, 2001), a characteristic that was confirmed by the sequencing of other S. Typhi strains (Deng et al., 2003; Holt et al., 2009). We will point out the different pseudogenes in each of the following sections. Surprisingly, most of the pseudogenes in S. Typhi are intact and fully functional in S. Typhimurium (McClelland et al., 2001) and could explain in part the loss of host range for serovar S. Typhi. Interestingly, many pseudogenes from S. Typhi are also LDE225 cost conserved in Paratyphi A, a serovar that has the ability to cause enteric fever that afflicts only humans (McClelland et al., 2004; Holt et al., 2009). Most S. Typhimurium strains contain a self-transmissible
virulence plasmid (pSLT) of about 90 kb harbouring virulence genes such as the spv operon, involved in intramacrophage survival, and the plasmid-encoded fimbriae (pef) fimbrial operon (Gulig & Doyle, 1993; Ahmer et al.,
1999; Rotger & Casadesús, 1999). When S. Typhimurium is cured selleck of the plasmid, virulence in the mouse is decreased (Jones et al., 1982) and can be complemented by the sole addition of the spv operon (Gulig et al., 1992) encoding the SpvB toxin (Lesnick et al., 2001). Additionally, S. Typhimurium can also carry multidrug-resistance plasmids of high molecular weight (up to 200 kb) and much smaller plasmids (<20 kb) with unknown functions (Rychlik et al., 2006). The pSLT virulence plasmid is absent in S. Typhi strains. In S. Typhi, incHI plasmids involved in multiple-drug resistance are commonly found (Maher & Taylor, 1993; Fica et al., 1997; Wain et al., 2003). Salmonella enterica serovar Typhi strain CT18 harbours plasmid pHCM1, an incHI1 plasmid of about 218 kb with genes for resistance to antibiotics PAK5 and heavy metals (Parkhill et al., 2001). Salmonella enterica serovar Typhi can also carry cryptic plasmids. Salmonella enterica serovar Typhi strain CT18 harbours the cryptic plasmid pHCM2 of
about 106 kb whose function is unknown, but it is rarely present in other strains (Parkhill et al., 2001; Kidgell et al., 2002a, b). Additionally, a 27-kb linear plasmid was recently isolated in S. Typhi strains originating from Indonesia. This plasmid carries the fljBz66 gene, encoding a flagellin antigen known as H:z66 (Baker et al., 2007b). However, no plasmid has been identified yet in S. Typhi that has been associated with virulence. Integrated bacteriophages represent major loci of genetic diversity in bacterial genomes (Brüssow et al., 2004). Salmonella genomes contain several prophages or prophage remnants with similarity to the lambda, Mu, P2 and P4 families (Thomson et al., 2004; Bossi & Figueroa-Bossi, 2005). The contribution of prophages to S. enterica virulence has been recognized only recently. Some prophages carry nonessential ‘cargo’ genes involved in fitness and/or virulence, including several type three secreted effectors (Ehrbar & Hardt, 2005). Each strain of S.