Support data for "Global distribution and large-scale genetic landscape of Salmonella Typhimurium: An epidemiological, spatial, comparative genomic study"

AbstractSalmonella Typhimurium has been an emerging concern in public health and food safety due to its increasing prevalence and multidrug resistance (MDR). However, its population structure remains broadly unknown, which hinders the efficient tracing of its transmission and evolution. In this study, 864 non-duplicated isolates were sequenced and all publicly available 34,590 S. Typhimurium genomes were retrieved. Applying cgMLST scheme and UMAP bedding approach, a total of 48 high-density genetic clusters of strains were identified and the relationship between genetic cluster, sequence type (ST) and antimicrobial resistance (AMR) was clearly demonstrated. ST19 and ST34 were the predominant ST types, however, two ST types displayed different evolution and transmission patterns. The ST19 strains exhibited significant geographic and host preference, with isolates from particular continents and hosts being limited in circulation to specific regions and hosts. The ST34 strains have been observed to exhibit a worldwide spread distribution and a continuous increase in prevalence over the past decades. The detection rates of multiple clinically important ARGs increased over time and demonstrated remarkable diverse across continents. A positive correlation was observed between ARGs and IncHI2 plasmid. Furthermore, we identified a unique cluster of carrying MDR IncHI2 plasmid in China. Subsequent analysis revealed that specific gene gain events within this specific cluster are linked to adaptations to plasmid. This study provides much-needed insights into the population structure, transmission routes, and pan-genomes of S. Typhimurium, which has the potential to improve infection control strategies and public health policy.