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from the firm's production facility to WGS of L. monocytogenes from five cases who were ill. Overall there
were five confirmed cases of illness, and two deaths
were reported (8).
Flour: FDA/CDC traced back a multistate outbreak
of Shiga toxin-producing E. coli infections linked to
a specific brand of flour. FDA and CDC matched
WGS of the pathogen isolated from the patient to the
WGS isolated from an open flour pack. Following this
revelation, a recall for the product was issued (11).
Dairy products: FDA's inspection of an ice cream
manufacturing facility isolated 15 isolates of L.
monocytogenes and found them be comprised of one
strain group. On comparison of the strains isolated
from the facility to the Genome Trakr database, it
was seen that they matched three other isolates: two
isolates from finished products tested by a commercial laboratory, and one isolate from an ingredient.
FDA urged for a recall and issued the 483 form for
corrective actions (9).
Inspection by FDA in an ice cream plant found
L. monocytogenes isolated twice over a two-year period. WGS showed that the same strain was isolated
both times. FDA suggested that repeated isolation
was from an in-house strain that had grown resistant
to cleaning and sanitization in place. The company
halted its production and incurred a $2.5 million loss
from recall, destroying 265 tons of ice cream (14).
FDA urged a voluntary recall of milk after finding
Salmonella from a routine inspection. WGS of strains
isolated from this visit was compared to that of strains
collected over time from the facility. The strains were
identical, pointing to the presence of a persistent
strain of Salmonella contaminating the facility for
nearly 7 years (10).
Poultry: CDC reported that a multistate Salmonellarelated outbreak that sickened 300 people was
associated with handling of live poultry (4). WGS,
along with other detection methods, was used in the
detection of the Salmonella outbreak.
Restaurants: An outbreak of Shiga-toxin producing
E. coli linked to a Mexican grill caused illness in 55
people in multiple states, as per CDC reports (5).
WGS performed on isolates from ill people showed
them to be highly related. Interviews of ill people
affected by this multistate event revealed that they
had consumed food from this particular Mexican grill
chain (13). The chain had to shut its outlets in many
states until the root cause of the outbreak could be
found.
Catering: FDA inspected an airline catering facility
and found L. monocytogenes isolates from food
environmental swabs. WGS analysis confirmed
that the isolates collected were identical to the L.

monocytogenes isolated previously by FDA from the
same facility. FDA suggested that the pathogen has
become established and has persisted over time and
declared that the cleaning procedures in the facility
were inadequate to remove the pathogen (7).
8. Seafood: FDA suspended the seafood facility registration because of repeated finding of L. monocytogenes in
their facility. WGS matched strains isolated from the
seafood to the strains isolated from ill people who had
consumed the seafood produced by the facility (16).
9. Bridging past and new cases: CDC and FDA matched
WGS of L. monocytogenes isolates obtained from FDA
inspection in 2015 of a soft cheese distribution facility
to WGS of a multistate L. monocytogenes outbreak
caused by contaminated soft cheese. When ill people
were interviewed, the only link between all the cases
was that they had consumed a specific brand of cheese
distributed by the same cheese distributer (3).
WORKING TOWARDS AN FDA VISIT
FDA has stepped up its inspection and foodbornepathogen surveillance by employing new cutting-edge
molecular technologies and the Swab-a-thon sampling
program. It is up to the food processing facilities to improve
their sanitation and routine surveillance of the processing
facilities, incoming ingredients and finished products.
Food manufacturers can be prepared for the FDA visit by
employing an internal Swab-a-Thon approach to finding
potential issues and taking action accordingly. The advantage
of conducting periodic swabbing with a view to gaining a
thorough understanding of the facility can be best described
as surveillance pathways to potential quality concerns. While
it is likely that spoilage organisms and pathogens of concern
will be found, this data is far more useful in identifying the
modes by which these may be transported in the facility, as
well as identifying the characteristics of the niches in which
problems may persist. It is vital to know where ingredients,
packaging and supplies come from and ensure the integrity
of the supplier's food safety compliance to protect the
business. From the many cases reported by FDA, there is a
pattern indicating that many food production facilities could
have harborage points and niches that protect pathogens
from being removed through standard sanitation protocols.
They may persist in the environment and evolve to acquire
a unique genetic signature pertinent to that environment.
To circumvent this issue of harborage, amplicon sequencing
can be used as an investigative tool to study the efficacy of
sanitation procedures so as to have a more targeted approach
towards the battle against harborage. Employing these
genomics tools in a periodic surveillance testing program can
avoid any surprises during the FDA visit, and provide the
facility with valuable data for internal improvement, serve as
a source of historic data and demonstrate one measure of a
preventive culture.

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