Trends in Salmonella Dublin over time in Denmark from food and animal related isolates.

Salmonella enterica serovar Dublin is highly adapted to cattle and a relatively rare cause of human infections. In Denmark S. Dublin has been endemic in the cattle population for many years. A national surveillance program in the cattle population was established at herd-level to reduce the occurrence of S. Dublin. In this study, we analyzed 421 S. Dublin genomes from cattle and food in order to determine the trend of S. Dublin's population size over time in Denmark and the impact of intervention in the cattle industry on the bacterial population size. A phylogenetic tree based on SNPs exhibited two major clades and one small cluster. All isolates were ST10. The temporal phylogenetic tree for the S. Dublin isolates showed that the most recent common ancestor was estimated to be in ~1980 for the two major clades. An effective population size over time based on a Bayesian skyline plot showed that the population size of S. Dublin decreased significantly between 2014 and 2019 in both major clades. This result was concordant with the decrease of infected human cases by S. Dublin in Denmark. The strengthening of a surveillance program in Denmark could be the cause for the reduction of S. Dublin's effective population size. This study showed that whole genome sequencing combined with computer intensive phylogenetic analysis estimating the effective size of the S. Dublin's population over time is a strongly relevant measure with respect to assessing the impact of control measures aiming to reduce the bacterial population in the reservoir and the risk for human infection.