Phenotypic Prediction: Linking Virulence to the Genomics of 59 Strains.

The increased availability of whole-genome-sequencing techniques generates a wealth of DNA data on numerous organisms, including foodborne pathogens such as . However, how these data can be used to improve microbial risk assessment and understanding of epidemiology remains a challenge. The aim of this study was to assess variability in virulence and genetic characteristics between and within different serovars. The phenotypic behavior of 59 strains of 32 different serovars from animal, human and food origin was assessed in an 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 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 virulence. Results showed that the (average) P(inf) of serovars ranged from 5.3E-05 ( Kedougou) to 5.2E-01 ( 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. P(inf) was found to be positively associated with the presence of specific plasmid related virulence genes (-5, , , and ). However, not all serovars with a relatively high P(inf), > 1E-02, could be linked with these specific genes. Moreover, some outbreak related strains ( Heidelberg and Thompson) did not reveal this association with P(inf). No clear association with virulence P(inf) was identified when grouping serovars with the same virulence gene profile (virulence plasmid, Typhoid toxin, operon and operon). This study shows that the P(inf) variation among individual strains from the same serovar is larger than that found between serovars. Therefore, ranking P(inf) of 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 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.