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. 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. 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.

中文翻译：

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利用比较基因组学对巴西不同来源鼠伤寒沙门氏菌流行病学的见解

沙门氏菌肠亚种。鼠伤寒鼠伤寒沙门氏菌（S. Typhimurium）是全世界重要的人畜共患病病原体。这项工作的目的是比较巴西30年来使用不同基因组学策略从不同来源分离得到的117鼠伤寒沙门氏菌。通过核心基因组多基因座序列分型，将研究的117种鼠伤寒沙门氏菌菌株中的大多数分为单个簇（约占90％），通过单拷贝标记基因分为（约占77％）。基于单核苷酸多态性（SNP）的系统发育分析将人类的大多数菌株分为一个簇（约93％），而从食物和猪中分离出的菌株则分为三个簇。从人类和食物中分离出的鼠伤寒沙门氏菌发现了不同的直系同源蛋白质簇，它们参与了代谢和调节过程。对于来自猪的26个分离株，序列类型（ST）19和ST1921是最流行的，并且还检测到ST14，ST64，ST516和ST639。先前的结果将人类和食物中的91种鼠伤寒沙门氏菌分离株分为ST19，ST313，ST1921，ST3343和ST1649。检测到的主要原发菌为：79株（67.5％）中的Gifsy-2和63株（54％）中的Gifsy-1。鼠伤寒沙门氏菌的所有分离株均含有acrA，acrB，macA，macB，mdtK，emrA，emrB，emrR和tolC外排泵基因。系统发育树将来自人类的大多数鼠伤寒沙门氏菌分离物归为一个簇，这表明巴西有一种流行的亚型。关于从食物和猪中分离出的毒株，SNPs的结果表明该国在过去30年中有一种以上的亚型流行。直系同源蛋白质簇分析揭示了所研究菌株中的独特基因，其主要与细菌代谢有关。与分离自人和食物的菌株相比，来自猪的鼠伤寒沙门氏菌菌株显示出更大的ST和噬菌体多样性。鼠伤寒沙门氏菌菌株的致病潜能被该血清型毒力的唯一噬菌体的存在所证实。与外排泵相关的大量抗性基因令人担忧，当需要临床治疗时可能导致治疗失败。鼠伤寒毒株被这种血清型毒力的唯一预言存在所证实。与外排泵相关的大量抗性基因令人担忧，当需要临床治疗时可能导致治疗失败。鼠伤寒毒株被这种血清型毒力的唯一预言存在所证实。与外排泵相关的大量抗性基因令人担忧，当需要临床治疗时可能导致治疗失败。