The availability of bacterial genome sequences raises an important new problem - how can one move from completely sequenced microorganisms as a reference to the hundreds and thousands of other strains or isolates of the same or related species that will not be sequenced in the near future? An efficient way to approach this task is the comparison of genomes by subtractive hybridization. Recently we developed a sensitive and reproducible subtraction procedure for comparison of bacterial genomes, based on the method of suppression subtractive hybridization (SSH). In this work we demonstrate the applicability of subtractive hybridization to the comparison of the related but markedly divergent bacterial species Escherichia coli and Salmonella typhimurium. Clone libraries representing sequence differences were obtained and, in the case of completely sequenced E. coli genome, the differences were directly placed in the genome map. About 60% of the differential clones identified by SSH were present in one of the genomes under comparison and absent from the other. Additional differences in most cases represent sequences that have diverged considerably in the course of evolution. Such an approach to comparative bacterial genomics can be applied both to studies of interspecies evolution - to elucidate the "strategies" that enable different genomes to fit their ecological niches - and to development of diagnostic probes for the rapid identification of pathogenic bacterial species.

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The development of gastroenteritis caused by non-typhoidal Salmonella (NTS) is mediated by the action of effectors that belong to the Type three secretory systems (T3SS) of Salmonella enterica. These effectors are expressed by Salmonella pathogenicity islands 1 and 2 located in the genome. The effectors of T3SS-1 provide invasion of salmonella into host cell, take part in the development of inflammatory diarrhea some and may act as a predisposing factor in oncogenesis leading to the development of colorectal cancer (CRC). The T3SS-2 effectors provide intracellular survival of bacteria in the host cell and evading from the host adaptive immune response that may lead to the prolonged persistence.