Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella enterica serovar Typhimurium clone.
Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella enterica serovar Typhimurium clone.
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DOI：
10.1099/mgen.0.000456
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发表时间：
2020-11
影响因子：
3.9
通讯作者：
Kingsley RA
中科院分区：
文献类型：
--
作者：
Tassinari E;Bawn M;Thilliez G;Charity O;Acton L;Kirkwood M;Petrovska L;Dallman T;Burgess CM;Hall N;Duffy G;Kingsley RA
具有独特特征的细菌病原体的流行性和大流行性克隆不断出现，通过仍然不清楚的机制取代了以前占主导地位的克隆。在这里，全基因组测序驱动的流行病学将毒力基因sopE的水平转移与一种新的流行性肠道沙门氏菌鼠伤寒血清型（S。Typhimurium）克隆。sopE基因在沙门氏菌属中零星分布，在沙门氏菌中罕见。 enterica Typhimurium谱系，但在目前占主导地位的流行性嗜水气单胞菌的克隆扩增期间多次获得。鼠伤寒序列型（ST）34克隆。祖先的状态重建和时间尺度的系统发育分析表明，SOPE是不存在的流行分支的共同祖先，但后来收购导致增加的克隆扩张的SOPE含有克隆，时间上与出现的流行病，符合健身增加。sopE基因主要与温带噬菌体mTmV相关，但与其它噬菌体的重组和sopE基因盒的明显水平基因转移导致sopE基因在嗜热链球菌中至少分布在4个移动的遗传元件中。 肠伤寒ST34流行分支。mTmV原噬菌体溶原性转移到其他S.肠道沙门氏菌血清型有限，但包括常见的猪相关沙门氏菌。 enterica Derby（S. Derby）。这可以解释S中的mTmV。在农场上，德比与嗜水气单胞菌S。鼠伤寒沙门氏菌ST 34，强调了sopE毒力基因在自然界中进一步转移的潜力。我们的结论是，全基因组流行病学查明病原体出现过程中的进化和流行病学动态的潜在驱动因素，并确定了流行病学和细菌致病机制的后续研究目标。
Epidemic and pandemic clones of bacterial pathogens with distinct characteristics continually emerge, replacing those previously dominant through mechanisms that remain poorly characterized. Here, whole-genome-sequencing-powered epidemiology linked horizontal transfer of a virulence gene, sopE, to the emergence and clonal expansion of a new epidemic Salmonella enterica serovar Typhimurium (S. Typhimurium) clone. The sopE gene is sporadically distributed within the genus Salmonella and rare in S . enterica Typhimurium lineages, but was acquired multiple times during clonal expansion of the currently dominant pandemic monophasic S. Typhimurium sequence type (ST) 34 clone. Ancestral state reconstruction and time-scaled phylogenetic analysis indicated that sopE was not present in the common ancestor of the epidemic clade, but later acquisition resulted in increased clonal expansion of sopE-containing clones that was temporally associated with emergence of the epidemic, consistent with increased fitness. The sopE gene was mainly associated with a temperate bacteriophage mTmV, but recombination with other bacteriophage and apparent horizontal gene transfer of the sopE gene cassette resulted in distribution among at least four mobile genetic elements within the monophasic S . enterica Typhimurium ST34 epidemic clade. The mTmV prophage lysogenic transfer to other S. enterica serovars in vitro was limited, but included the common pig-associated S . enterica Derby (S. Derby). This may explain mTmV in S. Derby co-circulating on farms with monophasic S. Typhimurium ST34, highlighting the potential for further transfer of the sopE virulence gene in nature. We conclude that whole-genome epidemiology pinpoints potential drivers of evolutionary and epidemiological dynamics during pathogen emergence, and identifies targets for subsequent research in epidemiology and bacterial pathogenesis.
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影响因子：
3.3
作者：
Hoffmann M;Zhao S;Pettengill J;Luo Y;Monday SR;Abbott J;Ayers SL;Cinar HN;Muruvanda T;Li C;Allard MW;Whichard J;Meng J;Brown EW;McDermott PF
通讯作者：
McDermott PF
影响因子：
56.9
作者：
Diard, Mederic;Bakkeren, Erik;Hardt, Wolf-Dietrich
通讯作者：
Hardt, Wolf-Dietrich
影响因子：
5.8
作者：
Dallman, Timothy;Ashton, Philip;Grant, Kathie
通讯作者：
Grant, Kathie
DOI：
10.1093/bioinformatics/btq413
发表时间：
2010-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Guy L;Kultima JR;Andersson SG
通讯作者：
Andersson SG
影响因子：
3.7
作者：
Gilcrease EB;Casjens SR
通讯作者：
Casjens SR