enterica (Grassl & Finlay, 2008; Haraga et al., 2008;

Tsolis et al., 2008; McGhie et al., 2009). This review presents a comparative analysis of the major genetic differences between S. Typhimurium and S. Typhi and how this may contribute RGFP966 chemical structure to our understanding of typhoid pathogenesis. 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 Methisazone & Casadesús, 1999; Boyd & Brüssow, 2002) and will be discussed below. The low level of genetic FK506 variation observed in S. Typhi genomes of distinct isolates from around the world revealed a highly conserved and clonal relation, suggesting that they emerged from a single progenitor, making S. Typhi a monomorphic organism (Baker & Dougan, 2007; Holt et al., 2008). Clonality is often encountered in human-restricted pathogens (Achtman, 2008). There is very little evidence of adaptive selection in S. Typhi genes, with the exception of a recent evolution in phenotypic traits that includes the acquisition of resistance to fluoroquinolones (Chau et al., 2007; Le et al., 2007). Examination of DNA sequences and the rate of change of single-nucleotide polymorphisms suggest that S. Typhi may be only 50 000 years old, a short time frame for bacteria to accumulate diversity (Selander et al., 1990; Kidgell et al., 2002a, b; Roumagnac et al., 2006). This situation strongly suggests that evolution in the S. Typhi strain population is mainly characterized by loss of gene function. Salmonella enterica serovar Typhi is an example of reductive evolution, where the adaptation to its human niche has led to the functional inactivation of genes, due to certain needs that have been satisfied by the host (Dagan et al., 2006). Annotation of the first completed S.