Study of the population structure of Salmonella Infantis and the effect of prophages in the population

BackgroundSalmonella Infantis (S. Infantis) is one of the most frequent Salmonella serovars isolated from human cases of salmonellosis and the most detected serovar from animal and food sources in Europe. The serovar is commonly associated with poultry and there is increasing concern over multidrug resistant clones spreading worldwide, facilitated by the presence of large plasmids carrying multiple resistance genes. Increasing the knowledge of the S. Infantis population and evolution is important for understanding and preventing further spread. In this study, we analysed a collection of strains representing different decades, sources and geographic locations. We analysed the population structure and we identified prophages with a view to understand the role of prophages in relation to the evolution of this serovar. ResultsWe sequenced a global collection of 100 strains S. Infantis. A core-genome SNP analysis separated five strains in e-Burst Group (eBG) 297 with a deep branch. The remaining strains all in eBG31, were divided into two lineages that were estimated to have separated approximately 150 years ago. One lineage contained six genetic clusters comprising the vast majority of strains. In five of six clusters, no obvious correlation with source or geographical locations was seen. However, one cluster contained mostly strains from human and avian sources, indicating a host-adapted clone. The majority of strains within this cluster harboured a pESI-like plasmid with multiple resistance genes. The other identified lineage contained two genetic clusters with more rarely isolated strains of mainly animal origin, possibly less infectious clones. Conserved prophages were identified in all lineages, likely representing bacteriophages which integrated into the chromosome of a common ancestor to S. Infantis. We also saw that some prophages were specific to clusters and were probably introduced when the clusters were formed, underlining the important role of prophages in shaping the Infantis population.ConclusionsThis study gives insight into a global S. Infantis population and highlights its genetic structure. We hypothesize that the population has evolved in two separate lineages, with one more successfully emerging lineage. We furthermore underlined the importance of prophages in the shaping of the population structure.