AUTHOR=Kuijpers Angelina F. A. , Bonacic Marinovic Axel A. , Wijnands Lucas M. , Delfgou-van Asch Ellen H. M. , van Hoek Angela H. A. M. , Franz Eelco , Pielaat Annemarie 

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

JOURNAL=Frontiers in Microbiology

VOLUME=9

YEAR=2019

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2018.03182

DOI=10.3389/fmicb.2018.03182

ISSN=1664-302X

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