Genomic methods for enhanced surveillance and persistence investigations of foodborne pathogens

The globalized food supply chain became a vast and complex network leading to an increased risk of spread of known and emerging foodborne pathogens, Listeria monocytogenes and Salmonella enterica serovar Typhimurium variant 4,[5],12:i:-. Based on a previous study of persistence of L. monocytogenes, 27 ST14 and 6 ST121 newly sequenced genomes collected over one year on the same rabbit meat processing plant were investigated in comparison to a selection of public genomes. cgMLST analysis of sequenced genomes showed higher discriminatory power in comparison to conventional typing methods. wgSNPs phylogeny inferred on 273 newly sequenced and publicly available ST121 and ST14 genomes confirmed that a persistent clone was circulating in the Italian rabbit-meat plant along with not persistent strains. Mass screening of a novel dataset of genes involved in physiological adaptation to food-processing environment showed a significant enrichment in ST121 genomes concerned genetic features related to sanitizing procedures adaptation, whereas genes related to biofilm forming enhanced ability and cadmium resistance was associated to ST14, as confirmed by phenotypic tests. Genomic data of 148 Salmonella enterica ser. Typhimurium monophasic variant 4,[5],12:i:- (MVSTm) isolates circulating in human and swine in Italy have been investigated in comparison to publicly available S. Typhimurium/ MVSTm strains collected in Italy and worldwide. The innovative genome-wide approach applied in this study allowed to mine population structure of a large Salmonella serovars dataset (~4,000 genomes) including Italian MVST strains belonging to a large population of ~1,300 clonal S. Typhimurium/ MVSTm isolates (2.5% of allele differences) isolated from a wide-range of countries in last two decades. cgSNPs phylogeny revealed and Genome-Wide Association Study suggested that discrete geographical segregation has had a strong impact on the accessory gene content with particular significance for a large SopE-containing prophage associated to Italian population and constituting specific biomarkers relevant in course of large epidemics.