Gene mapping used by US scientists to combat food poisoning
US disease detectives to decode DNA of potentially deadly bacteria
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?
US disease detectives are beginning a programme 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 is especially dangerous to pregnant women. Already, the government credits the technology with helping to solve a listeria outbreak 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 of the US Centres for Disease Control and Prevention (CDC). "One way to think of it is: is it identifying a suspect by a line-up or by a fingerprint?"
Whole genome sequencing, or mapping all of an organism's DNA, has become a staple of medical research. In public health, 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 are not as precise. Now, with genome sequencing becoming faster and cheaper, the CDC is armed with US$30 million from Congress to broaden its use with a programme 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.
As a first step, federal and state officials are rapidly decoding the DNA of all the listeria infections diagnosed in the US this year, along with samples found in tainted foods or factories.
It is 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 would increase investigators' ability to nab the right culprit, he said.
"This is going to change everything as far as source attribution," Price added.
Today's standard tests sometimes miss linked cases or provide false leads. For example, officials in 2012 initially thought a salmonella outbreak in the Netherlands, associated with smoked salmon, was linked to cases in the US. Later sequencing showed the bugs were different.