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TABLE 1. NCBI accession numbers and metadata for S. I 4,[5],12:i:- isolates included in
Figure 1
Strain ID
PNUSAS027931
PNUSAS026252
NY84671838
NY84671873
PNUSAS037576
PNUSAS036486
PNUSAS034333
PNUSAS038526
PNUSAS030104
PNUSAS040819*

BioSample Accession⁰

SRA Run Accession+

Isolation Source

Collection Date

SAMN08134123
SAMN08134060
SAMN08513397
SAMN08513396
SAMN09429145
SAMN08964172
SAMN08964080
SAMN09430482
SAMN08513667
SAMN09260941

SRR6371606
SRR6380788
SRR6761221
SRR6761464
SRR7346617
SRR7049885
SRR7049814
SRR7348240
SRR6703791
SRR7218800

stool
stool
ground turkey
ground turkey
stool
stool
stool
stool
stool
stool

10/17/17
9/26/2017
2018
2018
3/6/2018
2/22/2018
1/23/2018
2/28/2018
11/15/2017
4/2/2018

⁰unique identifier to access sample metadata.
+
unique identifier to access sample sequence data within the SRA (sequence read archive).
*related within 4-7 SNPs from isolates in WGS Cluster 1 (not pictured in Fig. 1).

Once requested, either a NYSDOH epidemiologist or a
trained student interviewer team member will attempt case
contact. For initial interviews, a minimum of three call
attempts are completed during business hours, followed
by at least one attempt afterhours (evening or weekend)
before closeout as lost to follow-up. For outbreak or focused
questionnaire interviews, in addition to the multiple daytime
attempts, at least two afterhours attempts are completed
before closeout. State and student team assistance has had a
tremendous positive impact on interview completion rates
for salmonellosis cases in NYS overall and played a key role
in data collection for the investigation described here. A case
was defined as an individual with an infection of Salmonella
I 4,[5],12:i:- pattern JPXX01.0621, highly related to the
WGS outbreak clade within 0 to 8 SNPs, and with an isolate
collection date on or after 1 September 2017.
RESULTS
In November 2017, NYSDOH began investigating two
cases of Salmonella I 4,[5],12:i:- with isolates matching
PFGE pattern JPXX01.0621. By May 2018, NYSDOH
WCL had identified 10 cases of Salmonella I 4,[5],12:i:- in
NYS (excluding NYC) with PFGE pattern JPXX01.0621.
A retrospective look at surveillance data indicated that this
number of cases, within the given timeframe, was not above
the baseline average for this PFGE pattern in the state. Each
case was contacted by the NYSDOH via phone, and all
cases consented to interview using an extensive hypothesisgenerating questionnaire consisting of questions regarding
grocery shopping locations, foods eaten outside the home,

food allergies, and special diets. For the 7-day food history
before illness onset, cases were questioned about 120 food
items (poultry, seafood, eggs, dairy, cheese, beef, other meat
or meat alternatives, vegetables, herbs, fruit, frozen foods,
nuts, cereals, and processed foods), in addition to other
exposure pertaining to sources of drinking water, travel
history, and animal exposures. Cases were geographically
dispersed across the state, and available epidemiologic
exposure histories did not yield leading hypotheses about the
source of infection among cases.
In June 2018, NYSDOH WCL used WGS data generated
from an in-house bioinformatic pipeline to further distinguish the genetic relatedness among the 10 case isolates
involved in the cluster. The initial report sent by NYSDOH
WCL to NYSDOH epidemiology staff illustrates how a single
PFGE cluster type can be resolved by WGS (Fig. 1). Within
the Salmonella I 4,[5],12:i:- PFGE pattern JPXX01.0621
cluster, WGS analysis defined a subcluster of four clinical
isolates, which were highly related within 0 to 6 SNPs (WGS
cluster 1) and would later be linked to a common food
source. Three other clinical isolates included in the original PFGE cluster (PNUSAS036486 and WGS cluster 3)
appeared genetically unrelated to the isolates in WGS cluster
1, distanced by 12 to 14 and 66 to 72 SNPs, respectively.
Isolates in WGS cluster 2 (of ground turkey origin) also appeared genetically unrelated to the isolates in WGS cluster 1
(44 to 62 SNP difference) and furthermore were not isolates
previously associated with the original PFGE cluster. One
additional clinical isolate associated with the original PFGE
cluster (PNUSAS040819, not pictured) was from a NYS

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Food Protection Trends - March/April 2021

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