Food Protection Trends - September/October 2020 - 323

TABLE 1. Listeria monocytogenes sequence information from the National Center for
Biotechnology Information (NCBI) Pathogen Detection database (50)

NCBI biosample

Retailer

SAMN08437793

A

SAMN08437795

B

SAMN08437792

C

SAMN08438037

D

SAMN08437794

D

Location

Deli case
girding
Slicer control
meat
Deli slicing
table
Meat
department
floor drain
Cutting
board on
floor

SNP range
in cluster

SNP distance
to closest
environmental
isolate

SNP
distance
to closest
clinical
isolate

Collection
date range
within
cluster

2

1-1 (1)

1

NAa

2018

PDS000025424

2

1-1 (1)

1

NA

2018

PDS000003255

31

0-59 (14)

1

3

2014-2018

PDS000003204

126

0-83 (35)

11

11

2013-2019

PDS000000366

1,109

0-108 (41)

22

20

2013-2019

SNP cluster
identification

No. of
isolates
in cluster

PDS000025424

NA, not applicable.

a

Sequence data analysis
Overall run quality was evaluated with the Illumina
Sequencing Analysis Viewer v.1.9.1 software (Illumina
Inc.) and FastQ files were inspected with FastQC v.0.11.3
(Babraham Institute, Cambridge, UK). Good-quality
sequences were shared with the FDA GenomeTrakr
Network via BaseSpace (Illumina Inc.). Raw sequence data
were submitted to the National Center for Biotechnology
Information (U.S. National Library of Medicine, Bethesda,
MD) Pathogen Detection database (50) (see Table 1 for
biosample numbers). Data were automatically analyzed
through the Pathogen Detection pipeline, which includes
single nucleotides polymorphism (SNP) comparisons
to find clusters of closely related isolates. Isolates were
placed in clusters by single-linkage clustering, with a
maximum 50 SNPs distance. SNP clusters to which this
study's isolates belong can be visualized on the Pathogen
Detection Web page (Table 1) (50). To obtain an overview
of relationship between the five isolates, analysis was
also performed by using a reference-free whole-genome
sequencing bioinformatics pipeline (30) (Utah Public
Health Laboratory, Salt Lake City, UT) as implemented on
the Google Virtual Machine at the Colorado Department of
Public Health and Environment (Denver, CO).
Environmental assessment
For insight into retail deli practices and environmental
data, a Listeria self-assessment form was developed and
pilot tested twice, prior to use. The assessment form was
a modified version of the Listeria monocytogenes deli self-

assessment tool (46). All inspectors collecting data used the
assessment tool; however, each was first trained on how to
use it. In addition, "mark-up" instructions were provided to
assure consistency in completion. One example illustrating
the detail and clarity of these instructions is as follows:
Item: RTE meat or poultry products refrigerated promptly
after use. Mark-up instructions: This item must be marked
YES or NO based on direct observations. The item must be
marked YES when the regulatory authority determines that
RTE products are promptly returned to refrigerated units
after slicing. This item may be marked NOT OBSERVED
when the establishment is not working with RTE products.
Promptly refrigerated after use means: a food product is
not left unattended when the food employee changes task
unless the task only creates a brief interruption before
returning to the product such as serving a retail customer.
Data analysis was conducted by using SPSS (version 23,
IBM Corporation, Armonk, NY) software. Descriptive
statistics (mean and standard deviation) were calculated. For
comparison purposes, the federal retail deli data set related
to adherence of eight recommendations was obtained from
the presentation "Listeria Controls at Retail: Nationwide
Surveillance Results" (17). To compare differences between
delis on the basis of size and location, retail delis were
divided into two groups: small retail delis and large retail
delis. Small delis were defined as those with less than 10
stores in the brand, and large were those with 10 or more
stores in the brand. Frequency statistics and t-tests were

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