Transcriptomes of genetically distinct E. coli O157:H7 strains

Transcriptomes of 24 clinical strains of E. coli O157:H7 that differ phylogenetically and by Shiga toxin profiles were compared after 30 min co-incubation with epithelial cells. Total RNA was harvested from the 24 O157:H7 strains exposed to, but not attached to, MAC-T epithelial cell monolayers for 30 min, using a previously described in vitro model of O157:H7 exposure to MAC-T cells. The microarray platform (Operon E. coli oligo set version 1.0.2) probes for 5978 ORFs from E. coli O157:H7 Sakai, O157:H7 EDL 933, and K12 MG1655, and for 110 ORFs from the pO157 plasmid. Thirty-six dye-swap hybridizations were performed between four groups with six strains per group, according to a balanced double loop design. Strains were grouped based on cladestx profiles and each strain was considered an independent biological replicate of its group (n=6). The six strains from each group were randomly hybridized with six strains from every other group; each hybridization compared a pair of strains that differed in either clade or stx profile, or both.