Food Protection Trends - September/October 2017 - 372

The nature of FDA inspections of food production
facilities has changed drastically. In the past, results of visual
observations and review of food safety record keeping
were the main criteria for FDA inspection activities. If
there were any discrepancies, form 483s were issued and
the manufacturers would have to employ corrective action
and send a written letter to FDA, including descriptions of
actions that had been undertaken. In the past couple of years,
with the new Food Safety Modernization act (FSMA), along
with visual observations and review of food safety records,
FDA would look for invisible evidence by employing a Swaba-thon, or heavy swabbing approach. These Swab-a-thons
include obtaining a wide range of samples from all parts of
the facility (hygienic zones 1, 2, 3, 4) and can collect up to
200 swabs from various zones, depending on the size of the
processing facility. Depending on the number and location of
positive samples obtained for pathogenic bacteria of concern,
this can result in a recall or even a temporary or long-term
shutdown of the facility. The positive swabs are subjected to
WGS and compared to Genome Trakr, and if there is a match
with the clinical WGS reported, FDA may take legal action
leading to criminal prosecution.
CASES WHERE WGS WAS USED AS A TOOL IN
IDENTIFICATION OF PATHOGENS
The FDA has used WGS to match pathogens found in
food to pathogens collected from people who became ill
from consuming the food or pathogens found as a part of

FDA's routine surveillance. Following are cases where FDA
and CDC employed WGS analysis as part of their outbreak
or routine investigation:
1. Fresh fruits and vegetables: There have been a number
of outbreaks/ recalls related to fresh produce (1).
During their inspection of a fresh produce facility,
FDA isolated 19 strains of Listeria monocytogenes and
performed WGS on the isolates. Seven strains were
from food contact surfaces and the rest were either in
close proximity to the food contact surface or from
a non-food contact surface. The WGS analysis of the
19 strains fell into two distinct strain types, one strain
type dominating, with seventeen identical WGS, and
the other strain type with two identical WGS. When
all the WGS sequences were compared with the WGS
sequences on Genome Trakr, the strain type with
two identical WGS were found to be associated with
eight cases of human illness. Six of the 8 ill individuals
were hospitalized for L. monocytogenes related illness
(15). The company received a form 483 from the FDA
requiring a response for corrective action.
FDA and Center for Disease Control (CDC)
performed WGS of isolates obtained from the clinical outbreaks and matched it with a specific brand
of salad (12). FDA urged for a recall of the salad,
curbing the outbreak.
Wholesome soy was under scrutiny when FDA
and CDC matched WGS of L. monocytogenes isolated

Figure 4. Workflow for WGS sequence comparison to Genome Trakr

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Food Protection Trends September/October

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