Author(s): Min Yue 1 , Shelley C. Rankin 1 , Ryan T. Blanchet 2 , James D. Nulton 2 , Robert A. Edwards 2 , 3 , Dieter M. Schifferli 1 , *
Salmonella infections result in substantial human and livestock morbidity and mortality worldwide . In humans S. enterica serovars Typhi and Paratyphi cause systemic diseases (typhoid and paratyphoid fever), globally with an estimated 12-33 million cases of illness and 216,00-600,000 deaths per year . Non-typhoidal salmonellae cause foodborne diarrheal illness, with approximately 1.3 billion cases of gastroenteritis per year, resulting in 3 million deaths . Salmonella remains the most frequent bacterial agent of foodborne diseases ,  and was the leading foodborne microbe causing hospitalizations and deaths in the US . Salmonella affects also animals, and immunologically unprepared young, stressed or periparturient farm animals are particularly susceptible to Salmonella enterica strains capable of causing systemic infections -. More frequently following an enteric infection, farm animals become asymptomatic carriers that shed bacteria contaminating carcasses, milk, eggs and agricultural products grown on land fertilized with manure . Undetected animal reservoirs best explain why CDC surveillance programs aimed at reducing food contamination remain mostly unsuccessful for Salmonella , .
Salmonella e are thought to have diverged from a common ancestor with Escherichia coli 100~160 million years ago . Although the latest accepted nomenclature divides Salmonella in only two species, bongori and enterica, and the latter species in 6 main named or numbered subspecies (enterica or I, salamae or II, arizonae or IIIa, diarizonae or IIIb, houtenae or IV and indica or VI; V is now S. bongori ) , over 2,600 serovars have been identified . Serovars are defined by the antigenic properties of the polysaccharide chains of LPS (O-antigens) and of the proteinaceous flagella (H antigens). Salmonella inhabit and multiply in an environment that is highly propitious for horizontal gene transfer (HGT): the intestine of carrier animals which is extremely rich in mobile DNA. O- and H-antigen gene studies indicated that the acquisition of DNA played a major role in the diversification of the Salmonella serovar antigens , . Newly acquired serovar-modifying DNA, together with the elimination or inactivation of unnecessary or interfering DNA, has been suggested to direct serovar-specific adaptation for successful competition with the host-specific intestinal flora, and provide the defense against predatory protozoa, lytic phages and host-specific immunity -. Diagnostic and epidemiological focus on the serovars of Salmonella has led to the distinction of serovars that are host-restricted (e.g. serovar Gallinarum in birds or Typhi in humans), host-adapted (e.g. serovar Choleraesuis in swine, more rarely in other animals or in humans), and broad range (e.g. serovar Typhimurium). However, the exact genetic components that determine host range and specialized adaptation remain to be identified.
A variety of methods have been used to dissect evolutionary links between serovars such as multi-locus enzyme electrophoresis  and multi-locus sequence typing (MLST), typically based on up to 7 housekeeping genes (http://mlst.ucc.ie/mlst/dbs/Senterica). The latter approach was able to demonstrate that not all Salmonella subspecies are clonal...