Lineage II Escherichia coli O157:H7: genomes, prophages, colicins, and the absence of detectable Stx2

The genomes of three lineage II strains of E. coli O157:H7 (FRIK2069, FRIK2455, and FRIK2533) with different pulsed-field gel electrophoresis patterns were sequenced, assembled, and compared. The genomes were closely related, with overall synteny, with the exception of a 302 kbp inversion in FRIK2069. FRIK2533 lacked pO157, which may account for its limited isolation. FRIK2455 was the dominant strain isolated over several years and was selected for comparison with lineage I (Sakai) and lineage I/II (EC4115) strains. Distinct polymorphisms were identified in prophages and MGEs among the three lineages. All lineages contained stx1 prophages and the locus of enterocyte effacement. The stx2a prophage was present in Sakai and EC4115, while the stx2c prophage was found in EC4115 and FRIK2455. Eleven geographically disparate LII strains from the United States were tested for functional phage and Stx2. Three of the 11 LII strains underwent delayed lysis after 24 h post-mitomycin C treatment. stx2 transcription was observed in two of the three lytic strains, but Stx2 was not detected in the lytic or non-lytic LII strains by Western blot. The supernatant of lysates from eight lineage II strains inhibited growth of the phage host ( E. coli strain MG1655) due to the production of a colicin (D, B, or M). These findings add to the body of evidence that LII EHEC do not produce functional phage or a detectable level of Stx2. Additionally, colicin production and pO157 may be key characteristics to the persistence of EHEC strains in the bovine host and farm environment. IMPORTANCE Escherichia coli O157:H7 is a human pathogen that is phylogenetically separated into three lineages. Strains belonging to lineages I and I/II are isolated from both clinical and bovine samples, whereas lineage II strains are only isolated from bovine and environments they occupy. This study sequenced, assembled, and compared the genomes of three lineage II strains. The genomes were closely related and syntenic, with differences in plasmid content and a chromosomal inversion. Comparison of the genome from FRIK2455 (lineage II strain) with the genomes of lineage I and I/II strains found distinct polymorphisms in prophages and mobile genetic elements. None of the lineage II strains examined produced functional phage or Stx2, but eight strains produced a colicin. Results from this study support previous reports that lineage II strains do not produce a detectable level of Stx2. Additionally, colicin production and pO157 may contribute to the persistence of EHEC in bovine.