Case Identification

Figure 1. Figure 1. Number of Case Patients, According to State of Residence.

Figure 2. 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.

Figure 3. Figure 3. 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 isolates from flour samples (flour). The source of each isolate (type of sample and state abbreviation) is provided after the identification number of each isolate. The numbers 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.

A total of 56 cases were identified in 24 states (Figure 1 and Figure 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) (Figure 3). These 40 isolates were all positive 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 female. 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 they might have baked during that period. Of the 5 case patients who remembered baking, 4 reported 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 identified 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

Table 1. Table 1. Selected Exposures among Case Patients in the Shiga Toxin–Producing Escherichia coli (STEC) Infection Outbreak and Comparison Patients with Non-STEC Illness.

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 completed this questionnaire, as did 84 comparison patients with non-STEC illness. Among these patients, 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 significantly 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 or batter (odds ratio, 36.02; 95% CI, 4.63 to 280.17), irrespective of brand, and eating chocolate 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 exposures in the multivariable model (Table 1). Several brands of chocolate chips were reported, however, 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 Colorado was unbleached all-purpose flour manufactured on November 14, 2015, and the flour from Washington was bleached all-purpose flour manufactured 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, California, 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 samples. 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, and Oklahoma; of these five samples, four were in original brand A packaging, whereas the Michigan 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) (Figure 3, and Table S1 in the Supplementary Appendix, 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 sequencing on these isolates and identified one STEC O26 strain that was closely related genetically (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 genetic 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