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

Abstract

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.

Pathogenicity and Competitive Fitness of Salmonella enterica Serovar 4,[5],12:i:- Compared to Salmonella Typhimurium and Salmonella Derby in Swine

“…A recent study attempted to determine the pathogenicity potential of various isolates of Salmonella in humans by comparing whole genome sequencing and the presence of known virulence genes to a phenotypic assessment of in vitro virulence (60). Within that study, S. 4, [5],12:i:-was considered to have a high probability of in vitro infection [P (inf)], similar to but slightly less than that of S. Typhimurium, which had the highest probability of all isolates studied.…”

“…In our study, only one of the S. Typhimurium isolates (ISU-SAL243-14) displayed these genes. The sodC1 gene, however, was present in the S. Typhimurium and S. 4, [5],12:i:-strains tested but absent in S. Derby; this gene was associated with high P (inf) and has been previously described to be present in S. 4, [5],12:i:-and S. Typhimurium (60). That study focused on the genetic determinates of disease in humans and it is unclear how transferrable these results are to swine, therefore, further work is needed to better understand the genetic determinates of virulence within the swine host.…”

Phenotypic and genotypic characterization of Salmonella Typhimurium isolates from humans and foods in Brazil

“…Interestingly, plasmid genes (spvABCDR, pefABCD, rck and mig-5) were detected in the present work in equal numbers and its location was confirmed in the plasmid pSLT, being that the S. Typhimurium strains isolated from humans and food studied had all the plasmid genes mentioned previously or none (Tables 3 and 4). According to Kuijpers and collaborators (2019), the spvABCDR, pefABCD, rck and mig-5 plasmids genes were detected only in the human cases associated with serovars Typhimurium and Enteritidis [38].…”

Association of Virulence and Antibiotic Resistance in Salmonella—Statistical and Computational Insights into a Selected Set of Clinical Isolates

“…Traditional serotyping may be replaced by more robust in silico platforms such as SeqSero, which allows the integration of the Salmonella classical serotyping scheme into a whole-genome sequencing (WGS)-based serotyping inference [ 66 ]. Recent genomics-based studies reveal that the attribution of phenotypical characteristics to individual Salmonella strains or serovars is not enough to improve the hazard characterization [ 67 ]. Studies have shown that the genomics data (without serotyping) of Salmonella isolates can efficiently be used in epidemiological and prevalence-related risk assessments [ 65 , 68 ].…”

“…Studies have shown that the genomics data (without serotyping) of Salmonella isolates can efficiently be used in epidemiological and prevalence-related risk assessments [ 65 , 68 ]. Moreover, a recent paper reports that the variation in the phenotypical characteristics (such as in vitro virulence) among individual strains from the same serovar is more significant than that found between serovars [ 67 ]. Therefore, the lack of serotype information in our study does not confound our findings of the relationship between phenotypic AR and virulence genes.…”