Insights about the Epidemiology of Salmonella Typhimurium Isolates from different Sources in Brazil using Comparative Genomics

Abstract Background: Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is an important zoonotic agent worldwide. In Brazil, there are few published studies that have characterized the possible differences of S. Typhimurium strains isolated from humans, foods and animal by whole genome sequencing (WGS). The aim of this work was to compare genetically 117 S. Typhimurium isolates from different sources from 30 years (1983 to 2013) in Brazil using different genomics strategies, including: phylogenetic analysis; orthologous protein clusters analysis; Multi-locus sequence typing (MLST); prophages and resistance genes screening related to efflux pumps. Results: The majority of the 117 S. Typhimurium strains studied were grouped into a single cluster (≅90%) by the genome core (cgMLST) and (≅77%) by single copy marker genes (ggTree). The different orthologous protein clusters found for some S. Typhimurium strains isolated from humans and food are involved in metabolic and regulatory processes. For 26 S. Typhimurium isolates from swine the sequence type (ST) 19 was the most common, the ST1921 was the second most prevalent and the STs 14, 64, 516 and 639 were also detected. The main prophages detected were: Gifsy-2 in 79 (67.5%) and Gifsy-1 in 63 (54%) S. Typhimurium isolates. All of the S. Typhimurium isolates contained the acrA, acrB, macA, macB, mdtK, emrA, emrB, emrR and tolC efflux pump genes. Conclusions: Phylogenetic analyses grouped the majority of the S. Typhimurium isolates into a single cluster suggesting that there is one prevalent subtype that has successful contaminated human, food and animal sources for 30 years in Brazil. The orthologous protein clusters analysis revealed unique genes in the S. Typhimurium studied mainly related to bacterial metabolism and that may be important in their pathogenicity. S. Typhimurium isolates from swine showed greater diversity of STs and prophages in comparison to S. Typhimurium strains isolated from humans and foods. The pathogenic potential of S. Typhimurium strains was corroborated by the presence of exclusive prophages of this serovar involved in their virulence. The high number of resistance genes related to efflux pumps is worrying and may lead to therapeutic failures when treatment is needed.