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The degree to which molecular epidemiology reveals information
about the sources and transmission patterns of an outbreak
depends on the resolution of the technology used and the samples
studied. Isolates of Escherichia coli O104:H4 from the outbreak centered
in Germany in May?July 2011, and the much smaller outbreak
in southwest France in June 2011, were indistinguishable by standard
tests. We report a molecular epidemiological analysis using
multiplatform whole-genome sequencing and analysis of multiple
isolates from the German and French outbreaks. Isolates from the
German outbreak showed remarkably little diversity, with only
two single nucleotide polymorphisms (SNPs) found in isolates from
four individuals. Surprisingly, we found much greater diversity (19
SNPs) in isolates from seven individuals infected in the French outbreak.
The German isolates form a clade within the more diverse
French outbreak strains. Moreover, five isolates derived from a single
infected individual from the French outbreak had extremely
limited diversity. The striking difference in diversity between the
German and French outbreak samples is consistent with several
hypotheses, including a bottleneck that purged diversity in the
German isolates, variation in mutation rates in the two E. coli outbreak
populations, or uneven distribution of diversity in the seed
populations that led to each outbreak.
food-borne outbreak | Shiga toxin | enteroaggregative E. coli |