Salmonella enterica serovar Typhimurium strain LT2 harbours four prophages, including Gifsy-1, Gifsy-2, Fels-1 and Fels-2 (McClelland et al., 2001; Brüssow et al., 2004). Both the Gifsy-3 and the SopE prophages, found in S. Typhimurium strains 14028 and SL1344, respectively, are absent in S. Typhimurium strain LT2 (Figueroa-Bossi et al., 2001; Brüssow et al., 2004; Thomson et al., 2004). Salmonella enterica serovar Typhimurium strains SL1344

and 14028 both contain Gifsy-1 and Gifsy-2, but not Fels-1 and Fels-2 (Figueroa-Bossi et al., Tyrosine Kinase Inhibitor Library 2001). Salmonella enterica serovar Typhi harbours seven distinct prophage-like elements, spanning >180 kb, that are generally conserved between strains (Fig. 2) (Thomson et al., 2004). The modular nature of prophage genomes makes a significant contribution to serovar variation

and comprises most of the variation in gene content among strains of the same serovar (Boyd et al., 2003; Vernikos et al., 2007). Salmonella has many virulence-associated genes found within clusters in its genome, which are known as SPIs (Mills et al., 1995). Virulence factors encoded by SPI genes tamper with host cellular mechanisms and are thought to dictate the host specificity of the different S. enterica serovars (Eswarappa et al., 2008). Many of the SPIs are found next to a tRNA gene (Supporting Information, Fig. S1) and their G+C content differs from the rest of the genome (Fig. 2). Hence, such genomic islands were most likely inserted into the DNA of Salmonella by horizontal transfer events, although Tolmetin this explanation remains uncertain (Amavisit Epacadostat mouse et al., 2003). Twenty-one SPIs are known to date in Salmonella (McClelland et al., 2001; Parkhill et al., 2001; Chiu et al., 2005; Shah et al., 2005; Vernikos & Parkhill, 2006; Fuentes et al., 2008; Blondel et al., 2009). The S. Typhimurium and S. Typhi genomes contain 11 common SPIs (SPIs-1 to 6, 9, 11, 12, 13 and 16) (Fig. 2). SPIs-8 and 10 were initially found in S. Typhi, and considered as absent in S. Typhimurium. However, at both locations in S. Typhimurium, there is a completely different set of genes. There is only one SPI specific to S. Typhimurium, SPI-14 (Shah et

al., 2005), and four SPIs are specific to S. Typhi (SPIs-7, 15, 17 and 18) (Fig. 2). SPIs-19, 20 and 21 are absent in both of these serovars and will not be discussed further (Blondel et al., 2009). Even if many of these islands are found in both serovars, differences emerge when comparing equivalent SPIs. In the following section, the genomic differences between S. Typhimurium and S. Typhi are described for each SPI using S. Typhimurium strain LT2 and S. Typhi strain CT18 as the genomic references. Amino acid alignments of SPIs between these strains were performed using the xbase software (Chaudhuri & Pallen, 2006) and can be seen in Fig. S1. SPI-1 is a 40 kb locus located at centisome 63 encoding a type three secretion system (T3SS) (Mills et al.