Abstract
BackgroundSalmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is an important zoonotic agent worldwide. The aim of this work was to compare genetically 117 S. Typhimurium isolated from different sources over 30 years in Brazil using different genomics strategies.ResultsThe majority of the 117 S. Typhimurium strains studied were grouped into a single cluster (≅ 90%) by the core genome multilocus sequence typing and (≅ 77%) by single copy marker genes. The phylogenetic analysis based on single nucleotide polymorphism (SNP) grouped most strains from humans into a single cluster (≅ 93%), while the strains isolated from food and swine were alocated into three clusters. The different orthologous protein clusters found for some S. Typhimurium isolated from humans and food are involved in metabolic and regulatory processes. For 26 isolates from swine the sequence types (ST) 19 and ST1921 were the most prevalent ones, and the ST14, ST64, ST516 and ST639 were also detected. Previous results typed the 91 S. Typhimurium isolates from humans and foods as ST19, ST313, ST1921, ST3343 and ST1649. The main prophages detected were: Gifsy-2 in 79 (67.5%) and Gifsy-1 in 63 (54%) strains. All of the S. Typhimurium isolates contained the acrA, acrB, macA, macB, mdtK, emrA, emrB, emrR and tolC efflux pump genes.ConclusionsThe phylogenetic trees grouped the majority of the S. Typhimurium isolates from humans into a single cluster suggesting that there is one prevalent subtype in Brazil. Regarding strains isolated from food and swine, the SNPs’ results suggested the circulation of more than one subtype over 30 years in this country. The orthologous protein clusters analysis revealed unique genes in the strains studied mainly related to bacterial metabolism. S. Typhimurium strains from swine showed greater diversity of STs and prophages in comparison to 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 its virulence. The high number of resistance genes related to efflux pumps is worrying and may lead to therapeutic failures when clinical treatment is needed.
Highlights
IntroductionTyphimurium) is an important zoonotic agent worldwide
Cluster B comprised a total of 108 genomes comprising strains isolated from humans, different foods and swine of ST19, ST1649, ST3343, ST1921 and ST313 in the case of strains isolated from humans and food, besides ST19, ST639, ST14, ST516, ST64 and ST1921 concerning strains isolated from swine
The phylogenetic analysis based on single nucleotide polymorphism (SNPs) grouped most strains from humans into a single cluster (≅ 93%), while the strains isolated from food and swine were grouped into three clusters (Fig. 3)
Summary
Typhimurium) is an important zoonotic agent worldwide. Typhimurium isolated from different sources over 30 years in Brazil using different genomics strategies. Nontyphoidal Salmonella (NTS) strains have been an important enteric agent transmitted mainly by contaminated foods worldwide [1]. According to Kirk and collaborators [2], it was estimated that 153 million infections and 56,969 deaths occurred around the globe due to salmonellosis in 2010. Data from the Centers for Disease Control and Prevention (CDC), estimated that 1.35 million infections, 26,500 hospitalizations and 420 deaths occur in the United States every year due to Salmonella [3]. Until now there are few published studies that have characterized the possible differences between Brazilian Salmonella enterica subsp. Typhimurium) strains isolated from human, food and animal sources by whole genome sequencing (WGS)
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