Salmonella enterica serotype Typhimurium (S. Typhimurium) is a leading cause of gastroenteritis and bacteraemia worldwide, and a model organism for the study of host-pathogen interactions. Two S. Typhimurium strains (SL1344 and ATCC14028) are widely used to study host-pathogen interactions, yet genotypic variation results in strains with diverse host range, pathogenicity and risk to food safety. The population structure of diverse strains of S. Typhimurium revealed a major phylogroup of predominantly sequence type 19 (ST19) and minor of ST36. The major phylogroup had a population structure with two high order clades (α and β) and multiple subclades on extended internal branches, that exhibited distinct signatures of host adaptation and anthropogenic selection. Clade α contained a number of subclades composed of strains from well characterized epidemics in domesticated animals, while clade β contained multiple subclades associated with wild avian species. The contrasting epidemiology of strains in clade α and β was reflected by the distinct distribution of antimicrobial resistance (AMR) genes, accumulation of hypothetically disrupted coding sequences (HDCS), and signatures of functional diversification. These observations were consistent with elevated anthropogenic selection of clade α lineages from adaptation to circulation in populations of domesticated livestock, and the predisposition of clade β lineages to undergo adaptation to an invasive lifestyle by a process of convergent evolution with of host adapted Salmonella serotypes. Gene flux was predominantly driven by acquisition and recombination of prophage and associated cargo genes, with only occasional loss of these elements. The acquisition of large chromosomally-encoded genetic islands was limited, but notably, a feature of two recent pandemic clones (DT104 and monophasic S. Typhimurium ST34) of clade α (SGI-1 and SGI-4).

肠沙门氏菌血清型鼠伤寒（ S.Typhimurium ）是全世界胃肠炎和菌血症的主要原因，也是研究宿主与病原体相互作用的模式生物。两个S。鼠伤寒菌株（SL1344 和 ATCC14028）广泛用于研究宿主与病原体的相互作用，但基因型变异导致菌株具有不同的宿主范围、致病性和食品安全风险。 S不同菌株的种群结构。鼠伤寒揭示了主要的序列类型 19 (ST19) 和次要的 ST36 的主要系统群。主要系统群的种群结构具有两个高阶进化枝（α和β）和扩展内部分支上的多个亚进化枝，表现出宿主适应和人为选择的独特特征。 α 进化枝包含许多由来自家养动物中已明确流行的菌株组成的亚进化枝，而 β 进化枝包含多个与野生鸟类相关的亚进化枝。抗菌素耐药性（AMR）基因的独特分布、假设破坏的编码序列（HDCS）的积累以及功能多样化的特征反映了α和β进化枝中菌株的流行病学对比。这些观察结果与进化枝 α 谱系从适应驯养牲畜种群中的循环过程中人为选择的增加相一致，以及进化枝 β 谱系通过与宿主适应的沙门氏菌血清型的趋同进化过程来适应入侵生活方式的倾向是一致的。基因流动主要是由原噬菌体和相关货物基因的获取和重组驱动的，这些元素只是偶尔丢失。 大型染色体编码遗传岛的获得是有限的，但值得注意的是，α 进化枝（SGI-1 和 SGI-4）的两个最近大流行克隆（DT104 和单相鼠伤寒沙门氏菌 ST34）的一个特征。