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

Herbert Schmidt^1,

¹ Institut für Medizinische Mikrobiologie und Hygiene der TU Dresden, Germany
² Institut für Hygiene und Mikrobiologie der Bayerischen Julius Maximilians Universität Würzburg, Germany
³ Lehrstuhl für Lebensmittelchemie der Bayerischen Julius Maximilians Universität Würzburg, Germany

Correspondence
Herbert Schmidt
hschmidt{at}uni-hohenheim.de

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-1639 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 O103 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 MG1655 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.

The GenBank/EMBL/DDBJ accession numbers for the sequences determined in this work are AJ304858 (phage CP-1639 and chromosomal integration site) and AJ831374 (integrative element of E. coli O103 : H2 strain 2905/96).

Present address: Department of Food Microbiology, Institute of Food Technology, University of Hohenheim, Garbenstrasse 28, 70599 Stuttgart, Germany.

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