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The increased availability of whole-genome-sequencing techniques generates a wealth of DNA data on numerous organisms, including foodborne pathogens such as  Salmonella . However, how these data can be used to improve microbial risk assessment and understanding of  Salmonella  epidemiology remains a challenge. The aim of this study was to assess variability in  in vitro  virulence and genetic characteristics between and within different serovars. The phenotypic behavior of 59 strains of 32 different  Salmonella enterica  serovars from animal, human and food origin was assessed in an  in vitro  gastro-intestinal tract (GIT) system and they were analyzed for the presence of 233 putative virulence genes as markers for phenotypic prediction. The probability of  in vitro  infection, P(inf), defined as the fraction of infectious cells passing from inoculation to host cell invasion at the last stage of the GIT system, was interpreted as the  in vitro  virulence. Results showed that the (average) P(inf) of  Salmonella  serovars ranged from 5.3E-05 ( S.  Kedougou) to 5.2E-01 ( S.  Typhimurium). In general, a higher P(inf) on serovar level corresponded to higher reported human incidence from epidemiological reporting data. Of the 233 virulence genes investigated, only 101 showed variability in presence/absence among the strains.  In vitro  P(inf) was found to be positively associated with the presence of specific plasmid related virulence genes ( mig -5,  pef ,  rck , and  spv ). However, not all serovars with a relatively high P(inf), > 1E-02, could be linked with these specific genes. Moreover, some outbreak related strains ( S.  Heidelberg and  S.  Thompson) did not reveal this association with P(inf). No clear association with  in vitro  virulence P(inf) was identified when grouping serovars with the same virulence gene profile (virulence plasmid, Typhoid toxin,  peg  operon and  stk  operon). This study shows that the  in vitro  P(inf) variation among individual strains from the same serovar is larger than that found between serovars. Therefore, ranking P(inf) of  S. enterica  on serovar level alone, or in combination with a serovar specific virulence gene profile, cannot be recommended. The attribution of single biological phenomena to individual strains or serovars is not sufficient to improve the hazard characterization for  S. enterica.  Future microbial risk assessments, including virulence gene profiles, require a systematic approach linked to epidemiological studies rather than revealing differences in characteristics on serovar level alone.

Phenotypic Prediction: Linking in vitro Virulence to the Genomics of 59 Salmonella enterica Strains