The metaphor that I like to use when we think about
moving from conventional approaches to the next
generation of food borne outbreak response is the
Hubble Telescope.
Can you imagine how people felt when they went from
just a simple backyard like telescope to flicking
on the Hubble for the first time and were able
to see deep into the stars?
Using whole genome sequencing which drives
the Genome Trakr network, we can now look deep into
food borne outbreaks and track them back to their
source exactly.
When you go out to eat, if you are going to a
restaurant, say a salad bar, you can think how
many different ingredients are you actually eating?
And for each different kind of food they come
from a different part of the world and so they have
different pathogens that are associated with that
particular kind of food.
And so when you eat at a salad bar, you might
easily eat 50 or 100 different ingredients,
which means you are really exposing yourself to the
potential risk of a global pathogen exposure.
So what we have been doing for Genome Trakr is we are
sequencing pathogens from known foods and from known
environments, and we are building up a database of
the genomes of the pathogens from these
particular places.
And then when you get sick and it's uncertain what
you got sick from, we compare the pathogen from
you to the database and then we can say hey, this
looks like a pathogen we've seen before in
California spinach, or Chinese shrimp.
And so this is a kind of microbial investigative
lead.
One of the most powerful examples that we have
recently uncovered in the use of whole genome
sequencing and our Genome Trakr network, actually
happened this past summer.
We noticed that there were illnesses associated with
peanut butter or nut butter and they were in
different states and different parts of the
country and it was not clear that they were
related.
At the same time FDA field inspectors had done a
random survey of a plant that made nut butter and
found salmonella in the facility.
When we sequenced those salmonella and put them in
the database, they were almost perfect matches
across 4.6 million data points to the two
illnesses in different parts of the country.
So we had actually used it in this case to detect the
source of an outbreak just as the outbreak was
starting.
We were able to stop the food product from going
further into the consumer's food supply and
we were able to stop the outbreak before it
advanced to many dozens or hundreds of illnesses.
And that was a very powerful application for
Genome Trakr.
At the end of 2014 we'll have sequenced 10,000 new
bacterial genomes and made them all publicly
available.
This is equivalent to 100 million file cabinets
stuffed full of documents that are available to the
public.
And this is growing.
We are going to double again in this year, the
next year and double again.
And this is becoming a global phenomenon where
laboratories, hospitals, academics and public
health laboratories are going to be all collecting
and making this data publicly available.
Whole genome sequencing is also telling us things
that we never thought we could learn about
bacterial pathogens.
We've learned things that we never thought possible,
things like certain salmonella are now
resistant to heavy metals and they live in tuna and
other top predators in the sea where heavy metals
accumulate.
These are adaptations or changes in the germ that
we never knew existed.
And by learning how the germ itself is evolving
and changing, we will be able to come up with
better preventive controls for the food supply and
for food manufacturers to stop the contamination in
their plants, in their facilities before it
spreads.