Plesiomonas shigelloides is an emerging pathogen that has been shown to be involved in gastrointestinal diseases and extraintestinal infections in humans. However, the taxonomic position, evolutionary dynamics, and pathogenesis of P. shigelloides remain unclear. We reported the draft genome sequences of 12 P. shigelloides strains representing different serogroups. We were able to determine a clear distinction between P. shigelloides and other members of Enterobacterales via core genome phylogeny, Neighbor-Net network, and average genome identity analysis. The pan-genome analysis of P. shigelloides revealed extensive genetic diversity and presented large flexible gene repertoires, while the core genome phylogeny exhibited a low level of clonality. The discordance between the core genome phylogeny and the pan-genome phylogeny indicated that flexible accessory genomes account for an important proportion of the evolution of P. shigelloides, which was subsequently characterized by determinations of hundreds of horizontally transferred genes (horizontal genes), massive gene expansions and contractions, and diverse mobile genetic elements (MGEs). The apparently high levels of horizontal gene transfer (HGT) in P. shigelloides were conferred from bacteria with novel properties from other taxa (mainly Vibrionaceae and Aeromonadaceae), which caused the historical taxonomic confusion and shaped the virulence gene pools. Furthermore, P. shigelloides genomes contain many macromolecular secretion system genes, virulence factor genes, and resistance genes, indicating its potential to cause intestinal and invasive infections. Collectively, our work provides insights into the phylogenetic position, evolutionary dynamic, and pathogenesis of P. shigelloides at the genomic level, which could facilitate the observation and research of this important pathogen.

中文翻译：

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水平基因转移澄清了分类学上的混乱，并促进了志贺氏假单胞菌的遗传多样性和致病性。

志贺氏假单胞菌是一种新兴病原体，已被证明与人类胃肠道疾病和肠外感染有关。但是，志贺假单胞菌的分类位置，进化动力学和发病机理仍然不清楚。我们报告了代表不同血清群的12个志贺氏志贺氏菌菌株的基因组序列草案。通过核心基因组系统发育，Neighbor-Net网络和平均基因组同一性分析，我们能够确定志贺氏疟原虫和肠杆菌的其他成员之间有明显的区别。志贺假单胞菌的全基因组分析揭示了广泛的遗传多样性，并提出了灵活的大型基因库，而核心基因组系统发育显示出低水平的克隆性。核心基因组系统发育和全基因组系统发育之间的不一致表明，柔性辅助基因组在志贺假单胞菌进化中占重要比例，其特征是随后测定了数百个水平转移基因（水平基因），大量基因扩张和收缩，以及多样化的移动遗传元件（MGE）。显然高水平水平基因转移（HGT）在P. shigelloides从细菌赋予与来自其他生物（主要是新的性质弧菌和Aeromonadaceae），这造成了历史上的分类学混乱，并塑造了毒力基因库。此外，志贺疟原虫的基因组包含许多大分子分泌系统基因，毒力因子基因和抗性基因，表明其可能引起肠道和侵袭性感染。总的来说，我们的工作在基因组水平上为志贺假单胞菌的系统发生位置，进化动力学和发病机理提供了见解，这可以促进对该重要病原体的观察和研究。