Organization of genomes allows us to gain a better understanding of the mechanisms by which species or serovars have evolved. Analysis of the chromosomal gene arrangement revealed that the genomic backbone of S. Typhimurium is very similar to the Escherichia coli genome. However, major differences in gene order have been observed in the S. Typhi chromosome. Differences in the S. Typhi genome occur mainly because of genomic rearrangements involving recombination between different rRNA operons (Liu & Sanderson, 1995; Liu & Sanderson, 1996) or IS200 elements (Alokam et al., 2002). Each serovar evolves through the acquisition of genetic elements by horizontal gene transfer or by gene degradation. The genomes of S. Typhimurium strain LT2 and S. Typhi strain CT18 are composed of 4 857 432 and 4 809 037 bp, respectively (Fig. 2) (McClelland et al., 2001; Parkhill et al., 2001). Both serovars share about 89% of genes (McClelland et al., 2001). Differences between S. Typhimurium and S. Typhi include ≈480 genes unique to S. Typhimurium and ≈600 genes unique to S. Typhi (Parkhill et al., 2001). Salmonella pathogenicity islands (SPIs), plasmids, functional prophages and phage remnants contribute significantly to the genetic diversity among S. enterica strains (Rotger & Casadesús, 1999; Boyd & Brüssow, 2002) and will be discussed below.
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 this explanation remains uncertain (Amavisit 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., 1995) and the sit metal transport system (Janakiraman & Slauch, 2000). The T3SS is involved in the invasion of nonphagocytic cells and proinflammatory responses (Galán & Curtiss, 1989; Mills et al., 1995; Galán & Collmer, 1999). T3SS are used by the bacteria to inject proteins, called effectors, directly inside the host cells that will act as mediators of cell invasion and modifications contributing to intracellular growth. Effectors can be encoded by genes located inside or outside SPI-1. Genomic comparison confirmed a high degree of identity between the two serovars and revealed the presence of four additional ORFs in S. Typhimurium, including the bacterial effector avrA (Hardt & Galán, 1997) and three distal ORFs (STM2901, STM2902 and STM2903) encoding putative cytoplasmic proteins (Fig. S1a) (Parkhill et al., 2001). In S. Typhi, a partial insertion sequence and transposase are present at the end of the locus. Therefore, the major difference in SPI-1 between both serovars may be at the functional level, as some genes coding effectors located outside SPI-1 are missing (sspH1, steB) or are pseudogenes (sopA, sopE2 and slrP) in S. Typhi. All known SPI-1 and SPI-2 effectors of the two serovars are listed in Table S1. Amino acid substitutions in the SipD translocon and the SptP effector were identified between these serovars and may reflect a potential functionality difference (Eswarappa et al., 2008).
SPI-2 is a 40 kb locus inserted next to the valV tRNA gene at centisome 30 and encodes a second T3SS, which is involved in intracellular survival (Shea et al., 1996; Hensel et al., 1998). Using comparative genomics, no major differences in SPI-2 were observed between both serovars (Fig. S1b). Three ORFs (STY1735, STY1739 and STY1742) are pseudogenes in S. Typhi. These ORFs, however, are not part of the T3SS, but part of a tetrathionate reductase complex. As with SPI-1, some genes encoding effectors in S. Typhimurium that are located outside SPI-2 are missing (sseI, sseK1, sseK2 and sseK3) or are pseudogenes (sopD2, sseJ) in S. Typhi (Table S1). Molecular differences were observed in translocon genes sseC and sseD, and effectors sseF and sifA (Eswarappa et al., 2008), reflecting a probable difference in functionality between these serovars.
SPI-3 is a 36 kb locus inserted next to the selC tRNA gene located at centisome 82, is involved in intracellular survival and encodes a magnesium transporter (Blanc-Potard & Groisman, 1997). SPI-3 shows extensive variations in its structure in various S. enterica serovars and can be divided into three regions (Fig. S1c) (Blanc-Potard et al., 1999; Amavisit et al., 2003). The region found next to the selC tRNA gene is where variations between S. Typhimurium and S. Typhi are the highest, including deletions and insertions. This region contains many pseudogenes in S. Typhi: STY4024 (cigR), STY4027 (marT), STY4030 (misL), STY4034, STY4035 and STY4037. A few more pseudogenes in S. Typhi are found in the second and third portions of SPI-3, including STY4012, STY4007 and STY4003 (Fig. S1c). In brief, the autotransporter MisL involved in intestinal colonization (Dorsey et al., 2005), its regulator MarT (Tükel et al., 2007) and an unknown putative transcriptional regulator (STY4012) are inactivated in S. Typhi.
SPI-4 is a 24 kb fragment located next to a potential tRNA-like gene at centisome 92 (Fig. S1d) and involved in adhesion to epithelial cells (Wong et al., 1998). SPI-4 harbours the siiABCDEF gene cluster encoding a type one secretion system (T1SS) for SiiE, a giant nonfimbrial adhesin of 595 kDa (Morgan et al., 2004; Gerlach et al., 2007; Morgan et al., 2007). SiiE mediates a close interaction with microvilli found on the apical side of epithelial cells, thereby aiding efficient translocation of SPI-1 effectors required for apical membrane ruffling (Gerlach et al., 2008). SiiE is encoded by one ORF in S. Typhimurium (STM4261), but is segmented into two ORFs in S. Typhi (STY4458 and STY4459) because of a stop codon, also present in S. Typhi strain Ty2 (Fig. S1d) (Deng et al., 2003). This suggests that siiE is a pseudogene in S. Typhi (Parkhill et al., 2001; Morgan et al., 2004), which correlates with a loss of function for an adhesin that contributes to intestinal colonization by S. Typhimurium (Morgan et al., 2007).
SPI-5 is an island <8 kb in size, inserted next to the serT tRNA gene at centisome 25, and is required for enteropathogenicity (Wood et al., 1998). SPI-5 encodes effectors of both SPI-1 and SPI-2. No difference is observed between the two serovars, except that an additional ORF (STY1114) is predicted to encode a transposase in S. Typhi (Fig. S1e).
SPI-6 is located next to the aspV tRNA gene at centisome 7 and is a 47 kb island in S. Typhimurium (Folkesson et al., 1999; Folkesson et al., 2002), whereas it is rather 59 kb in S. Typhi (Parkhill et al., 2001). It was previously shown that the complete deletion of this island reduced the entry of S. Typhimurium in Hep2 cells (Folkesson et al., 2002). Located on this island are a type six secretion system (T6SS), the safABCD fimbrial gene cluster and the invasin pagN (Lambert & Smith, 2008), all present in both serovars (Folkesson et al., 1999; Townsend et al., 2001; Porwollik & McClelland, 2003). A 10 kb fragment downstream of the saf operon is found only in S. Typhi, and includes probable transposase remnants (STY0343 and STY0344, both pseudogenes), the fimbrial operon tcfABCD and genes tinR (STY0349) and tioA (STY0350) (Fig. S1f) (Folkesson et al., 1999; Townsend et al., 2001; Porwollik & McClelland, 2003). The T6SS of S. Typhi contains two pseudogenes, sciI (STY0298) and sciS (STY0308), and some ORFs are missing or divergent, probably rendering its T6SS nonfunctional. Interestingly, sciS was shown to limit the intracellular growth of S. Typhimurium in macrophages at a late stage of infection and to decrease virulence in mice (Parsons & Heffron, 2005).
SPI-7 remains the largest island identified to date and is absent in S. Typhimurium, but present in S. Typhi (Parkhill et al., 2001; Pickard et al., 2003; Bueno et al., 2004). In S. Typhi, it is 134 kb in size, corresponding to approximately 150 genes inserted between duplicated pheU tRNA sequences (Hansen-Wester & Hensel, 2002; Pickard et al., 2003). This island contains the Vi capsule biosynthesis genes (Hashimoto et al., 1993), whose production is associated with virulence (see section below), a type IVB pilus operon (Zhang et al., 2000) and the SopE prophage (ST44) encoding the SPI-1 effector SopE (Mirold et al., 1999). SopE is also encoded in S. Typhimurium's genome, but within the temperate SopE prophage (Hardt et al., 1998) located at a different location (sopE is absent in most S. Typhimurium strains, including S. Typhimurium strain LT2, but present and located on a prophage in S. Typhimurium strains SL1344 and 14028) (Hardt et al., 1998; Mirold et al., 1999; Pelludat et al., 2003). At the SPI-7 location in S. Typhimurium LT2, we find a single complete pheU tRNA sequence and STM4320 (a putative merR family bacterial regulatory protein) (Fig. S1g).
SPI-8 is an 8 kb DNA fragment found next to the pheV tRNA gene that is part of SPI-13 and will be discussed in that section (Fig. S1l) (Parkhill et al., 2001; Hensel, 2004).
SPI-9 is a 16 kb locus present in both serovars (Fig. S1h). This island contains three genes encoding for a T1SS and one for a large protein, sharing an overall 40% nucleotide identity to siiCDEF genes from SPI-4 (Morgan et al., 2004, 2007). The large protein-coding ORF (STM2689) in S. Typhimurium strain LT2 was first suggested to be a pseudogene (McClelland et al., 2001; Morgan et al., 2004). However, a subsequent study showed an undisrupted gene coding a putative 386 kDa product renamed BapA (Latasa et al., 2005).
SPI-10 is an island found next to the leuX tRNA gene at centisome 93. This locus is completely different in each serovar and has been termed SPI-10 only in S. Typhi. In S. Typhimurium, it is substituted by a 20 kb uncharacterized island without any SPI annotation (Fig. S1i), comprising functionally unrelated genes that share little homology to sequences from the genomic databases (Edwards et al., 2001; Bishop et al., 2005). However, a possible relationship of these genes with DNA repair has been proposed (Porwollik & McClelland, 2003). Deletion of this island in S. Typhimurium strain 14028 caused attenuation of virulence in mice (Haneda et al., 2009). In S. Typhi's genome, this island corresponds to a 33 kb fragment (Parkhill et al., 2001) carrying a full P4-related prophage, termed ST46 (Edwards et al., 2001; Thomson et al., 2004; Bishop et al., 2005). ST46 harbours the prpZ cluster as cargo genes encoding eukaryotic-type Ser/Thr protein kinases and phosphatases involved in S. Typhi survival in macrophages (Faucher et al., 2008). There is also a complete, but inactivated sefABCDR (S. Enteritidis fimbriae) fimbrial operon (Fig S1i). Many pseudogenes are found in S. Typhi: STY4835 (IS1230), STY4836 (sefA), STY4839 (sefD), STY4841 (sefR), STY4845 (a thiol : disulphide interchange protein) and STY4848 (putative transposase) (Fig. S1i). Interestingly, ORFs STY4842–4846 of S. Typhi are homologues to S. Typhimurium genes located on the virulence plasmid, including srgA (Rodríguez-Peña et al., 1997). srgA encodes a functional disulphide oxidoreductase in S. Typhimurium and is a pseudogene in S. Typhi (STY4845) (Bouwman et al., 2003). It was shown that SrgA acts in concert with DsbA, another disulphide oxidoreductase, to target SipA (a SPI-2 effector), and that an srgA dsbA double mutant had a stronger attenuation than either single mutants, with a level of attenuation similar to a SPI-2 mutant (Miki et al., 2004).
SPI-11 was initially identified in the genome sequencing of serovar Choleraesuis as a 14 kb fragment inserted next to the Gifsy-1 prophage (Chiu et al., 2005). This SPI is shorter in S. Typhimurium (6.7 kb) and in S. Typhi (10 kb) (Fig. S1j). SPI-11 includes the phoP-activated genes pagD and pagC involved in intramacrophage survival (Miller et al., 1989; Gunn et al., 1995). The putative envelope lipoprotein envF is absent in S. Typhi, while six additional ORFs (STY1884–1891), including the typhoid toxin cdtB, are present in S. Typhi (Fig. S1j) (Spanòet al., 2008).
SPI-12, located next to the proL tRNA gene at centisome 48, is 15.8 kb long in S. Typhimurium and 6.3 kb long in S. Typhi (Fig. S1k) (Hansen-Wester & Hensel, 2002). It contains the effector SspH2 (Miao et al., 1999). The additional 9.5 kb fragment in S. Typhimurium contains 11 ORFs, which include some putative and phage-associated genes as well as oafA, encoding a Salmonella-specific gene for O-antigen acetylase (Fig. S1k) (Slauch et al., 1996; Hansen-Wester & Hensel, 2002). SPI-12 was shown to be required for systemic infection of mice in S. Typhimurium strain 14028 (Haneda et al., 2009). In S. Typhi, three ORFs are pseudogenes (STY2466a, STY2468 and STY2469), leaving only the sspH2 gene as functional on this island.
SPI-13 was initially identified in serovar Gallinarum (Shah et al., 2005). This 25 kb gene cluster is found next to the pheV tRNA gene at centisome 67 in S. Typhimurium and in S. Typhi. However, an 8 kb portion is different in each serovar and corresponds to SPI-8 only in S. Typhi (Fig. S1l). In S. Typhimurium, this region contains the ORFs STM3117 to STM3123, a cluster unique to S. Typhimurium, coding genes for a putative lyase, hydrolase, oxidase, arylsulphatase and arylsulphatase regulator as well as two putative LysR family transcriptional regulators (Fig. S1l). In strain S. Typhimurium 14028, STM3117–STM3121 are novel virulence-associated genes, as they were shown to be involved in systemic infection of mice (Haneda et al., 2009) and replication inside murine macrophages (Shi et al., 2006). In S. Typhi, the virulence function of SPI-8 is unknown and it harbours two bacteriocin immunity proteins (STY3281 and STY3283) and four pseudogenes (Fig. S1l) (Parkhill et al., 2001). The 17 kb conserved portion of SPI-13 has not been shown to contribute to virulence (Haneda et al., 2009).
SPI-14 corresponds to 9 kb present in S. Typhimurium at centisome 19 and is absent in S. Typhi (Shah et al., 2005; Morgan, 2007). It harbours seven ORFs encoding putative cytoplasmic proteins (Fig. S1m). The function of genes on this island is unknown, but gene upregulation was observed in macrophages infected by S. Typhimurium strain SL1344 (Eriksson et al., 2003).
SPI-15 is a 6.5 kb island of five ORFs encoding hypothetical proteins, is inserted near the glyU tRNA gene in S. Typhi and is absent in S. Typhimurium (Fig. S1n) (Vernikos & Parkhill, 2006). Different genes are found at the same location in S. Typhi strain Ty2 (Fig. S1n) (Vernikos & Parkhill, 2006). SPI-15, as well as SPI-16 and 17, were identified by bioinformatic work (Vernikos & Parkhill, 2006).
SPI-16 is found in S. Typhimurium and S. Typhi as a 4.5 kb fragment inserted next to an argU tRNA site, and encodes five or seven ORFs, respectively, four of which are pseudogenes in S. Typhi (Fig. S1o). The three remaining ORFs show a high level of identity with P22 phage genes involved in seroconversion (Vernikos & Parkhill, 2006) and were suggested to mediate O-antigen glycosylation (Mavris et al., 1997; Guan et al., 1999) and cell surface variation (Allison & Verma, 2000; Bogomolnaya et al., 2008). These ORFs (genes yfdH, rfbI and STM0557) were required for the intestinal persistence of S. Typhimurium in mice (Bogomolnaya et al., 2008).
SPI-17 is a 5 kb island encoding six ORFs inserted next to an argW tRNA site and is absent in S. Typhimurium, but present in S. Typhi (Fig. S1p) (Vernikos & Parkhill, 2006). Seroconversion genes homologous to P22 phage are present and showed high homology to genes of SPI-16, including a putative lipopolysaccharide modification acyltransferase. Most of these genes (four) are pseudogenes in S. Typhi (Fig. S1p).
SPI-18 was recently identified in S. Typhi as a 2.3 kb fragment harbouring only two ORFs: STY1498 and STY1499 (Fig. S1q) (Fuentes et al., 2008). clyA (STY1498), also known as hlyE or sheA, encodes a 34 kDa pore-forming secreted cytolysin found in E. coli and S. enterica serovars Typhi and Paratyphi A (del Castillo et al., 1997; Green & Baldwin, 1997; Oscarsson et al., 1999, 2002). clyA is important for invasion of human epithelial cells in vitro, with its heterologous expression in S. Typhimurium leading to colonization of deep organs in a murine model (Fuentes et al., 2008). taiA (STY1499) is a secreted 27 kDa invasin that increases bacterial uptake by human macrophages (Faucher et al., 2009). Both genes are part of a common operon and are controlled by the virulence-related regulator PhoP (Faucher et al., 2009).
Other pathogenicity islands are found in the S. Typhimurium and S. Typhi genomes and have not been identified as SPIs, but encode genes responsible for virulence in the host, such as CS54. The CS54 island is a 25 kb region found between xseA and yfgJ at centisome 54 in S. Typhimurium (Kingsley et al., 2003) and S. Typhi (Fig. S1r). Five genes are found within this island, which are shdA, ratB, ratA, sinI and sinH (sivH). In S. Typhimurium, ShdA was shown to be an outer membrane protein of the autotransporter family that binds fibronectin, RatB is a predicted secreted protein of unknown function and SinH is a putative outer membrane protein (Kingsley & Bäumler, 2002; Kingsley et al., 2003; Abd El Ghany et al., 2007). shdA, ratB and sinH (sivH) are all implicated in intestinal colonization of BALB/c mice by S. Typhimurium, but are all pseudogenes in S. Typhi (Kingsley et al., 2003).