Spontaneous recombination between homologous prophage regions causes large-scale inversions within the Escherichia coli O157:H7 chromosome

Abstract

It is known that XbaI-digested chromosomal DNAs of strains of Escherichia coli O157:H7 exhibit a wide variety in pulsed-field gel electrophoresis (PFGE) fragment patterns, which is used for epidemiological surveillance of this important pathogen. The variety in the restriction enzyme-digestion patterns suggests a wide genomic diversity, however, only a few studies have been conducted to investigate involvement of large-scale chromosomal rearrangements in development of the diversity. In this study, through rounds of subculturing E. coli O157:H7 strain EDL933, naturally occurring genome variation in the isolated derivatives was investigated. By comparing the PFGE patterns among clonally related derivatives, we found five types of large-scale inversions taking place within the chromosome. The five inversions found were across the replication axis and ranged from 250-kb to 1.4-Mb long, and all the corresponding recombination sites were associated with prophages or phage-like regions. Four inversions out of the five were resulted from recombination between pairs of lambda-like prophages disturbing the symmetry of the origin and terminus of the replication axis. These observations indicate that those prophage regions represent some of the hot spots for intrachromosomal recombination within the E. coli O157:H7 chromosome, where recombination between the prophage regions results not only in the large chromosomal inversions but might also in generation of chimeric phages.

Optical maps distinguish individual strains of Escherichia coli O157 : H7

“…Carefully detailed PFGE analysis of inversions occurring during passage of E. coli O157 : H7 EDL933 in the laboratory (Iguchi et al, 2006) found most of the inversions identified by optical mapping. An additional inversion between an EDL933 P4-like prophage M located at O-island 43 and another P4-like prophage at O-island 48 was also found after laboratory passage of EDL933.…”

“…There are, of course, chromosomal constraints that will modulate inversion formation, e.g. the positions of the origin and termination of chromosome replication (Iguchi et al, 2006).…”

“…In addition to showing that a single isolate of EDL933, during subculture in the laboratory, produced a number of different PFGE profiles derived from chromosomal inversions (Iguchi et al, 2006), three other E. coli O157 : H7 strains, including Sakai, showed changes in PFGE patterns after repeated subculture and prolonged storage (Shima et al, 2006). Chromosomal inversions in these strains were implicated in some of the changed PFGE profiles.…”

Optical mapping and 454 sequencing of Escherichia coli O157 : H7 isolates linked to the US 2006 spinach-associated outbreak

“…Genomic variability of E. coli O157 : H7 strains is mainly due to differences within prophages and in chromosomal inversions (Kudva et al, 2002a, b;Brüssow et al, 2004;Iguchi et al, 2006;Kotewicz et al, 2007). Most of the chromosomal markers demonstrated by optical mapping would not have been detected by microarray and simple sequence-based techniques such as SNP analysis.…”

“…Variations among dozens of prophage integrations and excisions, as well as prophage deletions and substitutions, have changed restriction sites and PFGE and PCR profiles for otherwise similar E. coli O157 : H7 isolates. Notably, large, and often double, chromosomal inversions are prevalent in E. coli O157 : H7 isolates (Iguchi et al, 2006;Shima et al, 2006;Kotewicz et al, 2007) and the inversions have occurred within resident prophages.…”