Geographic source attribution of Salmonella serovar Infantis REPJFX01 through core SNP and phylogeographic analyses

Salmonella enterica subsp. enterica serovar Infantis is globally widespread. Salmonella Infantis REPJFX01 is a persisting multidrug-resistant strain associated with U.S. sporadic illnesses and outbreaks linked to chicken consumption and international travel. Previous work demonstrated that REPJFX01 isolates from the United States and South America are closely related. Here, we expanded that work to show that REPJFX01 isolates are distributed beyond the United States and that distinct single nucleotide polymorphisms (SNPs) are associated with certain locations. Phylogenetic analysis revealed that REPJFX01 isolates formed two major groups: (i) a paraphyletic group primarily containing South American and Asian isolates, and (ii) a monophyletic group primarily containing U.S. isolates. We identified one core SNP that can be used to assign REPJFX01-like isolates to the South America/Asia group with 99% sensitivity and 96% specificity. Time-calibrated phylogenetic analysis indicated that the most recent common ancestor of REPJFX01 existed in Peru circa 2009. Phylogeographic analysis suggests that REPJFX01 spread from South America to the United States in a single dissemination event circa 2010. Hence, our results suggest that SNP identification can be used to generate hypotheses on whether an infection with REPJFX01 was acquired domestically or outside of the United States prior to case interviews. Furthermore, identifying potential events leading to the dissemination of REPJFX01 can support the development and deployment of specific public health actions, like enhanced surveillance of imported products.IMPORTANCESalmonella Infantis REPJFX01 is a persisting multidrug-resistant (MDR) strain that has caused thousands of human illnesses in the United States linked to consumption of chicken and international travel. Here, we demonstrate through phylogeographic analyses that REPJFX01 has spread beyond the United States due to three major spread events originating from Peru, the United States, and South Korea. We also identified genetic markers (SNPs) that can be used for fast geographic attribution of new clinical isolates, facilitating prioritization of cluster investigations. Thus, this study indicates that S. Infantis REPJFX01 is a global hazard and highlights the possible role of import and export events in the dissemination of MDR Salmonella across the globe.