Food Protection Trends - March/April 2021 - 240

of contaminated food, predominantly of animal origin (4).
The timely identification of disease clusters and attribution
of foodborne illness cases to specific food sources is vital
to halting disease transmission, preventing additional cases
of human illness, and developing prevention and control
strategies to improve food safety. To that end, and in an
effort to improve surveillance for enteric disease outbreaks,
laboratory subtyping methods to determine the relatedness
of clinical isolates have become a rapidly evolving science,
with various advanced molecular techniques on the horizon.
Epidemiologists and laboratorians at state and local health
departments nationwide, including those at the New York
State Department of Health (NYSDOH), transitioned in
2019 from using pulsed-field gel electrophoresis (PFGE)
to whole-genome sequencing (WGS) for enteric disease
surveillance and outbreak detection. Although PFGE can
show relatedness among isolates in a cluster, WGS is able to
provide added resolution for assessing genetic relatedness.
As such, WGS analysis is based on the inference that closely
related isolates likely share a common ancestor and the
corresponding cases likely had exposure to a common source
of infection. The NYSDOH Wadsworth Center Laboratory
(WCL) began using PFGE for enteric disease cluster
detection on a national scale in 1997 and implemented
WGS for local cluster surveillance in 2013. In March 2019,
NYSDOH WCL discontinued the use of PFGE for isolate
subtyping. This transition from PFGE-WGS tandem analysis
to analysis exclusively by WGS has required constant
communication among NYSDOH epidemiologists, public
health laboratorians, and environmental health specialists
to determine workflow and thresholds for enteric disease
outbreak investigations of local and national scale.
By way of the Food Safety Modernization Act (2011),
NYSDOH, in partnership with Cornell University, was
established as an Integrated Food Safety Center of Excellence
(NY CoE) in 2015 with a mission to support, enhance, and
improve foodborne outbreak investigations at state and
metropolitan public health departments across the nation.
NY CoE, a recognized subject matter expert in WGS, has
made it a priority to advance knowledge on the subject,
particularly among those in public health who interpret
WGS results for cluster detection and investigation. Training
and education efforts to improve food safety and assist with
cluster identification are multidisciplinary in approach,
targeting epidemiologists, public health laboratorians, and
environmental health specialists. This investigation (i)
describes how WGS was able to define a subcluster of cases
within an endemic Salmonella serotype I 4,[5],12:i:- cluster
in New York state (NYS) linked to a commercially available
raw poultry product; (ii) highlights how WGS can narrow
the focus of an epidemiology investigation, particularly when
highly related clinical and food isolates have been identified;
(iii) demonstrates successful communication of WGS

240

Food Protection Trends March/April

analysis and collaboration among local, state, and federal
partners; and (iv) demonstrates how WGS, along with
epidemiologic information, provided a strong foundation for
communication with consumers and industry.
MATERIALS AND METHODS
Salmonella surveillance: laboratory
Clinical laboratories in NYS, exclusive of New York
City (NYC), are required to submit confirmed Salmonella
isolates to the NYSDOH WCL for confirmatory testing,
subtyping, and serotyping. At the time of this investigation,
PFGE analysis was still being performed at the NYSDOH
WCL. Results of the PFGE analysis were uploaded through
BioNumerics (Applied Maths, Austin, TX) to the PulseNet
National Database for comparison with national PFGE
data. WGS and bioinformatic data for all NYS Salmonella
serotype Typhimurium isolates (including I 4,[5],12:i:-)
were analyzed via an in-house-developed, reference-based
single-nucleotide polymorphism (SNP) pipeline for local
cluster detection (8). Salmonella Typhimurium LT2 was
used as a reference genome to map the sequence reads
and find positions with SNPs. For a SNP to be identified,
a genome position was required to have at least 20× depth
of coverage of high-quality mapped reads with 95% of the
reads in agreement. SNPs that failed these requirements
or that mapped over phage-associated islands and repeat
were excluded. In addition, sequence data were shared with
CDC PulseNet through the web-based utility BaseSpace
(Illumina, Inc.) to facilitate PulseNet enteric disease
surveillance activities. The sequence data, along with
minimal sample metadata, were also uploaded to the
National Center for Biotechnology Information (NCBI)
and analyzed on the NCBI Pathogen Detection isolates
browser, which enabled searching for genetically related
clinical, food, and environmental isolates on a national level
(13). The sequence data and metadata for isolates included
in the study can be accessed on NCBI using the accession
numbers provided in Table 1.
Salmonella surveillance: epidemiology
Reporting of all culture-confirmed cases of salmonellosis
in NYS is mandated under the NYS Sanitary Code
(10NYCRR 2.10 and 2.14) and the NYC Health Code. All
cases are reported electronically to the NYSDOH, and it
is the responsibility of the local health department of the
case's county of residence to initiate follow-up. All cases of
salmonellosis are contacted by a local health department
official and interviewed using a detailed questionnaire
to capture demographic data, clinical illness and medical
care details, and a 7-day (before illness onset) history
of food, water, animal, and travel exposures. Since 2016,
NYSDOH has offered interviewing assistance to local
health departments with completion of Salmonella initial
hypothesis generation and/or outbreak questionnaires.



Food Protection Trends - March/April 2021

Table of Contents for the Digital Edition of Food Protection Trends - March/April 2021

Presence of Listeria monocytogenes and Sanitation Controls in Cold-Smoked Salmon Facilities during FDA Inspections
Sensitivity of Planktonic Cells and Biofilm of Wild- Type and Pressure-Stressed Cronobacter sakazakii and Salmonella enterica Serovars to Sodium Hypochlorite
I Read It on Reddit: Food Safety Information-Seeking Preferences and Practices of Young Adults Online
Food Safety Knowledge and Self-Reported Practice among Campers in the United States
Consumer Handling of Whole Turkeys: Identification of Common Mishandling Practices
Ability of Whole-Genome Sequencing to Refine a Salmonella I 4,[5],12:i:- Cluster in New York State and Detect a Multistate Outbreak Linked to Raw Poultry
Beyond the Bio Nadia Narine
PDG Highlight Food Safety Assessment, Audit and Inspection Professional Development Group
Industry Products
Coming Events
Food Protection Trends - March/April 2021 - Cover1
Food Protection Trends - March/April 2021 - Cover2
Food Protection Trends - March/April 2021 - 177
Food Protection Trends - March/April 2021 - 178
Food Protection Trends - March/April 2021 - 179
Food Protection Trends - March/April 2021 - 180
Food Protection Trends - March/April 2021 - 181
Food Protection Trends - March/April 2021 - 182
Food Protection Trends - March/April 2021 - 183
Food Protection Trends - March/April 2021 - Presence of Listeria monocytogenes and Sanitation Controls in Cold-Smoked Salmon Facilities during FDA Inspections
Food Protection Trends - March/April 2021 - 185
Food Protection Trends - March/April 2021 - 186
Food Protection Trends - March/April 2021 - 187
Food Protection Trends - March/April 2021 - 188
Food Protection Trends - March/April 2021 - 189
Food Protection Trends - March/April 2021 - 190
Food Protection Trends - March/April 2021 - 191
Food Protection Trends - March/April 2021 - 192
Food Protection Trends - March/April 2021 - 193
Food Protection Trends - March/April 2021 - 194
Food Protection Trends - March/April 2021 - Sensitivity of Planktonic Cells and Biofilm of Wild- Type and Pressure-Stressed Cronobacter sakazakii and Salmonella enterica Serovars to Sodium Hypochlorite
Food Protection Trends - March/April 2021 - 196
Food Protection Trends - March/April 2021 - 197
Food Protection Trends - March/April 2021 - 198
Food Protection Trends - March/April 2021 - 199
Food Protection Trends - March/April 2021 - 200
Food Protection Trends - March/April 2021 - 201
Food Protection Trends - March/April 2021 - 202
Food Protection Trends - March/April 2021 - 203
Food Protection Trends - March/April 2021 - I Read It on Reddit: Food Safety Information-Seeking Preferences and Practices of Young Adults Online
Food Protection Trends - March/April 2021 - 205
Food Protection Trends - March/April 2021 - 206
Food Protection Trends - March/April 2021 - 207
Food Protection Trends - March/April 2021 - 208
Food Protection Trends - March/April 2021 - 209
Food Protection Trends - March/April 2021 - 210
Food Protection Trends - March/April 2021 - 211
Food Protection Trends - March/April 2021 - 212
Food Protection Trends - March/April 2021 - 213
Food Protection Trends - March/April 2021 - 214
Food Protection Trends - March/April 2021 - 215
Food Protection Trends - March/April 2021 - Food Safety Knowledge and Self-Reported Practice among Campers in the United States
Food Protection Trends - March/April 2021 - 217
Food Protection Trends - March/April 2021 - 218
Food Protection Trends - March/April 2021 - 219
Food Protection Trends - March/April 2021 - 220
Food Protection Trends - March/April 2021 - 221
Food Protection Trends - March/April 2021 - 222
Food Protection Trends - March/April 2021 - 223
Food Protection Trends - March/April 2021 - 224
Food Protection Trends - March/April 2021 - 225
Food Protection Trends - March/April 2021 - 226
Food Protection Trends - March/April 2021 - 227
Food Protection Trends - March/April 2021 - 228
Food Protection Trends - March/April 2021 - 229
Food Protection Trends - March/April 2021 - 230
Food Protection Trends - March/April 2021 - 231
Food Protection Trends - March/April 2021 - Consumer Handling of Whole Turkeys: Identification of Common Mishandling Practices
Food Protection Trends - March/April 2021 - 233
Food Protection Trends - March/April 2021 - 234
Food Protection Trends - March/April 2021 - 235
Food Protection Trends - March/April 2021 - 236
Food Protection Trends - March/April 2021 - 237
Food Protection Trends - March/April 2021 - 238
Food Protection Trends - March/April 2021 - Ability of Whole-Genome Sequencing to Refine a Salmonella I 4,[5],12:i:- Cluster in New York State and Detect a Multistate Outbreak Linked to Raw Poultry
Food Protection Trends - March/April 2021 - 240
Food Protection Trends - March/April 2021 - 241
Food Protection Trends - March/April 2021 - 242
Food Protection Trends - March/April 2021 - 243
Food Protection Trends - March/April 2021 - 244
Food Protection Trends - March/April 2021 - 245
Food Protection Trends - March/April 2021 - 246
Food Protection Trends - March/April 2021 - 247
Food Protection Trends - March/April 2021 - Beyond the Bio Nadia Narine
Food Protection Trends - March/April 2021 - 249
Food Protection Trends - March/April 2021 - 250
Food Protection Trends - March/April 2021 - PDG Highlight Food Safety Assessment, Audit and Inspection Professional Development Group
Food Protection Trends - March/April 2021 - 252
Food Protection Trends - March/April 2021 - 253
Food Protection Trends - March/April 2021 - 254
Food Protection Trends - March/April 2021 - 255
Food Protection Trends - March/April 2021 - Industry Products
Food Protection Trends - March/April 2021 - 257
Food Protection Trends - March/April 2021 - Coming Events
Food Protection Trends - March/April 2021 - Cover3
Food Protection Trends - March/April 2021 - Cover4
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