Genomic Database Helps FDA Discover
Origin of Food Contamination Outbreaks
The GenomeTrakr project is a network of state and federal public health labs that sequences
microbial foodborne pathogens and uploads the data to a common public database in real-time
The Food and Drug Administration (FDA) is tasked with promoting and protecting public health in
many different areas, including ensuring
a safe food supply. Over the past 25 years,
FDA and its sister agencies have worked
side-by-side identifying outbreaks (CDC)
and tracing back (FDA and USDA) the
contamination sources that caused them.
Until recently the gold-standard technology
for subtyping, or strain identification, of
foodborne bacteria has been a molecular
technique that reveals a set of banding
patterns for each isolate. These patterns are
used to identify bacteria and to compare one
bacterial isolate to another.
However, in the past five
years, technology advances
have allowed us to rapidly
collect data on a foodborne
pathogen’s entire genomic
sequence, using a process
known as whole genome
sequencing (WGS). WGS is
rapid, precise, automatable,
cost-effective, can be
universally applied across all
foodborne pathogens, and
offers higher resolution data
for analysis than banding
patterns provide. WGS data
also allows us to infer the
evolutionary history of a
set of isolates, which can
provide powerful clues for
health officials trying to
identify the contamination
source of an outbreak.
In 2012 FDA began the
Genome Trakr project, a
distributed network of state
and federal public health
labs sequencing microbial
foodborne pathogens and uploading the data
to a common public database in real-time.
The result has been a continuously growing
database of genomic sequence information
and accompanying metadata (e.g.
geographic location, source, and date) from
food, environmental, and clinical isolates.
Whenever new sequences are submitted
they are analyzed and compared to existing
sequences in the Genome Trakr database.
Close “matches” between isolates could
reveal a foodborne illness outbreak or food
contamination event and lead investigators
trying to determine how the pathogen got
into the food supply.
There are two major paradigm shifts
with the Genome Trakr network. One is
the advancement in technology. WGS
data provides precise high-resolution
information about a pathogen, often enabling
us to distinguish which farm or factory
a particular pathogen originated from.
This discriminatory power, along with full
epidemiological concordance, enables us to
confidently determine the root cause of more
foodborne illness outbreaks than ever before.
The second major paradigm shift is
perhaps more significant. Genome Trakr
data is made public immediately after data
As of August 2017, the five foodborne pathogens under surveillance within Genome Trakr are: Salmonella enterica, Listeria
monocytogenes, Escherichia coli/Shigella, Campylobacter jejuni, and Vibrio parahaemolyticus. Credit: U.S. FDA