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. 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. Results The 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. Conclusions The 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.

Prevalence and Characteristics of Salmonella spp. Isolated from Raw Chicken Meat in the Republic of Korea

“…isolated from domestic chicken sold in Chungcheong Province showed specific sequence types as the ST of Salmonella spp., which several studies reported were isolated from Brazilian poultry. Salmonella Typhimurium isolated from poultry revealed ST-19 [41,42] and most of the Salmonella Dublin isolates (n = 112) from human and animal presented ST-10 (n = 68), ST-3734 (n = 28), and ST-4030 (n = 9) [43].…”

Global Spread and Molecular Characterization of CTX-M-Producing Salmonella Typhimurium Isolates

“…However, ST19 isolates were resistant to fewer antibiotic classes than ST34 isolates [ 27 ]. Thus far, ST19 has been reported from humans, reptiles, ovine, swine, poultry, food, and bovine from France, Mexico, China, Germany, Scotland, Portugal, Qatar, Korea, Ireland, the United States, the United Kingdom, and Denmark, according to Enterobase [ 28 ]. ST313 is a relatively newly emerged sequence type and closely related to the ST19 group of S. Typhimurium, which has caused a devastating epidemic of bloodstream infections across sub-Saharan Africa [ 29 ].…”

The rare Salmonella enterica serovar Isangi: genomic characterization of the antimicrobial resistance, virulence potential and epidemiology of Brazilian strains in comparison to global isolates

“…In NTS, prophages have been demonstrated not only to play a role in virulence, but also to be an indicator of genetic diversity [53,54]. The different types of prophage detected in the 11 S. Isangi strains studied are related to bacteria of the genus Salmonella (SW9, Fels_1, SPN3UB and SEN8), Escherichia (phiV10 and vB_EcoM_12474III), Yersinia (L_413C) and Edwardsiella (GF_2) (Table 1).…”

“…In NTS, prophages have been demonstrated not only to play a role in virulence, but also to be an indicator of genetic diversity [53, 54]. The different types of prophage detected in the 11 S .…”