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Background   Salmonella paratyphi  C, like  S. typhi , is adapted to humans and causes typhoid fever. Previously we reported different genome structures between two strains of  S. paratyphi  C, which suggests that  S. paratyphi  C might have a plastic genome (large DNA segments being organized in different orders or orientations on the genome). As many but not all host-adapted  Salmonella  pathogens have large genomic insertions as well as the supposedly resultant genomic rearrangements, bacterial genome plasticity presents an extraordinary evolutionary phenomenon. Events contributing to genomic plasticity, especially large insertions, may be associated with the formation of particular  Salmonella  pathogens.    Results  We constructed a high resolution genome map in  S. paratyphi  C strain RKS4594 and located four insertions totaling 176 kb (including the 90 kb SPI7) and seven deletions totaling 165 kb relative to  S. typhimurium  LT2. Two rearrangements were revealed, including an inversion of 1602 kb covering the  ter  region and the translocation of the 43 kb I-CeuI F fragment. The 23 wild type strains analyzed in this study exhibited diverse genome structures, mostly as a result of recombination between  rrn  genes. In at least two cases, the rearrangements involved recombination between genomic sites other than the  rrn  genes, possibly homologous genes in prophages. Two strains had a 20 kb deletion between  rrlA  and  rrlB , which is a highly conservative region and no deletion has been reported in this region in any other  Salmonella  lineages.    Conclusion   S. paratyphi  C has diverse genome structures among different isolates, possibly as a result of large genomic insertions, e.g., SPI7. Although the  Salmonella  typhoid agents may not be more closely related among them than each of them to other  Salmonella  lineages, they may have evolved in similar ways, i.e., acquiring typhoid-associated genes followed by genome structure rearrangements. Comparison of multiple  Salmonella  typhoid agents at both single sequenced genome and population levels will facilitate the studies on the evolutionary process of typhoid pathogenesis, especially the identification of typhoid-associated genes.

Diverse genome structures of Salmonella paratyphi C