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The new engl and jour nal of medicine
n engl j med 377;21 nejm.org  November 23, 20172036
From the Centers for Disease Control
and Prevention (S.J.C., L.B., L.W., A.B.,
M.N.S., D.W., E.T., M.E.W., K.P.N.), and
IHRC (L.B., D.W.), Atlanta; Food and
Drug Administration, College Park, MD
(L.N.S., B.M.W., J.B., S.V.); Colorado De-
partment of Public Health and Environ-
ment, Denver (N.C.); Washington State
Department of Health, Shoreline (B.M.),
and Food and Drug Administration,
Bothell (J.W., L.A.N.) — both in Wash-
ington; Michigan Department of Health
and Human Services, Lansing (K.D.A.,
D.D.); Oklahoma State Department of
Health, Oklahoma City (J.S.); and Virginia
Department of Health, Richmond (K.A.,
J.R.). Address reprint requests to Dr. Crowe
at the Centers for Disease Control and
Prevention, 1600 Clifton Rd. NE, MS C-09,
Atlanta, GA 30329, or at ­yeo2@​­cdc​.­gov.
N Engl J Med 2017;377:2036-43.
DOI: 10.1056/NEJMoa1615910
Copyright © 2017 Massachusetts Medical Society.
BACKGROUND
In 2016, a multijurisdictional team investigated an outbreak of Shiga toxin–producing
Escherichia coli (STEC) serogroup O121 and O26 infections linked to contaminated
flour from a large domestic producer.
METHODS
A case was defined as infection with an outbreak strain in which illness onset was
between December 21, 2015, and September 5, 2016. To identify exposures associated
with the outbreak, outbreak cases were compared with non-STEC enteric illness
cases, matched according to age group, sex, and state of residence. Products sus-
pected to be related to the outbreak were collected for STEC testing, and a common
point of contamination was sought. Whole-genome sequencing was performed on
isolates from clinical and food samples.
RESULTS
A total of 56 cases were identified in 24 states. Univariable exact conditional logistic-
regression models of 22 matched sets showed that infection was significantly
associated with the use of one brand of flour (odds ratio, 21.04; 95% confidence
interval [CI], 4.69 to 94.37) and with tasting unbaked homemade dough or batter
(odds ratio, 36.02; 95% CI, 4.63 to 280.17). Laboratory testing isolated the out-
break strains from flour samples, and whole-genome sequencing revealed that the
isolates from clinical and food samples were closely related to one another ge-
netically. Trace-back investigation identified a common flour-production facility.
CONCLUSIONS
This investigation implicated raw flour as the source of an outbreak of STEC infec-
tions. Although it is a low-moisture food, raw flour can be a vehicle for foodborne
pathogens.
ABSTR ACT
Shiga Toxin–Producing E. coli Infections
Associated with Flour
Samuel J. Crowe, Ph.D., M.P.H., Lyndsay Bottichio, M.P.H.,
Lauren N. Shade, B.S., Brooke M. Whitney, Ph.D., Nereida Corral, M.P.H.,
Beth Melius, M.N., M.P.H., Katherine D. Arends, M.P.H.,
Danielle Donovan, M.S., Jolianne Stone, M.P.H., Krisandra Allen, M.P.H.,
Jessica Rosner, M.P.H., Jennifer Beal, M.P.H., Laura Whitlock, M.P.H.,
Anna Blackstock, Ph.D., June Wetherington, M.S., Lisa A. Newberry, Ph.D.,
Morgan N. Schroeder, M.P.H., Darlene Wagner, Ph.D., Eija Trees, D.V.M., Ph.D.,
Stelios Viazis, Ph.D., Matthew E. Wise, M.P.H., Ph.D.,
and Karen P. Neil, M.D., M.S.P.H.​​
Original Article
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n engl j med 377;21 nejm.org  November 23, 2017 2037
E. coli Infections Associated with Flour
F
lour has been a suspected outbreak
vehicle for Shiga toxin–producing Escherichia
coli (STEC) infections since 2009, when a
multistate outbreak of foodborne disease was
linked to prepackaged cookie dough.1,2
However,
flour was not definitively identified as the source
of infection in that outbreak or in subsequent
outbreaks of STEC infection. Flour is a raw,
minimally processed product intended to be mixed
with other ingredients and cooked before con-
sumption. It is a low-water-content ingredient
and typically does not support bacterial growth.
Nevertheless, pathogenic microorganisms on the
wheat or other ingredients in flour can survive
the drying process and remain viable in flour for
months in a desiccated state.3,4
STEC, which is
estimated to cause 265,000 infections in the
United States each year, has been identified as
one of a group of pathogens that can contami-
nate flour.5,6
Symptoms typically appear 3 to 4 days
after infection and include mild fever, abdominal
pain, vomiting, and diarrhea, which is often
bloody. The hemolytic–uremic syndrome, a form
of kidney failure, also develops in some patients
with STEC infection.7
In 2016, a multistate outbreak investigation
in the United States linked infection with STEC
serogroups O121 and O26 to contaminated flour
from a large domestic producer. We describe the
epidemiologic, laboratory, and trace-back aspects
of the investigation and discuss the public health
implications of our findings.
Methods
Overview of the Investigation
In February 2016, the Centers for Disease Con-
trol and Prevention (CDC) and state health depart-
ments began investigating a cluster of patients
who were infected with STEC O121. All the pa-
tients were infected with a strain of STEC O121
that had the same uncommon pulsed-field gel
electrophoresis (PFGE) pattern combination,
which suggested a common source of illness.
CDC and state and local health officials inter-
viewed the patients to obtain demographic,
clinical, and exposure information. As the inves-
tigation developed, patients who were infected
with STEC O121 characterized by other PFGE
pattern combinations, as well as patients infected
with STEC that had a PFGE pattern of an addi-
tional serogroup, O26, were identified as part of
the outbreak. After the investigation, members
of the investigation team prepared this report
for submission; the authors vouch for the accu-
racy and completeness of the data collected and
of the subsequent analyses.
Case Identification
Cases were identified by PulseNet, the national
molecular subtyping network for foodborne dis-
ease surveillance.8,9
CDC and state laboratory
personnel further subtyped selected clinical iso-
lates by means of whole-genome sequencing.
The QIAGEN DNeasy Blood and Tissue Kit (Qia-
gen) was used to extract genomic DNA. The DNA
libraries were created with the Nextera XT DNA
Library Preparation Kit (Illumina). DNA sequenc-
ing was performed on the Illumina MiSeq Se-
quencing System. The Lyve-SET pipeline was
used to perform high-quality single-nucleotide
polymorphism (SNP) analysis.10
Two criteria
were used by CDC epidemiologists to define a
case. First, a case was an infection with E. coli
serogroup O121 that had PFGE pattern combina-
tionEXKX01.0001/EXKA26.0001,EXKX01.0001/
EXKA26.0313, EXKX01.0389/EXKA26.0001, or
EXKX01.0395/EXKA26.0001 or an infection with
E. coli serogroup O26 that had pattern combina-
tion EVCX01.2685/EVCA26.1686, with illness on-
set during the period from December 21, 2015,
through September 5, 2016. Second, when data
were available, the infecting E. coli strain in a case
was found by whole-genome sequencing to be
closely related genetically to other isolates from
clinical samples or to isolates from flour sam-
ples collected during the outbreak investigation.
Hypothesis Generation
On the basis of preliminary interview data col-
lected by local and state officials, CDC epidemi-
ologists created and deployed an initial ques-
tionnaire to identify common exposures. The
frequencies of exposures were compared with
those in the Foodborne Disease Active Surveil-
lance Network (FoodNet) Population Survey —
a survey in which data on food-consumption
frequencies during the previous 7 days are col-
lected from interviewees — with the use of a
binomial probability distribution.11
After the re-
sponses to the initial questionnaire did not lead
to the generation of a strong hypothesis regard-
ing the outbreak source, a CDC epidemiologist
conducted open-ended interviews with a subset
of patients. Inquiries were made about all foods
consumed during the week before illness onset
The New England Journal of Medicine
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The new engl and jour nal of medicine
and locations where the foods were eaten. Find-
ings from these interviews led to the develop-
ment of a second questionnaire that local and
state health officials then used to interview ad-
ditional case patients.
Case–Case Analysis
CDC and state epidemiologists conducted a
matched case–case analysis of the data collected
with the use of the second questionnaire to iden-
tify exposures associated with illness. Cases from
this outbreak were matched with cases of infec-
tion caused by non-STEC enteric pathogens, such
as salmonella, that had been reported to state
health departments during the outbreak period
(non-outbreak cases). Outbreak case patients
and patients with non-STEC illness were matched
according to state of residence, sex, and age group
(<1 to 9 years, 10 to 19 years, 20 to 29 years,
and ≥30 years). Four cases of non-STEC illness
were sought for each outbreak case. Odds ratios
and 95% confidence intervals were calculated
for food exposures with the use of univariable
and multivariable exact conditional logistic-­
regression models (clogit function from the Sur-
vival Analysis package in R software).12
The most
probable outbreak sources on the basis of the
results of the univariable analyses were included
in the multivariable model.
Product Trace-Back Investigation
and Testing
Local and state health officials collected data on
production lots and “better if used by” dates for
foods suspected to be involved in the outbreak
to determine whether they could be traced to a
common production location and time period.
The Food and Drug Administration (FDA) in-
spected production locations and collected prod-
ucts from these facilities for testing. The FDA
traced ingredients of the products to identify
potential sources of contamination. When avail-
able, the products were collected from the
homes of case patients and tested for STEC. The
implicated company also conducted product test-
ing and shared STEC isolates with the FDA.
FDA laboratory personnel used the primary
enrichment methods outlined in the Bacterio-
logical Analytical Manual to test foods for the
outbreak strain.13
The recovery of bacteria was
assisted through immunomagnetic separation
with the use of the Invitrogen Dynabead Max
EPEC/VTEC O121 Kit. The Applied Biosystems
Prepman Ultra Kit was used to prepare a tem-
plate for real-time polymerase chain reaction
(PCR). When a sample was found to be positive
for STEC by means of real-time PCR assay, the
immunomagnetic separation–concentrated pellet
was plated to a series of up to six isolation agars
(selective, differential, or both) and incubated at
37°C for 18 to 24 hours. Colonies were screened
with the Abraxis E. coli Latex Agglutination O121.
Isolates were confirmed as E. coli with the use of
a Vitek GN microbial identification test card,
and real-time PCR was repeated to verify the
toxin profile. Isolates were subjected to molecu-
lar serotyping by means of Bio-Plex analysis,
which was also used to determine the presence
of virulence markers. Isolates that were con-
firmed as E. coli serogroup O121 underwent PFGE
and whole-genome sequencing analysis.14
Results
Case Identification
A total of 56 cases were identified in 24 states
(Figs. 1 and 2); 55 were infections with STEC
O121, and 1 was an infection with STEC O26. Of
the 55 STEC O121 isolates, 40 underwent whole-
genome sequencing analysis and were found to
be closely related genetically (a difference of 0 to
2 SNPs) (Fig. 3). These 40 isolates were all posi-
tive for the gene stx2a; the lone O26 strain was
positive for stx1a only. All sequenced isolates
were positive for eaeA, and all but 3 of the O121
isolates were also positive for ehlA. Case patients
ranged in age from 1 to 95 years (median, 18).
A total of 43 of 56 case patients (77%) were fe-
male. Sixteen case patients were hospitalized.
The hemolytic–uremic syndrome developed in
one adolescent girl (infected with STEC O121
that was positive for stx2a, eaeA, and ehlA), but
she recovered. No deaths were reported.
Hypothesis Generation
Leafy green vegetables were commonly reported
as having been eaten by early case patients, but
the initial questionnaire did not identify any food
exposures among case patients that were eaten
at a significantly higher frequency than in the
FoodNet Population survey. Open-ended telephone
interviews then were conducted with 10 patients,
all of whom stated that they baked frequently or
regularly consumed home-baked foods. Five of
the patients recalled baking during the week
before illness onset, and 3 others reported that
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n engl j med 377;21 nejm.org November 23, 2017 2039
E. coli Infections Associated with Flour
they might have baked during that period. Of the
5 case patients who remembered baking, 4 re-
ported eating or tasting homemade batter or
dough, 3 of whom used brand A flour. The
fourth used either brand A or another brand.
Two of the patients (a resident of Colorado and
a resident of Washington) still had the bags of
brand A flour that they had used in the week
before illness onset.
Shortly thereafter, state investigators identi-
fied 3 ill children who had been exposed to raw
flour at restaurants in Maryland, Virginia, and
Texas. Restaurant staff had given them raw
dough to play with while they waited for their
food to be served.
Case–Case Analysis
The case–case questionnaire included questions
about baking, flour, and raw-dough exposures
and about other food exposures that had been
reported during hypothesis generation. Of the
56 case patients, 33 (59%) in the outbreak com-
pleted this questionnaire, as did 84 comparison
patients with non-STEC illness. Among these pa-
tients, there were 22 matched sets that each
contained one STEC outbreak case and one or
more comparison cases. Univariable matched
analysis showed that STEC infection was sig-
nificantly associated with baking (odds ratio,
8.79; 95% confidence interval [CI], 2.39 to 32.24)
and with the use of brand A flour (odds ratio,
21.04; 95% CI, 4.69 to 94.37), as well as with
tasting uncooked or unbaked homemade dough
Figure 1. Number of Case Patients, According to State of Residence.
No. of
Case Patients
0
1
2
3
≥4
Alabama
Arizona
Alaska
Hawaii
Arkansas
California
Connecticut
Delaware
Washington, D.C.
Florida
Georgia
Idaho
Illinois Indiana
Iowa
Kentucky
Louisi-
ana
Maine
Maryland
Massachusetts
Michigan
Missis-
sippi
Montana
Nevada
New Hampshire
New Jersey
New Mexico
North Carolina
Ohio
Oregon
Rhode Island
Tennessee
Utah
Washington
Wisconsin
Wyoming
Texas
Nebraska
South Dakota
Minnesota
North Dakota
Oklahoma
Missouri
South
Carolina
Virginia
West
Virginia
Pennsylvania
Colorado
Kansas
Vermont
New York
Figure 2. Number of Case Patients, According to Week of Illness Onset
(December 21, 2015, through September 5, 2016).
The data include both reported dates and estimated dates of illness onset.
Estimated dates of onset were calculated by subtracting 3 days from the
date of pathogen isolation.
No.ofCases
6
4
5
3
2
1
0
Week of Illness Onset
Dec. Jan. Feb. Sept.Aug.JulyJuneMayAprilMarch
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The new engl and jour nal of medicine
CFSAN051464 (Flour, CO)
CFSAN052207 (Flour, OK)
CFSAN051559 (Flour, AZ)
CFSAN051463 (Flour, CO)
PNUSAE002385 (Case, CO)
CFSAN051560 (Flour, AZ)
PNUSAE002568 (Case, MI)
PNUSAE003253 (Case, MI)
CFSAN051772 (Flour, MI)
PNUSAE002978 (Case, MD)
PNUSAE004359 (Case, MN)
CFSAN051461 (Flour, CO)
PNUSAE002762 (Case, VA)
PNUSAE002759 (Case, IA)
PNUSAE002540 (Case, WA)
PNUSAE002761 (Case, OK)
PNUSAE002420 (Case, VA)
2016C-3839 (Case, WA)
PNUSAE004457 (Case, VA)
PNUSAE002715 (Case, CO)
PNUSAE002161 (Case, MN)
CFSAN052208 (Flour, OK)
PNUSAE004147 (Case, TN)
CFSAN051771 (Flour, MI)
PNUSAE002184 (Case, WI)
PNUSAE005457 (Case, OK)
PNUSAE003214 (Case, IL)
PNUSAE003502 (Case, CA)
PNUSAE002179 (Case, NY)
2016C-3845 (Case, AZ)
PNUSAE004513 (Case, NY)
PNUSAE002383 (Case, CO)
PNUSAE002203 (Case, TX)
PNUSAE003180 (Case, WI)
PNUSAE002823 (Case, MA)
PNUSAE003551 (Case, IN)
PNUSAE002331 (Case, MA)
PNUSAE002632 (Case, CA)
PNUSAE002432 (Case, WA)
PNUSAE003279 (Case, MN)
PNUSAE002758 (Case, CO)
PNUSAE003499 (Case, MN)
PNUSAE003616 (Case, WI)
PNUSAE003908 (Case, NY)
PNUSAE004038 (Case, WA)
PNUSAE002570 (Case, MI)
PNUSAE002380 (Case, MI)
PNUSAE002592 (Case, MN)
PNUSAE002731 (Case, TX)
PNUSAE004545 (Excluded case, WA)
PNUSAE004562 (Excluded case, CA)
PNUSAE004046 (Excluded case, MN)
PNUSAE004488 (Excluded case, NY)
PNUSAE004517 (Excluded case, IA)
100
100
56
100
0.0001
0–2 SNPs (Outbreak clade)
110–130 SNPs
72–91 SNPs
69–88 SNPs
72–89 SNPs
58–70 SNPs
58–130 SNP
difference
from outbreak
clade
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E. coli Infections Associated with Flour
or batter (odds ratio, 36.02; 95% CI, 4.63 to
280.17), irrespective of brand, and eating choco-
late chips (odds ratio, 15.03; 95% CI, 3.31 to
68.36). Using brand A flour and eating chocolate
chips also were found to be significant expo-
sures in the multivariable model (Table 1). Several
brands of chocolate chips were reported, how-
ever, which made a common source less likely.
Product Trace-Back Investigation
and Testing
Trace-back investigation of the two bags of brand
A flour collected from patients in Colorado and
Washington revealed that the flour from Colo-
rado was unbleached all-purpose flour manufac-
tured on November 14, 2015, and the flour from
Washington was bleached all-purpose flour man-
ufactured on November 15, 2015. The two bags
were produced in the same facility. The flour
that was used in the raw dough given to the
children exposed in the Maryland, Virginia, and
Texas restaurants also was from this facility, as
was flour from three additional bags collected
from case patients residing in Arizona, Califor-
nia, and Oklahoma.
Initial testing of the flour collected from the
homes of case patients did not identify STEC
O121. After additional screening of colonies that
are not typical of E. coli, STEC O121 with delayed
lactose fermentation was recovered from the
Colorado flour sample. The laboratory protocol
was modified and used to test subsequent sam-
ples. The delayed lactose fermentation observed
in the isolates from flour samples was consistent
with what was reported for the isolates from
clinical samples associated with this outbreak.
In total, testing isolated the STEC O121 outbreak
strains from flour samples collected from case
patients in Arizona, Colorado, Indiana, Michigan,
Exposure Unmatched Patients Matched Sets of Patients
Case Patients
Patients with Non-
STEC Illness
Univariable
Analysis
Multivariable
Analysis†
no./total no. (%) odds ratio (95% CI)‡
Baked or made homemade cookies, muffins, pan-
cakes, cakes, or other foods containing flour
22/26 (85) 19/77 (25) 8.79 (2.39–32.24) —
Used brand A flour to make something homemade
or from scratch
19/30 (63) 7/78 (9) 21.04 (4.69–94.37) 6.87 (1.23–38.35)
Ate, tasted, or licked any uncooked or unbaked
homemade dough or batter
17/30 (57) 3/80 (4) 36.02 (4.63–280.17) —
Ate any chocolate chips or chunks by themselves
or in homemade foods
15/24 (62) 8/76 (11) 15.03 (3.31–68.36) 6.40 (1.04–39.28)
Ate any peanut butter 23/29 (79) 35/77 (45) 2.97 (0.92–9.60) 0.83 (0.14–5.11)
*	The questionnaire also included questions about exposure to five additional brands of flour, as well as five brands of baking mix. Exposure
to each of these brands among case patients did not differ significantly from that among patients with non-STEC illness, and therefore these
data were excluded from this table.
†	Variables were selected to compare the most probable sources of the outbreak.
‡	Shown are the odds ratios for the selected exposures among outbreak case patients versus patients with non-STEC illness, matched accord-
ing to state of residence, sex, and age group.
Table 1. Selected Exposures among Case Patients in the Shiga Toxin–Producing Escherichia coli (STEC) Infection Outbreak and Comparison
Patients with Non-STEC Illness.*
Figure 3 (facing page). Phylogenetic Tree of Selected
Shiga Toxin–Producing Escherichia coli Serogroup O121
Isolates Involved in the Outbreak.
The tree is based on 40 clinical isolates (case) and 9 iso-
lates from flour samples (flour). The source of each iso-
late (type of sample and state abbreviation) is provided
after the identification number of each isolate. The num-
bers at the tree nodes are bootstrap values that indicate
the confidence in the clustering on repeated analysis
of random subsets of the data (the closer the value is
to 100, the higher the confidence is in the clustering).
Additional details are provided in the Supplementary
Appendix. SNP denotes single-nucleotide polymorphism.
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The new engl and jour nal of medicine
and Oklahoma; of these five samples, four were
in original brand A packaging, whereas the Michi-
gan sample was reportedly brand A but was not
in original packaging. The isolates from Arizona,
Colorado, Michigan, and Oklahoma underwent
whole-genome sequencing analysis and were found
to be closely related genetically to 40 STEC O121
isolates from clinical samples that represented
three of the four outbreak O121 PFGE pattern
combinations (a difference of 0 to 2 SNPs)
(Fig. 3, and Table S1 in the Supplementary Ap-
pendix, available with the full text of this article
at NEJM.org).
FDA inspectors did not identify a source of
contamination at the implicated facility, which
suggested that the ingredients might have been
contaminated further back in the production
chain. Company A, the parent company of brand
A, also isolated STEC from flour produced at
that facility and shared the isolates with the
FDA. The FDA conducted whole-genome se-
quencing on these isolates and identified one
STEC O26 strain that was closely related geneti-
cally (a difference of 3 SNPs) to one clinical
isolate that had previously not been considered a
part of the outbreak. This case was subsequently
included in the case count on the basis of ge-
netic relatedness and additional epidemiologic
information collected.
Product Recall
This investigation identified flour produced at
a single facility as the source of the outbreak.
In response, company A issued three recalls of
multiple brands of flour produced at this facility.
Additional product recalls were issued by other
companies that had used the recalled flour in
their own products. In total, nearly 250 products
containing flour were recalled.15
Information
about these products is provided on the CDC
and FDA outbreak Web pages.15,16
Discussion
In this investigation, raw flour was identified as
the source of an outbreak of STEC infections. In
addition to STEC, other foodborne pathogens,
including salmonella, have been detected in raw
flour and implicated in outbreak investigations,
which suggests that, although it is a low-moisture
food, flour is a possible vehicle for foodborne
pathogens and a potential outbreak source.3,17,18
Linking this outbreak to flour was challeng-
ing. Consumption of raw or undercooked flour
is not included on most routine state and na-
tional foodborne disease questionnaires, so epi-
demiologists were not initially able to assess
whether case patients had consumed raw flour.
In addition, many case patients also reported
exposure to chocolate chips, but additional epi-
demiologic and laboratory evidence supporting
flour as the source helped to rule out this food.
These case patients were baking with both choco-
late chips and flour when they were exposed.
Some case patients did not report exposure to
flour in the week before illness onset, but this is
not uncommon in outbreak investigations. Inter-
views often occur weeks to months after the
illness, which makes it difficult for the patient
to recall exposures accurately. Another challenge
was the fact that most case patients had dis-
carded their flour packaging; therefore, informa-
tion regarding the production lot, which could
have been used to determine the manufacturing
location, was often not available. Moreover, the
trace-back investigation could not determine
whether the implicated flour shared a common
source of wheat, because wheat from several
states was used to produce the flour and grains
from different fields are frequently commingled
shortly after harvest and further mixed during
transport and milling.
The laboratory component of the investiga-
tion also faced difficulties. Laboratory personnel
needed to use immunomagnetic-separation tech-
niques to concentrate the pathogen cells in order
to isolate STEC from the leftover flour provided
by patients. They also used modified screening
criteria to isolate the STEC O121 strain, which
had delayed lactose fermentation, an unusual
characteristic for STEC. Investigations of future
outbreaks will need to account for the fact that
laboratory procedures using lactose fermenta-
tion as a screening step for STEC O121 may re-
duce the likelihood of recovering the pathogen.
This investigation also provided additional evi-
dence that clusters of illnesses with distinct PFGE
patterns can be closely related genetically and
caused by a common source.19
Apparent differ-
ences according to PFGE pattern among isolates
that are determined by whole-genome sequenc-
ing to be closely related probably resulted from
the exclusion of mobile genetic elements (e.g.,
plasmids and phages) from the whole-genome
sequencing analysis because they are less evolu-
tionarily informative.
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E. coli Infections Associated with Flour
Although the epidemiologic, trace-back, and
laboratory components of the investigation con-
firmed flour produced in a single facility as the
source of the outbreak, the source of the con-
tamination was never identified. On the basis of
what is known about the ingredients of flour,
wheat is the ingredient most likely to be con-
taminated, perhaps in the field before harvest.
Some farmers use manure from cattle, a reservoir
of STEC, to fertilize their wheat fields, which
could lead to contamination of the wheat if the
cattle are colonized.20
Another source might be
white-tailed deer, which are ubiquitous in the
United States and are also reservoirs for STEC.21
Given that a specific wheat field was not impli-
cated in this investigation, we could not evaluate
whether animal intrusion was a source of con-
tamination.
Since this outbreak resulted in the hospital-
ization of more than a quarter of case patients
and in the development of the hemolytic–uremic
syndrome in one, it serves as a reminder of the
substantial health consequences of STEC infec-
tions. The investigation also highlighted a number
of issues that contributed to this multistate out-
break. STEC O121 was introduced into a com-
mercially distributed product at a concentration
sufficient to cause a substantial number of ill-
nesses. However, the behaviors of both consum-
ers and retailers increased the risk of illnesses
resulting from the contaminated flour. These
behaviors included the consumption of raw or
undercooked homemade dough or batter, which
has long been discouraged because of the known
risk of salmonellosis from consuming raw eggs,
as well as allowing children to play with raw
dough in restaurants and using flour to make
play-dough for children at home. Our data show
that although it is a low-moisture food, raw
flour can be a vehicle for foodborne pathogens.
This article is based on a public health response by local,
state, and federal government staff. It did not receive any outside
financial support. The findings and conclusions in this report
are those of the authors and do not necessarily represent the
official position of the Centers for Disease Control and Preven-
tion or the Food and Drug Administration.
Disclosure forms provided by the authors are available with
the full text of this article at NEJM.org.
We thank all the outbreak investigation team members in
jurisdictions affected by the outbreak who contributed to this
investigation, including local and state partners in Alabama,
Arizona, Arkansas, California, Colorado, Illinois, Indiana, Iowa,
Maryland, Massachusetts, Michigan, Minnesota, Missouri, Mon-
tana, Nebraska, New York, Oklahoma, Oregon, Pennsylvania,
Tennessee, Texas, Virginia, Washington, and Wisconsin, as well
as partners at the FDA and CDC.
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Copyright © 2017 Massachusetts Medical Society.
The New England Journal of Medicine
Downloaded from nejm.org by DEBRA GOLDSCHMIDT on November 24, 2017. For personal use only. No other uses without permission.
Copyright © 2017 Massachusetts Medical Society. All rights reserved.

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E..coli.flour.nejmoa1615910

  • 1. The new engl and jour nal of medicine n engl j med 377;21 nejm.org  November 23, 20172036 From the Centers for Disease Control and Prevention (S.J.C., L.B., L.W., A.B., M.N.S., D.W., E.T., M.E.W., K.P.N.), and IHRC (L.B., D.W.), Atlanta; Food and Drug Administration, College Park, MD (L.N.S., B.M.W., J.B., S.V.); Colorado De- partment of Public Health and Environ- ment, Denver (N.C.); Washington State Department of Health, Shoreline (B.M.), and Food and Drug Administration, Bothell (J.W., L.A.N.) — both in Wash- ington; Michigan Department of Health and Human Services, Lansing (K.D.A., D.D.); Oklahoma State Department of Health, Oklahoma City (J.S.); and Virginia Department of Health, Richmond (K.A., J.R.). Address reprint requests to Dr. Crowe at the Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, MS C-09, Atlanta, GA 30329, or at ­yeo2@​­cdc​.­gov. N Engl J Med 2017;377:2036-43. DOI: 10.1056/NEJMoa1615910 Copyright © 2017 Massachusetts Medical Society. BACKGROUND In 2016, a multijurisdictional team investigated an outbreak of Shiga toxin–producing Escherichia coli (STEC) serogroup O121 and O26 infections linked to contaminated flour from a large domestic producer. METHODS A case was defined as infection with an outbreak strain in which illness onset was between December 21, 2015, and September 5, 2016. To identify exposures associated with the outbreak, outbreak cases were compared with non-STEC enteric illness cases, matched according to age group, sex, and state of residence. Products sus- pected to be related to the outbreak were collected for STEC testing, and a common point of contamination was sought. Whole-genome sequencing was performed on isolates from clinical and food samples. RESULTS A total of 56 cases were identified in 24 states. Univariable exact conditional logistic- regression models of 22 matched sets showed that infection was significantly associated with the use of one brand of flour (odds ratio, 21.04; 95% confidence interval [CI], 4.69 to 94.37) and with tasting unbaked homemade dough or batter (odds ratio, 36.02; 95% CI, 4.63 to 280.17). Laboratory testing isolated the out- break strains from flour samples, and whole-genome sequencing revealed that the isolates from clinical and food samples were closely related to one another ge- netically. Trace-back investigation identified a common flour-production facility. CONCLUSIONS This investigation implicated raw flour as the source of an outbreak of STEC infec- tions. Although it is a low-moisture food, raw flour can be a vehicle for foodborne pathogens. ABSTR ACT Shiga Toxin–Producing E. coli Infections Associated with Flour Samuel J. Crowe, Ph.D., M.P.H., Lyndsay Bottichio, M.P.H., Lauren N. Shade, B.S., Brooke M. Whitney, Ph.D., Nereida Corral, M.P.H., Beth Melius, M.N., M.P.H., Katherine D. Arends, M.P.H., Danielle Donovan, M.S., Jolianne Stone, M.P.H., Krisandra Allen, M.P.H., Jessica Rosner, M.P.H., Jennifer Beal, M.P.H., Laura Whitlock, M.P.H., Anna Blackstock, Ph.D., June Wetherington, M.S., Lisa A. Newberry, Ph.D., Morgan N. Schroeder, M.P.H., Darlene Wagner, Ph.D., Eija Trees, D.V.M., Ph.D., Stelios Viazis, Ph.D., Matthew E. Wise, M.P.H., Ph.D., and Karen P. Neil, M.D., M.S.P.H.​​ Original Article The New England Journal of Medicine Downloaded from nejm.org by DEBRA GOLDSCHMIDT on November 24, 2017. For personal use only. No other uses without permission. Copyright © 2017 Massachusetts Medical Society. All rights reserved.
  • 2. n engl j med 377;21 nejm.org  November 23, 2017 2037 E. coli Infections Associated with Flour F lour has been a suspected outbreak vehicle for Shiga toxin–producing Escherichia coli (STEC) infections since 2009, when a multistate outbreak of foodborne disease was linked to prepackaged cookie dough.1,2 However, flour was not definitively identified as the source of infection in that outbreak or in subsequent outbreaks of STEC infection. Flour is a raw, minimally processed product intended to be mixed with other ingredients and cooked before con- sumption. It is a low-water-content ingredient and typically does not support bacterial growth. Nevertheless, pathogenic microorganisms on the wheat or other ingredients in flour can survive the drying process and remain viable in flour for months in a desiccated state.3,4 STEC, which is estimated to cause 265,000 infections in the United States each year, has been identified as one of a group of pathogens that can contami- nate flour.5,6 Symptoms typically appear 3 to 4 days after infection and include mild fever, abdominal pain, vomiting, and diarrhea, which is often bloody. The hemolytic–uremic syndrome, a form of kidney failure, also develops in some patients with STEC infection.7 In 2016, a multistate outbreak investigation in the United States linked infection with STEC serogroups O121 and O26 to contaminated flour from a large domestic producer. We describe the epidemiologic, laboratory, and trace-back aspects of the investigation and discuss the public health implications of our findings. Methods Overview of the Investigation In February 2016, the Centers for Disease Con- trol and Prevention (CDC) and state health depart- ments began investigating a cluster of patients who were infected with STEC O121. All the pa- tients were infected with a strain of STEC O121 that had the same uncommon pulsed-field gel electrophoresis (PFGE) pattern combination, which suggested a common source of illness. CDC and state and local health officials inter- viewed the patients to obtain demographic, clinical, and exposure information. As the inves- tigation developed, patients who were infected with STEC O121 characterized by other PFGE pattern combinations, as well as patients infected with STEC that had a PFGE pattern of an addi- tional serogroup, O26, were identified as part of the outbreak. After the investigation, members of the investigation team prepared this report for submission; the authors vouch for the accu- racy and completeness of the data collected and of the subsequent analyses. Case Identification Cases were identified by PulseNet, the national molecular subtyping network for foodborne dis- ease surveillance.8,9 CDC and state laboratory personnel further subtyped selected clinical iso- lates by means of whole-genome sequencing. The QIAGEN DNeasy Blood and Tissue Kit (Qia- gen) was used to extract genomic DNA. The DNA libraries were created with the Nextera XT DNA Library Preparation Kit (Illumina). DNA sequenc- ing was performed on the Illumina MiSeq Se- quencing System. The Lyve-SET pipeline was used to perform high-quality single-nucleotide polymorphism (SNP) analysis.10 Two criteria were used by CDC epidemiologists to define a case. First, a case was an infection with E. coli serogroup O121 that had PFGE pattern combina- tionEXKX01.0001/EXKA26.0001,EXKX01.0001/ EXKA26.0313, EXKX01.0389/EXKA26.0001, or EXKX01.0395/EXKA26.0001 or an infection with E. coli serogroup O26 that had pattern combina- tion EVCX01.2685/EVCA26.1686, with illness on- set during the period from December 21, 2015, through September 5, 2016. Second, when data were available, the infecting E. coli strain in a case was found by whole-genome sequencing to be closely related genetically to other isolates from clinical samples or to isolates from flour sam- ples collected during the outbreak investigation. Hypothesis Generation On the basis of preliminary interview data col- lected by local and state officials, CDC epidemi- ologists created and deployed an initial ques- tionnaire to identify common exposures. The frequencies of exposures were compared with those in the Foodborne Disease Active Surveil- lance Network (FoodNet) Population Survey — a survey in which data on food-consumption frequencies during the previous 7 days are col- lected from interviewees — with the use of a binomial probability distribution.11 After the re- sponses to the initial questionnaire did not lead to the generation of a strong hypothesis regard- ing the outbreak source, a CDC epidemiologist conducted open-ended interviews with a subset of patients. Inquiries were made about all foods consumed during the week before illness onset The New England Journal of Medicine Downloaded from nejm.org by DEBRA GOLDSCHMIDT on November 24, 2017. For personal use only. No other uses without permission. Copyright © 2017 Massachusetts Medical Society. All rights reserved.
  • 3. n engl j med 377;21 nejm.org  November 23, 20172038 The new engl and jour nal of medicine and locations where the foods were eaten. Find- ings from these interviews led to the develop- ment of a second questionnaire that local and state health officials then used to interview ad- ditional case patients. Case–Case Analysis CDC and state epidemiologists conducted a matched case–case analysis of the data collected with the use of the second questionnaire to iden- tify exposures associated with illness. Cases from this outbreak were matched with cases of infec- tion caused by non-STEC enteric pathogens, such as salmonella, that had been reported to state health departments during the outbreak period (non-outbreak cases). Outbreak case patients and patients with non-STEC illness were matched according to state of residence, sex, and age group (<1 to 9 years, 10 to 19 years, 20 to 29 years, and ≥30 years). Four cases of non-STEC illness were sought for each outbreak case. Odds ratios and 95% confidence intervals were calculated for food exposures with the use of univariable and multivariable exact conditional logistic-­ regression models (clogit function from the Sur- vival Analysis package in R software).12 The most probable outbreak sources on the basis of the results of the univariable analyses were included in the multivariable model. Product Trace-Back Investigation and Testing Local and state health officials collected data on production lots and “better if used by” dates for foods suspected to be involved in the outbreak to determine whether they could be traced to a common production location and time period. The Food and Drug Administration (FDA) in- spected production locations and collected prod- ucts from these facilities for testing. The FDA traced ingredients of the products to identify potential sources of contamination. When avail- able, the products were collected from the homes of case patients and tested for STEC. The implicated company also conducted product test- ing and shared STEC isolates with the FDA. FDA laboratory personnel used the primary enrichment methods outlined in the Bacterio- logical Analytical Manual to test foods for the outbreak strain.13 The recovery of bacteria was assisted through immunomagnetic separation with the use of the Invitrogen Dynabead Max EPEC/VTEC O121 Kit. The Applied Biosystems Prepman Ultra Kit was used to prepare a tem- plate for real-time polymerase chain reaction (PCR). When a sample was found to be positive for STEC by means of real-time PCR assay, the immunomagnetic separation–concentrated pellet was plated to a series of up to six isolation agars (selective, differential, or both) and incubated at 37°C for 18 to 24 hours. Colonies were screened with the Abraxis E. coli Latex Agglutination O121. Isolates were confirmed as E. coli with the use of a Vitek GN microbial identification test card, and real-time PCR was repeated to verify the toxin profile. Isolates were subjected to molecu- lar serotyping by means of Bio-Plex analysis, which was also used to determine the presence of virulence markers. Isolates that were con- firmed as E. coli serogroup O121 underwent PFGE and whole-genome sequencing analysis.14 Results Case Identification A total of 56 cases were identified in 24 states (Figs. 1 and 2); 55 were infections with STEC O121, and 1 was an infection with STEC O26. Of the 55 STEC O121 isolates, 40 underwent whole- genome sequencing analysis and were found to be closely related genetically (a difference of 0 to 2 SNPs) (Fig. 3). These 40 isolates were all posi- tive for the gene stx2a; the lone O26 strain was positive for stx1a only. All sequenced isolates were positive for eaeA, and all but 3 of the O121 isolates were also positive for ehlA. Case patients ranged in age from 1 to 95 years (median, 18). A total of 43 of 56 case patients (77%) were fe- male. Sixteen case patients were hospitalized. The hemolytic–uremic syndrome developed in one adolescent girl (infected with STEC O121 that was positive for stx2a, eaeA, and ehlA), but she recovered. No deaths were reported. Hypothesis Generation Leafy green vegetables were commonly reported as having been eaten by early case patients, but the initial questionnaire did not identify any food exposures among case patients that were eaten at a significantly higher frequency than in the FoodNet Population survey. Open-ended telephone interviews then were conducted with 10 patients, all of whom stated that they baked frequently or regularly consumed home-baked foods. Five of the patients recalled baking during the week before illness onset, and 3 others reported that The New England Journal of Medicine Downloaded from nejm.org by DEBRA GOLDSCHMIDT on November 24, 2017. For personal use only. No other uses without permission. Copyright © 2017 Massachusetts Medical Society. All rights reserved.
  • 4. n engl j med 377;21 nejm.org November 23, 2017 2039 E. coli Infections Associated with Flour they might have baked during that period. Of the 5 case patients who remembered baking, 4 re- ported eating or tasting homemade batter or dough, 3 of whom used brand A flour. The fourth used either brand A or another brand. Two of the patients (a resident of Colorado and a resident of Washington) still had the bags of brand A flour that they had used in the week before illness onset. Shortly thereafter, state investigators identi- fied 3 ill children who had been exposed to raw flour at restaurants in Maryland, Virginia, and Texas. Restaurant staff had given them raw dough to play with while they waited for their food to be served. Case–Case Analysis The case–case questionnaire included questions about baking, flour, and raw-dough exposures and about other food exposures that had been reported during hypothesis generation. Of the 56 case patients, 33 (59%) in the outbreak com- pleted this questionnaire, as did 84 comparison patients with non-STEC illness. Among these pa- tients, there were 22 matched sets that each contained one STEC outbreak case and one or more comparison cases. Univariable matched analysis showed that STEC infection was sig- nificantly associated with baking (odds ratio, 8.79; 95% confidence interval [CI], 2.39 to 32.24) and with the use of brand A flour (odds ratio, 21.04; 95% CI, 4.69 to 94.37), as well as with tasting uncooked or unbaked homemade dough Figure 1. Number of Case Patients, According to State of Residence. No. of Case Patients 0 1 2 3 ≥4 Alabama Arizona Alaska Hawaii Arkansas California Connecticut Delaware Washington, D.C. Florida Georgia Idaho Illinois Indiana Iowa Kentucky Louisi- ana Maine Maryland Massachusetts Michigan Missis- sippi Montana Nevada New Hampshire New Jersey New Mexico North Carolina Ohio Oregon Rhode Island Tennessee Utah Washington Wisconsin Wyoming Texas Nebraska South Dakota Minnesota North Dakota Oklahoma Missouri South Carolina Virginia West Virginia Pennsylvania Colorado Kansas Vermont New York Figure 2. Number of Case Patients, According to Week of Illness Onset (December 21, 2015, through September 5, 2016). The data include both reported dates and estimated dates of illness onset. Estimated dates of onset were calculated by subtracting 3 days from the date of pathogen isolation. No.ofCases 6 4 5 3 2 1 0 Week of Illness Onset Dec. Jan. Feb. Sept.Aug.JulyJuneMayAprilMarch The New England Journal of Medicine Downloaded from nejm.org by DEBRA GOLDSCHMIDT on November 24, 2017. For personal use only. No other uses without permission. Copyright © 2017 Massachusetts Medical Society. All rights reserved.
  • 5. n engl j med 377;21 nejm.org  November 23, 20172040 The new engl and jour nal of medicine CFSAN051464 (Flour, CO) CFSAN052207 (Flour, OK) CFSAN051559 (Flour, AZ) CFSAN051463 (Flour, CO) PNUSAE002385 (Case, CO) CFSAN051560 (Flour, AZ) PNUSAE002568 (Case, MI) PNUSAE003253 (Case, MI) CFSAN051772 (Flour, MI) PNUSAE002978 (Case, MD) PNUSAE004359 (Case, MN) CFSAN051461 (Flour, CO) PNUSAE002762 (Case, VA) PNUSAE002759 (Case, IA) PNUSAE002540 (Case, WA) PNUSAE002761 (Case, OK) PNUSAE002420 (Case, VA) 2016C-3839 (Case, WA) PNUSAE004457 (Case, VA) PNUSAE002715 (Case, CO) PNUSAE002161 (Case, MN) CFSAN052208 (Flour, OK) PNUSAE004147 (Case, TN) CFSAN051771 (Flour, MI) PNUSAE002184 (Case, WI) PNUSAE005457 (Case, OK) PNUSAE003214 (Case, IL) PNUSAE003502 (Case, CA) PNUSAE002179 (Case, NY) 2016C-3845 (Case, AZ) PNUSAE004513 (Case, NY) PNUSAE002383 (Case, CO) PNUSAE002203 (Case, TX) PNUSAE003180 (Case, WI) PNUSAE002823 (Case, MA) PNUSAE003551 (Case, IN) PNUSAE002331 (Case, MA) PNUSAE002632 (Case, CA) PNUSAE002432 (Case, WA) PNUSAE003279 (Case, MN) PNUSAE002758 (Case, CO) PNUSAE003499 (Case, MN) PNUSAE003616 (Case, WI) PNUSAE003908 (Case, NY) PNUSAE004038 (Case, WA) PNUSAE002570 (Case, MI) PNUSAE002380 (Case, MI) PNUSAE002592 (Case, MN) PNUSAE002731 (Case, TX) PNUSAE004545 (Excluded case, WA) PNUSAE004562 (Excluded case, CA) PNUSAE004046 (Excluded case, MN) PNUSAE004488 (Excluded case, NY) PNUSAE004517 (Excluded case, IA) 100 100 56 100 0.0001 0–2 SNPs (Outbreak clade) 110–130 SNPs 72–91 SNPs 69–88 SNPs 72–89 SNPs 58–70 SNPs 58–130 SNP difference from outbreak clade The New England Journal of Medicine Downloaded from nejm.org by DEBRA GOLDSCHMIDT on November 24, 2017. For personal use only. No other uses without permission. Copyright © 2017 Massachusetts Medical Society. All rights reserved.
  • 6. n engl j med 377;21 nejm.org  November 23, 2017 2041 E. coli Infections Associated with Flour or batter (odds ratio, 36.02; 95% CI, 4.63 to 280.17), irrespective of brand, and eating choco- late chips (odds ratio, 15.03; 95% CI, 3.31 to 68.36). Using brand A flour and eating chocolate chips also were found to be significant expo- sures in the multivariable model (Table 1). Several brands of chocolate chips were reported, how- ever, which made a common source less likely. Product Trace-Back Investigation and Testing Trace-back investigation of the two bags of brand A flour collected from patients in Colorado and Washington revealed that the flour from Colo- rado was unbleached all-purpose flour manufac- tured on November 14, 2015, and the flour from Washington was bleached all-purpose flour man- ufactured on November 15, 2015. The two bags were produced in the same facility. The flour that was used in the raw dough given to the children exposed in the Maryland, Virginia, and Texas restaurants also was from this facility, as was flour from three additional bags collected from case patients residing in Arizona, Califor- nia, and Oklahoma. Initial testing of the flour collected from the homes of case patients did not identify STEC O121. After additional screening of colonies that are not typical of E. coli, STEC O121 with delayed lactose fermentation was recovered from the Colorado flour sample. The laboratory protocol was modified and used to test subsequent sam- ples. The delayed lactose fermentation observed in the isolates from flour samples was consistent with what was reported for the isolates from clinical samples associated with this outbreak. In total, testing isolated the STEC O121 outbreak strains from flour samples collected from case patients in Arizona, Colorado, Indiana, Michigan, Exposure Unmatched Patients Matched Sets of Patients Case Patients Patients with Non- STEC Illness Univariable Analysis Multivariable Analysis† no./total no. (%) odds ratio (95% CI)‡ Baked or made homemade cookies, muffins, pan- cakes, cakes, or other foods containing flour 22/26 (85) 19/77 (25) 8.79 (2.39–32.24) — Used brand A flour to make something homemade or from scratch 19/30 (63) 7/78 (9) 21.04 (4.69–94.37) 6.87 (1.23–38.35) Ate, tasted, or licked any uncooked or unbaked homemade dough or batter 17/30 (57) 3/80 (4) 36.02 (4.63–280.17) — Ate any chocolate chips or chunks by themselves or in homemade foods 15/24 (62) 8/76 (11) 15.03 (3.31–68.36) 6.40 (1.04–39.28) Ate any peanut butter 23/29 (79) 35/77 (45) 2.97 (0.92–9.60) 0.83 (0.14–5.11) * The questionnaire also included questions about exposure to five additional brands of flour, as well as five brands of baking mix. Exposure to each of these brands among case patients did not differ significantly from that among patients with non-STEC illness, and therefore these data were excluded from this table. † Variables were selected to compare the most probable sources of the outbreak. ‡ Shown are the odds ratios for the selected exposures among outbreak case patients versus patients with non-STEC illness, matched accord- ing to state of residence, sex, and age group. Table 1. Selected Exposures among Case Patients in the Shiga Toxin–Producing Escherichia coli (STEC) Infection Outbreak and Comparison Patients with Non-STEC Illness.* Figure 3 (facing page). Phylogenetic Tree of Selected Shiga Toxin–Producing Escherichia coli Serogroup O121 Isolates Involved in the Outbreak. The tree is based on 40 clinical isolates (case) and 9 iso- lates from flour samples (flour). The source of each iso- late (type of sample and state abbreviation) is provided after the identification number of each isolate. The num- bers at the tree nodes are bootstrap values that indicate the confidence in the clustering on repeated analysis of random subsets of the data (the closer the value is to 100, the higher the confidence is in the clustering). Additional details are provided in the Supplementary Appendix. SNP denotes single-nucleotide polymorphism. The New England Journal of Medicine Downloaded from nejm.org by DEBRA GOLDSCHMIDT on November 24, 2017. For personal use only. No other uses without permission. Copyright © 2017 Massachusetts Medical Society. All rights reserved.
  • 7. n engl j med 377;21 nejm.org  November 23, 20172042 The new engl and jour nal of medicine and Oklahoma; of these five samples, four were in original brand A packaging, whereas the Michi- gan sample was reportedly brand A but was not in original packaging. The isolates from Arizona, Colorado, Michigan, and Oklahoma underwent whole-genome sequencing analysis and were found to be closely related genetically to 40 STEC O121 isolates from clinical samples that represented three of the four outbreak O121 PFGE pattern combinations (a difference of 0 to 2 SNPs) (Fig. 3, and Table S1 in the Supplementary Ap- pendix, available with the full text of this article at NEJM.org). FDA inspectors did not identify a source of contamination at the implicated facility, which suggested that the ingredients might have been contaminated further back in the production chain. Company A, the parent company of brand A, also isolated STEC from flour produced at that facility and shared the isolates with the FDA. The FDA conducted whole-genome se- quencing on these isolates and identified one STEC O26 strain that was closely related geneti- cally (a difference of 3 SNPs) to one clinical isolate that had previously not been considered a part of the outbreak. This case was subsequently included in the case count on the basis of ge- netic relatedness and additional epidemiologic information collected. Product Recall This investigation identified flour produced at a single facility as the source of the outbreak. In response, company A issued three recalls of multiple brands of flour produced at this facility. Additional product recalls were issued by other companies that had used the recalled flour in their own products. In total, nearly 250 products containing flour were recalled.15 Information about these products is provided on the CDC and FDA outbreak Web pages.15,16 Discussion In this investigation, raw flour was identified as the source of an outbreak of STEC infections. In addition to STEC, other foodborne pathogens, including salmonella, have been detected in raw flour and implicated in outbreak investigations, which suggests that, although it is a low-moisture food, flour is a possible vehicle for foodborne pathogens and a potential outbreak source.3,17,18 Linking this outbreak to flour was challeng- ing. Consumption of raw or undercooked flour is not included on most routine state and na- tional foodborne disease questionnaires, so epi- demiologists were not initially able to assess whether case patients had consumed raw flour. In addition, many case patients also reported exposure to chocolate chips, but additional epi- demiologic and laboratory evidence supporting flour as the source helped to rule out this food. These case patients were baking with both choco- late chips and flour when they were exposed. Some case patients did not report exposure to flour in the week before illness onset, but this is not uncommon in outbreak investigations. Inter- views often occur weeks to months after the illness, which makes it difficult for the patient to recall exposures accurately. Another challenge was the fact that most case patients had dis- carded their flour packaging; therefore, informa- tion regarding the production lot, which could have been used to determine the manufacturing location, was often not available. Moreover, the trace-back investigation could not determine whether the implicated flour shared a common source of wheat, because wheat from several states was used to produce the flour and grains from different fields are frequently commingled shortly after harvest and further mixed during transport and milling. The laboratory component of the investiga- tion also faced difficulties. Laboratory personnel needed to use immunomagnetic-separation tech- niques to concentrate the pathogen cells in order to isolate STEC from the leftover flour provided by patients. They also used modified screening criteria to isolate the STEC O121 strain, which had delayed lactose fermentation, an unusual characteristic for STEC. Investigations of future outbreaks will need to account for the fact that laboratory procedures using lactose fermenta- tion as a screening step for STEC O121 may re- duce the likelihood of recovering the pathogen. This investigation also provided additional evi- dence that clusters of illnesses with distinct PFGE patterns can be closely related genetically and caused by a common source.19 Apparent differ- ences according to PFGE pattern among isolates that are determined by whole-genome sequenc- ing to be closely related probably resulted from the exclusion of mobile genetic elements (e.g., plasmids and phages) from the whole-genome sequencing analysis because they are less evolu- tionarily informative. The New England Journal of Medicine Downloaded from nejm.org by DEBRA GOLDSCHMIDT on November 24, 2017. For personal use only. No other uses without permission. Copyright © 2017 Massachusetts Medical Society. All rights reserved.
  • 8. n engl j med 377;21 nejm.org  November 23, 2017 2043 E. coli Infections Associated with Flour Although the epidemiologic, trace-back, and laboratory components of the investigation con- firmed flour produced in a single facility as the source of the outbreak, the source of the con- tamination was never identified. On the basis of what is known about the ingredients of flour, wheat is the ingredient most likely to be con- taminated, perhaps in the field before harvest. Some farmers use manure from cattle, a reservoir of STEC, to fertilize their wheat fields, which could lead to contamination of the wheat if the cattle are colonized.20 Another source might be white-tailed deer, which are ubiquitous in the United States and are also reservoirs for STEC.21 Given that a specific wheat field was not impli- cated in this investigation, we could not evaluate whether animal intrusion was a source of con- tamination. Since this outbreak resulted in the hospital- ization of more than a quarter of case patients and in the development of the hemolytic–uremic syndrome in one, it serves as a reminder of the substantial health consequences of STEC infec- tions. The investigation also highlighted a number of issues that contributed to this multistate out- break. STEC O121 was introduced into a com- mercially distributed product at a concentration sufficient to cause a substantial number of ill- nesses. However, the behaviors of both consum- ers and retailers increased the risk of illnesses resulting from the contaminated flour. These behaviors included the consumption of raw or undercooked homemade dough or batter, which has long been discouraged because of the known risk of salmonellosis from consuming raw eggs, as well as allowing children to play with raw dough in restaurants and using flour to make play-dough for children at home. Our data show that although it is a low-moisture food, raw flour can be a vehicle for foodborne pathogens. This article is based on a public health response by local, state, and federal government staff. It did not receive any outside financial support. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Preven- tion or the Food and Drug Administration. Disclosure forms provided by the authors are available with the full text of this article at NEJM.org. We thank all the outbreak investigation team members in jurisdictions affected by the outbreak who contributed to this investigation, including local and state partners in Alabama, Arizona, Arkansas, California, Colorado, Illinois, Indiana, Iowa, Maryland, Massachusetts, Michigan, Minnesota, Missouri, Mon- tana, Nebraska, New York, Oklahoma, Oregon, Pennsylvania, Tennessee, Texas, Virginia, Washington, and Wisconsin, as well as partners at the FDA and CDC. References 1. Neil KP, Biggerstaff G, MacDonald JK, et al. A novel vehicle for transmission of Escherichia coli O157:H7 to humans: multi- state outbreak of E.coli O157:H7 infections associated with consumption of ready-to- bake commercial prepackaged cookie dough — United States, 2009. Clin Infect Dis 2012;​54:​511-8. 2. Gieraltowski L, Schwensohn C, Meyer S, et al. Notes from the field: multistate outbreak of Escherichia coli O157:H7 infec- tions linked to dough mix — United States, 2016. MMWR Morb Mortal Wkly Rep 2017;​66:​88-9. 3. Beuchat LR, Komitopoulou E, Beck- ers H, et al. Low-water activity foods: increased concern as vehicles of food- borne pathogens. J Food Prot 2013;​76:​ 150-72. 4. Burgess CM, Gianotti A, Gruzdev N, et al. The response of foodborne patho- gens to osmotic and desiccation stresses in the food chain. Int J Food Microbiol 2016;​221:​37-53. 5. Thorpe CM. Shiga toxin-producing Escherichia coli infection. Clin Infect Dis 2004;​38:​1298-303. 6. Scallan E, Hoekstra RM, Angulo FJ, et al. Foodborne illness acquired in the United States — major pathogens. Emerg Infect Dis 2011;​17:​7-15. 7. General information:​ Escherichia coli. At- lanta:​Centers for Disease Control and Pre- vention (http://www​.cdc​.gov/​ecoli/​general/​ index​.html). 8. PulseNet home page. Atlanta:​Centers for Disease Control and Prevention (https:/​/​ www​.cdc​.gov/​pulsenet/​). 9. Ribot EM, Fair MA, Gautom R, et al. Standardization of pulsed-field gel elec- trophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet. Foodborne Pathog Dis 2006;​3:​59-67. 10. GitHub. Lyve-SET hqSNP pipeline (https:/​/​github​.com/​lskatz/​lyve-SET). 11. Foodborne Diseases Active Surveillance Network (FoodNet):​population survey. Atlanta:​Centers for Disease Control and Prevention (https:/​/​www​.cdc​.gov/​foodnet/​ surveys/​population​.html). 12. R:​a language and environment for statistical computing. Vienna:​R Core Team (http://www​.R-project​.org/​). 13. Bacteriological analytical manual:​chap- ter 4A — diarrheagenic Escherichiacoli. Silver Spring, MD:​Food and Drug Administra- tion, June 2016 (http://www​.fda​.gov/​Food/​ FoodScienceResearch/​LaboratoryMethods/​ ucm070080​.htm). 14. GenomeTrakr network. Silver Spring, MD:​Food and Drug Administration (http:// www​.fda​.gov/​Food/​FoodScienceResearch/​ WholeGenomeSequencingProgramWGS/​ ucm363134​.htm). 15. Multistate outbreak of Shiga toxin- producing Escherichia coli infections linked to flour (final update). Atlanta:​Centers for Disease Control and Prevention, Septem- ber 29, 2016 (http://www​.cdc​.gov/​ecoli/​2016/​ o121-06-16/​index​.html). 16. FDA investigates multistate outbreak of Shiga toxin-producing E. coli infections linked to flour. Silver Spring, MD:​Food and Drug Administration, September 29, 2016 (http://www​.fda​.gov/​Food/​RecallsOutbreaks Emergencies/​Outbreaks/​ucm504192​.htm). 17. McCallum L, Paine S, Sexton K, et al. An outbreak of Salmonella Typhimurium phage type 42 associated with the con- sumption of raw flour. Foodborne Pathog Dis 2013;​10:​159-64. 18. Richter KS, Dorneanu E, Eskridge KM, Rao CS. Microbiological quality of flours. Cereal Foods World 1993;​38:​367-9. 19. Jackson BR, Tarr C, Strain E, et al. Implementation of nationwide real-time whole-genome sequencing to enhance lis- teriosis outbreak detection and investiga- tion. Clin Infect Dis 2016;​63:​380-6. 20. Persad AK, LeJeune JT. Animal reser- voirs of Shiga toxin-producing Escherichia coli. Microbiol Spectr 2014;​2(4):​EHEC-0027. 21. Laidler MR, Tourdjman M, Buser GL, et al. Escherichia coli O157:H7 infections associated with consumption of locally grown strawberries contaminated by deer. Clin Infect Dis 2013;​57:​1129-34. Copyright © 2017 Massachusetts Medical Society. The New England Journal of Medicine Downloaded from nejm.org by DEBRA GOLDSCHMIDT on November 24, 2017. For personal use only. No other uses without permission. Copyright © 2017 Massachusetts Medical Society. All rights reserved.