A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

HE OUTBREAK OF SHIGA-TOXIgenic Escherichia coli (STEC), which struck Germany in May-June 2011, illustrated the effects of a bacterial epidemic on a wealthy, modern, industrialized society, with more than 3000 cases and more than 50 deaths. 1During an outbreak, rapid and accurate pathogen identification and characterization is essential for the management of individual cases and of an entire outbreak.Traditionally, clinical bacteriology has relied primarily on laboratory isolation of bacteria in pure culture as a prerequisite to identification and characterization of an outbreak strain.Often, however, in vitro culture proves slow, difficult, or even impossible, and recognition of an out-See also pp