(A) Bootstrap consensus maximum-likelihood phylogeny using the 21 SNPs, based on 500 bootstraps and rooted on the 2004 and 2009 isolates. No branch lengths are provided for the 2004 and 2009 isolates because this phylogeny is generated only from the 21 SNPs from the two outbreaks. The isolates associated with the German outbreak are C236-11, C227-11, Ec11-3677, and Ec11-3798. The 2004 and 2009 isolates are Ec04-8351 and Ec09-7901, respectively. The remaining isolates are associated with the French outbreak. Ec11-4632.1 to Ec11-4632.5 represent the five isolates from a single individual. The black numbers at nodes indicate bootstrap support. The maroon numbers along the branches indicate the locations, with respect to the TY2482 genome, of the SNPs that define each branch. (B) Bootstrap consensus maximum-likelihood phylogeny using SNPs derived from whole-genome alignment of assemblies of C227-11, 55989, 01–09591, Ec04-8351, Ec09-7901, and the commensal E. coli E1167, as described in Materials and Methods. The black numbers at nodes indicate bootstrap support.

Schematic of hypotheses to explain differences in E. coli SNP diversity seen in the French and German outbreaks. (A) At minimum, the contaminating population that gave rise to both the French and German outbreaks was polymorphic at location 1568661, and possibly other sites, indicating at least two types of genotypes in the original contaminating population (represented in green and blue). In the samples presented here, there is greater diversity in the French outbreak E. coli O104:H4 population than observed in the German outbreak population. Although the probability that our sample represents the majority of the German outbreak is high (see main text), unsampled diversity may exist in a minority of cases in the German outbreak. (B) By the physical separation hypothesis, there was uneven distribution of the diversity in the original contaminating E. coli O104:H4 population, with the 50-g seed packets that led to the French outbreak containing a greater degree of diversity than was present in the 75-kg of seed sent to the German sprout farm (7). (C) By the variable mutation rate hypothesis, the original seed population, comprising at least two genotypes, may have mutated more quickly along the route to the French outbreak because of environmental or other factors. (D) By the bottleneck hypothesis, the French outbreak diversity represents the original diversity present in the contaminated seeds. Either a subset or overlapping set of strains that led to the French outbreak were sent to the German sprout farm, followed by a bottleneck that restricted diversity in the German outbreak. A bottleneck could have taken place from the time of separation of the seeds from the original shipment to the German and English seed distributors through germination in the sprout facility. For discussion of factors favoring each hypothesis, see the main text.