Food Protection Trends - July/August 2020 - 269

collaboration, the USDA-FSIS uploads WGS data and
limited metadata such as sample type (food, environmental),
geographic location (state), and year to the NCBI. The
NCBI Pathogen Detection Browser is the public-facing
platform that the USDA-FSIS and other public health
partners use to share isolate genetic information. The USDAFSIS uploads sequences in real-time and is a significant
contributor of food and food processing environment isolate
sequences; however, other domestic and international
partners contribute sequences as well, making this a highly
diverse, robust database. As of 5 February 2020, there were
~255,000 Salmonella sequences, ~99,000 Escherichia coli
sequences, ~48,500 Campylobacter jejuni sequences, and
~32,000 Listeria monocytogenes sequences in the NCBI
Pathogen Detection Browser. With the transition to WGS,
the USDA-FSIS continues to explore options for sharing
WGS identifiers with stakeholders so they can use the
NCBI Pathogen Detection Browser as well. The USDAFSIS currently shares information with public health and
regulatory partners to investigate outbreaks in accordance
with an established information sharing processes. The
USDA-FSIS also shares information with establishments
from which isolates have been detected that match clinical
isolates in an investigated outbreak.
Surveillance and investigations
The USDA-FSIS Office of Public Health Science uses WGS
information uploaded to NCBI to conduct surveillance for
clinical isolates that may be associated with isolates derived
from USDA-FSIS-regulated products. Epidemiologists,
microbiologists, and other food safety professionals use
the NCBI Pathogen Detection Browser to determine
whether USDA-FSIS isolates are related genetically (via
single-nucleotide polymorphism analyses) to other isolates
in the database. This information can help guide further
investigation to determine whether USDA-FSIS-regulated
products are associated with human illness. Genetic
similarities between pathogens detected in food and humans
increase the likelihood that they share a common source,
but genetic similarity alone is not sufficient to determine
whether a specific food is causing human illness. WGS may
help to generate hypotheses and guide the investigation. It is
essential however to consider all investigative information,
such as epidemiologic (e.g., what product was consumed by
ill patients) and traceback (where product was purchased
and produced), as part of the decision-making process.
Depending on the evidence collected during an investigation,
the USDA-FSIS may take various actions to limit exposure
and prevent additional illnesses. Actions taken by the USDAFSIS at an establishment may include issuing a notice of
intended enforcement, retaining product, withholding marks
of inspection, or suspending a federal establishment. In
addition, the USDA-FSIS may notify the public of potential
food safety concerns through the issuance of a press release

announcing a public health alert or may request that an
establishment recall product linked to human illness.
The USDA-FSIS has successfully used WGS to investigate
and solve outbreaks in coordination with CDC and public
health and regulatory partners. Two Listeria monocytogenes
(L. monocytogenes) outbreaks investigated in 2018 highlight
how WGS was used in conjunction with epidemiologic
information to determine the source of illnesses and recall
product from commerce. In addition, WGS has been used
to detect outbreaks with a small number of cases and
isolates spread out over a long period. In both situations,
WGS, in conjunction with case interview and traceback
data, increased the confidence that illnesses were linked to
consumption of USDA-FSIS-regulated products.
The first outbreak involved clinical patients who became
sick in 2017 and 2018. WGS data showed that the L. monocytogenes strains obtained from the patients were genetically
similar to isolates collected from ready-to-eat ham samples
in an establishment in 2016 and 2018. Patient interviews
revealed that they had eaten deli ham or country ham
biscuits. USDA-FSIS investigators visited and reviewed
records from settings where patients purchased or consumed
these ham products and determined that the ham products
were received from the same establishment with the positive
samples. The USDA-FSIS evaluated the WGS, case exposure,
and traceback information to link illnesses to consumption
of the product and the establishment voluntarily recalled the
ready-to-eat ham products. In the second L. monocytogenes
outbreak example, WGS data showed genetic similarity
between clinical patient, food, and environmental isolates
collected between 2014 and 2018 from an establishment
that produced Asian-style pork products. Patients were not
able to provide detailed food histories but did report eating
Asian-style foods and shopping at Asian specialty grocery
stores. The grocery stores sold ready-to-eat pork products
manufactured at the establishment with the positive samples.
This was the only establishment where the USDA-FSIS had
isolated a strain that was closely related to the illness strain
by WGS. Along with available epidemiologic information,
this WGS evidence linked patients to the consumption of the
ready-to-eat pork products and the establishment voluntarily
recalled the products.
WGS has also been useful in investigations of illnesses
due to Salmonella. Between 2018 and 2019, the USDA-FSIS,
in coordination with the CDC and public health partners,
investigated a Salmonella Reading outbreak. Exposure
information from clinical patients suggested consumption of
turkey as the common cause of the illnesses. The outbreak
strain of Salmonella Reading was identified in samples of
ground turkey collected from homes of patients and from
raw turkey used for pet food. The outbreak strain was
also identified in samples of raw turkey products from 24
slaughter and 14 processing establishments through routine
USDA-FSIS testing and from an additional 120 retail turkey

July/August Food Protection Trends

269

Food Protection Trends - July/August 2020

Table of Contents for the Digital Edition of Food Protection Trends - July/August 2020