As it descended from Escherichia coli O55:H7, Shiga toxin (Stx)-producing E. coli (STEC) O157:H7 is believed to have acquired, in sequence, a bacteriophage encoding Stx2 and another encoding Stx1. Between these events, sorbitol-fermenting E. coli O157:H ؊ presumably diverged from this clade. We employed PCR and sequence analyses to investigate sites of bacteriophage integration into the chromosome, using evolutionarily informative STEC to trace the sequence of acquisition of elements encoding Stx. Contrary to expectations from the two currently sequenced strains, truncated bacteriophages occupy yehV in almost all E. coli O157:H7 strains that lack stx 1 (stx 1 -negative strains). Two truncated variants were determined to contain either GTT or TGACTGTT sequence, in lieu of 20,214 or 18,895 bp, respectively, of the bacteriophage central region. A single-nucleotide polymorphism in the latter variant suggests that recombination in that element extended beyond the inserted octamer. An stx 2 bacteriophage usually occupies wrbA in stx 1 ؉ /stx 2 ؉ E. coli O157:H7, but wrbA is unexpectedly unoccupied in most stx 1 -negative/stx 2 ؉ E. coli O157:H7 strains, the presumed progenitors of stx 1 ؉ /stx 2 ؉ E. coli O157:H7. Trimethoprim-sulfamethoxazole promotes the excision of all, and ciprofloxacin and fosfomycin significantly promote the excision of a subset of complete and truncated stx bacteriophages from the E. coli O157:H7 strains tested; bile salts usually attenuate excision. These data demonstrate the unexpected diversity of the chromosomal architecture of E. coli O157:H7 (with novel truncated bacteriophages and multiple stx 2 bacteriophage insertion sites), suggest that stx 1 acquisition might be a multistep process, and compel the consideration of multiple exogenous factors, including antibiotics and bile, when chromosome stability is examined.Shiga toxins 1 and 2 (Stx1 and Stx2) are cardinal virulence factors of Escherichia coli O157:H7. Stx1 is nearly identical to Stx, the principal extracellular cytotoxin of Shigella dysenteriae serotype 1 (8). Stx2 has 56% identity to Stx1 (36). The stx 1 and stx 2 A and B subunit genes exist as tandem open reading frames (ORFs) in the central portion of lambdoid bacteriophages in E. coli O157:H7 (19). In Sakai and EDL933, the two E. coli O157:H7 strains that have been completely sequenced, the bacteriophage that encodes Stx1 is integrated into yehV (57), which encodes a protein that positively regulates curli expression (7), and is flanked by duplications of CCCTGT CACGTTACGCGCGTG. The bacteriophage that encodes Stx2 is integrated into wrbA (32, 40), which encodes a novel multimeric flavodoxin-like protein (13), and is flanked by duplications of GACATATTGAAAC. Almost all E. coli O157:H7 strains possess stx 2 , and approximately three-quarters contain, in addition, stx 1 (strains lacking stx 1 are referred to hereafter as stx 1 -negative strains) (23,38,45). Most human non-O157:H7 Stx-producing E. coli (STEC) strains possess stx 1 but lack stx 2 (5, 6, 28, 51). Except for an Stx2...