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 Previously, samples from sick patients were sent to state and
federal labs, where disease detectives ran tests to see if the
infections were caused by the same bug. When enough matches emerged,
typically a dozen or so, epidemiologists interviewed sick people,
looking for a common food that was causing the outbreak.
But the testing wasn’t definitive, and linking one case to another
took time. "While all of this was going on, more contaminated
product was getting out into the public," said Dr. Steven Musser,
deputy director for scientific operations at the U.S. Food and Drug
Administration's Center for Food Safety and Applied Nutrition.
Now, the FDA is building a network of state and federal labs
equipped to map out the exact DNA sequence of strains of Listeria,
Salmonella and other foodborne pathogens found in sick patients.
These sequences are then uploaded to a public database housed at the
National Institutes of Health. The technology can not only
differentiate a pathogen from multiple related species, but can also
show slight mutations within the same strain.
 At the same time, the FDA has begun sequencing pathogens found
during routine plant inspections and adding those to the database.
One benefit of that, they say, is being able to quickly connect
patients within an outbreak. Another is the potential to identify
the source of an outbreak after just a few patients fall ill,
shortening the time it takes to get tainted food off store shelves.
To increase the odds of a match, the FDA wants manufacturers to
contribute samples of pathogens found during their own plant
inspections. Some contamination is common in food plants. When it is
found in the manufacturing facility, but not in food products,
companies generally are required only to clean it up without
recalling products.
But eliminating pathogens is tough, and convincing companies to
offer up potentially incriminating evidence has been a hard sell,
according to interviews with public health officials, food
manufacturers and experts on recalls.
"That is not something that we've solved yet," said Ruth Timme, an
FDA microbiologist who has talked to 10-15 companies over the past
year about the benefits of sequencing.
'BAM! YOU'VE GOT EM.'
The FDA became convinced of the superiority of the new approach
during a 2014 outbreak of salmonella affecting peanut butter made by
nSpired Natural Foods of Oregon.
The FDA had just activated a network of state, federal and academic
laboratories to do whole genome sequencing, and the agency had also
begun sequencing pathogens it collected from swabbing surfaces
during factory inspections. All of these codes were uploaded to the
database, known as GenomeTrakr.
When people started getting sick, FDA scientists and partners
searched GenomeTrakr, looking for matches with inspection samples.
They found the DNA of bugs taken from two sick patients were "almost
indistinguishable" from salmonella the FDA had found at nSpired
Foods, said Dr. Eric Brown, director of FDA’s Division of
Microbiology.
 The match allowed officials to quickly recall tainted peanut butter.
Only six people got sick.
"You catch things far earlier" with sequencing, said Dr. David
Lipman, director of the National Center for Biotechnology
Information. "It can be two cases. If you see a match, Bam! You've
got em."
A MORE PRECISE TOOL
Since the start of GenomeTrakr in 2012, 25,000 genomes from a
variety of pathogens have been added to the database, and several
state and federal partners, including the U.S. Department of
Agriculture and the U.S. Centers for Disease Control and Prevention,
have signed on.
The participants agree that sequencing offers huge advantages over
the 20-year-old genetic fingerprinting technique used previously,
known as PFGE.
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David Acheson, a former official at both the USDA and the FDA, who
now advises companies on food safety, likens the difference to a
witness in a hit and run accident. While PFGE might identify the
vehicle as a brown Toyota Corolla, whole genome sequencing provides
the license number and even the vehicle identification number.
"They both help identify the culprit," he said, but one identifies
the specific bug implicated.
The CDC began experimenting with whole genome sequencing in the fall
of 2013, joining the FDA and USDA in a pilot project to sequence all
reported cases of Listeriosis in patients and upload those sequences
on the GenomeTrakr database.
For the pilot, CDC compared whole genome sequencing to PFGE, and
found that sequencing reduced the number of red herrings - cases
that look similar but aren't.
In the first year of the Listeria project, whole genome sequencing
identified 19 Listeria clusters and solved four outbreaks. That
compared with identifying 14 dusters and solving one outbreak the
year earlier.
MIXED BLESSING
For the food industry, the ability to more quickly match bacteria
from a patient sample with their plants is a mixed blessing.
FDA's Musser thinks the technology will ultimately be embraced by
industry, which could use sequencing to see if suppliers are
bringing contamination into their plants or if bacteria has taken up
residence in a corner of the plant.
"These are things industry could just never get to before," Musser
said.
Bernie Steves of Aon Risk Solutions Crisis Management Practice, who
advises companies on product recalls, said sequencing is tying
illnesses in people to the source "faster than we've seen before,"
allowing companies to "nip things in the bud."
Conversely, he said, "it gives regulators another tool to find out
where a potential problem is being sourced from."
That could mean more recalls. According to the Center for Science in
the Public Interest, only about 40 percent of reported foodborne
disease outbreaks from 2002-2011 were ever solved, letting many
manufacturers off the hook.
To allay some of those concerns and still get more samples, the FDA
and its partners are working on ways to allow companies to provide
blind samples through a third party.
One such program called VoluntaryNet at the University of Georgia
would allow companies to provide samples anonymously. For companies,
the program could alert them pathogens residing in their plants. If
a submitted pathogen starts making people sick, public health
officials could alert companies about the problem, and possibly pull
food off market shelves more quickly.
FDA statistician Errol Strain said several companies have agreed in
principle to supply samples and they are working out details on how
to participate anonymously.
(Reporting by Julie Steenhuysen; Editing by Michele Gershberg and
Sue Horton)
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