The genus Salmonella contains a group of closely related pathogens that can be differentiated by serology into 2463 serotypes [1]. The genus contains two species, Salmonella bongori (containing 20 different serotypes) and Salmonella enterica (containing 2443 different serotypes). S. enterica is further subdivided into six subspecies: enterica (subspecies I), salamae (subspecies II), arizonae (subspecies IIIa), dia-rizonae (subspecies IIIb), houtenae (subspecies IV), and indica (subspecies VI) [1]. Unlike members of the closely related genus Escherichia, which contains both pathogenic and commensal organisms, all members of the genus Salmonella are considered pathogenic for humans. However, Salmonella serotypes vary with regard to their natural host range and the disease manifestations associated with infection of different host species.

Genomic comparison of Salmonella serotypes with closely related commensal organisms has revealed genetic differences that are important for their pathogenic lifestyle. Identification of genomic differences between Salmonella serotypes is beginning to provide new insights into the genetic basis of host adaptation and the pathogenesis of certain diseases. This chapter will review recent progress in understanding Salmonella pathogenesis and evolution as a result of whole genome sequencing.

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