Genomic island discovery in Shigella by tRNA site interrogation

Introduction: Shigella spp. are pathogenic variants of Escherichia coli that cause bacillary dysentery, resulting in more than 1 million deaths per year. E. coli bacteria demonstrate extensive intra-species genodiversity. The dynamic process of acquisition and loss of genomic islands (GIs), especially those associated with virulence (pathogenicity islands [PAIs]) is a driving force behind the emergence of new pathotypes. In Shigella only 4 GIs have been well characterised and there is currently no effective vaccine against the many serotypes of this pathogen. Therefore the development of an effective screen to detect GIs in unsequenced Shigella strains could be highly informative. In this study, 16 known E. coli tRNA gene integration hotspots in 10 strains representative of the 4 ‘species’ of Shigella were probed for the presence of island DNA using a high throughput PCR screen known as tRNA site Interrogation for PAIs, prophages and other GIs (tRIP). Putative GIs were then investigated using a chromosome walking technique known as single genome-specific primer-PCR (SGSP-PCR).