Genetic structure and chromosomal integration site of the cryptic prophage CP-1639 encoding Shiga toxin 1

The sequence of 50 625 bp of chromosomal DNA derived from Shiga-toxin (Stx)-producing Escherichia coli (STEC) O111 : H- strain 1639/77 was determined. This DNA fragment contains the cryptic Stx1-encoding prophage CP-1639 and its flanking chromosomal regions. The genome of CP-11639 basically resembles that of lambdoid phages in structure, but contains three IS629 elements, one of which disrupts the gene of a tail fibre component. The prophage genome lacks parts of the recombination region including integrase and excisionase genes. Moreover, a capsid protein gene is absent. CP-1639 is closely associated with an integrase gene of an ancient integrative element. This element consists of three ORFs of unknown origin and a truncated integrase gene homologous to intA of CP4-57. By PCR analysis and sequencing, it was shown that this integrative element is present in a number of non-O157 STEC serotypes and in non-STEC strains, where it is located at the 3'-end of the chromosomal ssrA gene. Whereas in most E coli O111 : H- strains, prophages are inserted in this site, E coli O26 strains contain the integrative element not connected to a prophage. In E coli 0103 strains, the genetic structure of this region is variable. Comparison of DNA sequences of this particular site in E coli O157: H7 strain EDL933, E coli O111 : H- strain 1639/77 and E coli K-12 strain MG 1655 showed that the ssrA gene is associated in all cases with the presence of foreign DNA. The results of this study have shown that the cryptic prophage CP-1639 is associated with an integrative element at a particular site in the E coli chromosome that possesses high genetic variability.