bacteria DNA while demonstrating a whole-genome sequencing machine called a MiSeq in a foodborne disease outbreak lab at the federal Centers for Disease Control and Prevention in Atlanta. The nation's disease detectives are beginning a program to try to outsmart outbreaks by routinely decoding the DNA of deadly bacteria and viruses. The initial target: Listeria, a kind of bacteria that's the third-leading cause of death from food poisoning, and one that's especially dangerous to pregnant women. Already, the technology has helped to solve a small listeria outbreak that killed one person in California and sickened seven others in Maryland.(AP Photo/David Goldman)

As a first step, federal and state officials are rapidly decoding the DNA of all the listeria infections diagnosed in the U.S. this year, along with samples found in tainted foods or factories.

It's the first time the technology has been used for routine disease surveillance, looking for people with matching strains who may have gotten sick from the same source.

If this pilot project works, the CDC says it sets the stage to eventually overhaul how public health laboratories around the country keep watch on food safety, and to use the technology more routinely against other outbreaks.

"Genome sequencing really is the ultimate DNA fingerprint," said George Washington University microbiologist Lance Price, who uses it to study the spread of antibiotic-resistant bacteria and says the CDC's move is long overdue.

Especially in foodborne outbreaks, the technology will increase investigators' ability to nab the right culprit, he said. The faster that happens, the fewer people may get sick.

"This is going to change everything as far as source attribution," Price added. "Recalls are expensive, the industry doesn't like them," and they've got to be accurate.

Today's standard tests sometimes miss linked cases or provide false leads. For example, U.S. officials in 2012 initially thought a salmonella outbreak in the Netherlands, associated with smoked salmon, was linked to cases here. Later sequencing showed the bugs were different.

"The current methods of subtyping salmonella aren't very good," said epidemiologist David Boxrud of the Minnesota Department of Health, part of a pilot Food and Drug Administration network that has begun sequencing that germ and certain others when they're discovered in food. State labs in Arizona, Florida, Maryland, New York, Virginia and Washington state also participate.

This photo taken Nov. 25, 2013 shows microbiologist Ashley Sabol extracting Listeria bacteria for genome sequencing in a foodborne disease outbreak lab at the federal Centers for Disease Control and Prevention in Atlanta. The nation's disease detectives are beginning a program to try to outsmart outbreaks by routinely decoding the DNA of deadly bacteria and viruses. The initial target: Listeria, a kind of bacteria that's the third-leading cause of death from food poisoning, and one that's especially dangerous to pregnant women. Already, the technology has helped to solve a small listeria outbreak that killed one person in California and sickened seven others in Maryland. (AP Photo/David Goldman)

Sequencing also promises to reveal drug resistance and how virulent a germ is more quickly than today's tests, and track how it's spreading from one person to another through tiny genetic changes that act like footprints.

Key to making it work is the computing power of a massive federal database being used to store the gene maps, said Duncan MacCannell, the CDC's senior adviser for bioinformatics. It's one thing to analyze bacterial DNA culled from a few dozen sick people during an outbreak, and another to compare samples from thousands.

Until recently, the CDC didn't have the "tools and approaches to make sense of this much data," he said.

The listeria project began as officials were investigating some sick Maryland newborns and their mothers. Genome sequencing showed those cases were linked to a California death, helping investigators determine which foods to focus on, said Dr. Robert Tauxe, CDC's leading foodborne disease sleuth.

Standard tests prompted recall of the FDA's suspect, a brand of Hispanic-style cheese. Last month, the government announced that sequencing also confirmed listeria from the recalled cheese matched germs from the patients.

"We expect to be able to match more and more of what we find in people to what we find in food," as the project grows, Tauxe said.

Explore further: One dead, babies ill from listeria linked to cheese

Related Stories

One dead, babies ill from listeria linked to cheese

February 22, 2014
One person has died and three newborns have become ill in an outbreak of listeria linked to Hispanic-style cheese.

Company recalls 16 varieties of cheese after death

February 24, 2014
(AP)—A Delaware company has recalled 16 varieties of cheese after some of the cheeses were linked to a death in California and illnesses in newborns.

Listeria food poisoning hits elderly, moms-to-be hardest: CDC

June 4, 2013
(HealthDay)—Soft cheese and raw produce have caused many recent listeria outbreaks in the United States, and at least 90 percent of cases typically occur among seniors, pregnant women, newborns and people with weakened ...

Listeria outbreak prompts cheese recall

July 8, 2013
(HealthDay)—A recent listeria outbreak that caused one death and sickened four other people seems to be linked to cheeses made by a Wisconsin firm, the U.S. Centers for Disease Control and Prevention reports.

21 deaths now linked to listeria in cantaloupe

October 7, 2011
(AP) -- Federal health authorities say a nationwide outbreak of listeria in cantaloupe is now responsible for 21 deaths and the number may continue to grow.

Recommended for you

MRSA emerged years before methicillin was even discovered

July 19, 2017
Methicillin resistant Staphylococcus aureus (MRSA) emerged long before the introduction of the antibiotic methicillin into clinical practice, according to a study published in the open access journal Genome Biology. It was ...

New test distinguishes Zika from similar viral infections

July 18, 2017
A new test is the best-to-date in differentiating Zika virus infections from infections caused by similar viruses. The antibody-based assay, developed by researchers at UC Berkeley and Humabs BioMed, a private biotechnology ...

'Superbugs' study reveals complex picture of E. coli bloodstream infections

July 18, 2017
The first large-scale genetic study of Escherichia coli (E. coli) cultured from patients with bloodstream infections in England showed that drug resistant 'superbugs' are not always out-competing other strains. Research by ...

Ebola virus can persist in monkeys that survived disease, even after symptoms disappear

July 17, 2017
Ebola virus infection can be detected in rhesus monkeys that survive the disease and no longer show symptoms, according to research published by Army scientists in today's online edition of the journal Nature Microbiology. ...

Mountain gorillas have herpes virus similar to that found in humans

July 13, 2017
Scientists from the University of California, Davis, have detected a herpes virus in wild mountain gorillas that is very similar to the Epstein-Barr virus in humans, according to a study published today in the journal Scientific ...

Vaccines protect fetuses from Zika infection, mouse study shows

July 13, 2017
Zika virus causes a mild, flu-like illness in most people, but to pregnant women the dangers are potentially much worse. The virus can reduce fetal growth, cause microcephaly, an abnormally small head associated with brain ...

1 comment

Adjust slider to filter visible comments by rank

Display comments: newest first

Jaeherys
not rated yet Apr 06, 2014
You can tell they are a rich lab because their 50 mL tubes are hinged :P.

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.