Didelot Xavier, Achtman Mark, Parkhill Julian, Thomson Nicholas R, Falush Daniel
Department of Statistics, University of Oxford, Oxford OX1 3SY, United Kingdom.
Genome Res. 2007 Jan;17(1):61-8. doi: 10.1101/gr.5512906. Epub 2006 Nov 7.
All Salmonella can cause disease but severe systemic infections are primarily caused by a few lineages. Paratyphi A and Typhi are the deadliest human restricted serovars, responsible for approximately 600,000 deaths per annum. We developed a Bayesian changepoint model that uses variation in the degree of nucleotide divergence along two genomes to detect homologous recombination between these strains, and with other lineages of Salmonella enterica. Paratyphi A and Typhi showed an atypical and surprising pattern. For three quarters of their genomes, they appear to be distantly related members of the species S. enterica, both in their gene content and nucleotide divergence. However, the remaining quarter is much more similar in both aspects, with average nucleotide divergence of 0.18% instead of 1.2%. We describe two different scenarios that could have led to this pattern, convergence and divergence, and conclude that the former is more likely based on a variety of criteria. The convergence scenario implies that, although Paratyphi A and Typhi were not especially close relatives within S. enterica, they have gone through a burst of recombination involving more than 100 recombination events. Several of the recombination events transferred novel genes in addition to homologous sequences, resulting in similar gene content in the two lineages. We propose that recombination between Typhi and Paratyphi A has allowed the exchange of gene variants that are important for their adaptation to their common ecological niche, the human host.
所有沙门氏菌都可致病，但严重的全身感染主要由少数谱系引起。甲型副伤寒沙门氏菌和伤寒沙门氏菌是最致命的人类限制性血清型，每年导致约60万人死亡。我们开发了一种贝叶斯变点模型，该模型利用两个基因组中核苷酸分歧程度的变化来检测这些菌株之间以及与肠炎沙门氏菌其他谱系之间的同源重组。甲型副伤寒沙门氏菌和伤寒沙门氏菌呈现出一种非典型且令人惊讶的模式。在其基因组的四分之三区域，无论是基因含量还是核苷酸分歧，它们似乎都是肠炎沙门氏菌物种中亲缘关系较远的成员。然而，其余四分之一在这两个方面则更为相似，平均核苷酸分歧为0.18%，而非1.2%。我们描述了两种可能导致这种模式的不同情形，趋同和趋异，并基于多种标准得出前者更有可能的结论。趋同情形意味着，尽管甲型副伤寒沙门氏菌和伤寒沙门氏菌在肠炎沙门氏菌中并非特别亲近的亲属，但它们经历了一阵涉及100多次重组事件的重组爆发。除了同源序列外，一些重组事件还转移了新基因，导致这两个谱系中的基因含量相似。我们提出，伤寒沙门氏菌和甲型副伤寒沙门氏菌之间的重组使得对它们适应共同生态位即人类宿主很重要的基因变体得以交换。
