FIG 3 .

Plasmid content of E. coli O104:H4 isolates. Heat map showing the degree of sequence identity between nonchromosomal scaffolds from each isolates and a reference set of plasmids associated with E. coli O104:H4 isolates. The shade of green indicates the degree of sequence identity (graded white to dark green, as per the legend). Plasmids considered present in the isolate on the basis of extent of sequence identity are outlined with a thick black border. Key contents of the plasmids, including the CTX-M-15 extended-spectrum beta-lactamase, AAF/I, and AAF/III, are denoted in representative sites. pHUSEC41-2 and p55989 are nearly identical (see Fig. S6C in the supplemental material), and pHUSEC41-3 (not shown) is not present in the isolates analyzed in this study. pTY3, pHUSEC41-4, pEc09-7901-c, and pEc12-0466-c represent cryptic plasmids. Of note, pTY2 was not in the sequenced genome of Ec11-9450; however, PCR analysis of multiple colonies from the original sample demonstrates that it was lost during laboratory culture steps. Its presence is therefore denoted by a dotted box.