Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation
Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation
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人为选择和生态位适应驱动的肠沙门氏菌血清型鼠伤寒进化
DOI：
10.1101/804674
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Bawn M
中科院分区：
文献类型：
--
作者：
Bawn M
鼠伤寒沙门氏菌（S. Typhimurium）是世界范围内引起肠胃炎和菌血症的主要原因，也是研究宿主-病原体相互作用的模式生物。2。鼠伤寒菌（Typhimurium）菌株SL1344和ATCC14028被广泛用于研究宿主-病原体相互作用，但基因型差异导致菌株具有不同的宿主范围、致病性和食品安全风险。不同菌株的种群结构。鼠伤寒菌主要系群为19型（ST19），次要系群为ST36。主要种群具有两个高阶分支（α和β）和多个扩展分支的种群结构，具有明显的宿主适应和人为选择特征。进化枝α包含许多由驯化动物流行病的菌株组成的亚枝，而进化枝β包含与野生鸟类物种相关的多个亚枝。α枝和β枝菌株的流行病学差异主要体现在抗微生物药物耐药性（AMR）基因的明显分布、假设破坏编码序列（HDCS）的积累和功能多样化特征上。这些观察结果与α枝系在驯化牲畜种群中适应循环的人为选择增加，以及β枝系通过与宿主适应的沙门氏菌型的趋同进化过程适应入侵生活方式的倾向相一致。基因通量主要是由前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。获得大的染色体编码遗传岛是有限的，但值得注意的是，这是最近两个大流行克隆（DT104和单相克隆）的一个特征。α枝（SGI-1和SGI-4）的鼠伤寒杆菌ST34。
Salmonella entericaserotype Typhimurium (S. Typhimurium) is a leading cause of gastroenteritis and bacteraemia worldwide, and a model organism for the study of host-pathogen interactions. TwoS. 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 ofS. Typhimurium revealed a major phylogroup of predominantly sequence type 19 (ST19) and a minor phylogroup 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 adaptedSalmonellaserotypes. 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 monophasicS. Typhimurium ST34) of clade α (SGI-1 and SGI-4).
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影响因子：
5.7
作者：
Ilyas B;Tsai CN;Coombes BK
通讯作者：
Coombes BK
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
影响因子：
3.6
作者：
Figueroa-Bossi, N;Uzzau, S;Bossi, L
通讯作者：
Bossi, L
影响因子：
3.8
作者：
Parsons BN;Humphrey S;Salisbury AM;Mikoleit J;Hinton JC;Gordon MA;Wigley P
通讯作者：
Wigley P
影响因子：
5.2
作者：
Mottawea W;Duceppe MO;Dupras AA;Usongo V;Jeukens J;Freschi L;Emond-Rheault JG;Hamel J;Kukavica-Ibrulj I;Boyle B;Gill A;Burnett E;Franz E;Arya G;Weadge JT;Gruenheid S;Wiedmann M;Huang H;Daigle F;Moineau S;Bekal S;Levesque RC;Goodridge LD;Ogunremi D
通讯作者：
Ogunremi D