Genetic analysis of Salmonella enterica serovar Typhimurium DT104 isolates in Japan

The global epidemic of multidrug resistant Salmonella Typhimurium DT104 provides an important example, both in terms of the agent and its resistance, of a type-specific epidemic occurring within an endemic infection pattern. Here, with a unique collection of isolates collected contemporaneously from humans and animals in Scotland, benchmarked against a sample of international-derived isolates, we have used whole genome sequencing to dissect the phylogenetic histories of the bacterium and its antimicrobial resistance genes through the entire course of the epidemic.