Investigating outbreaks of Salmonella enterica serovar Typhimurium and its monophasic variants in Denmark by whole-genome sequencing; getting ready for real-time surveillance

Whole genome sequencing (WGS) is rapidly replacing current molecular typing methods for surveillance purposes. Our study evaluates core-genome single nucleotide polymorphism (SNP) analysis for outbreak detection and linking of sources of S. enterica serovar Typhimurium and its monophasic variants in a 7 months surveillance period in Denmark. Previously defined outbreaks were re-analyzed and defined from the phylogenetic relation of the isolates, epidemiological data and food trace back investigations. All outbreaks were identified and we were able to exclude unrelated and include additional related human cases. We were furthermore able to link food and veterinary sources to the outbreaks, here sources mainly related to swine . Isolates clustered according to sequence types (ST) 19, 34 and 36. Outbreaks were well defined for ST19 and ST36 isolates, however, analysis on the accessory genome were needed to underline conclusions in the tight genetic cluster of ST34 isolates.