Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics
Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics
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DOI：
10.1371/journal.pntd.0007270
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发表时间：
2019-05-01
影响因子：
3.8
通讯作者：
Picardeau, Mathieu
中科院分区：
文献类型：
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作者：
Vincent, Antony T.;Schiettekatte, Olivier;Picardeau, Mathieu
钩端螺旋体病的病原体是世界范围内一种新出现的人畜共患病的原因。钩端螺旋体病的主要传播途径之一是被各种水库动物的尿液污染的自然环境。土壤和地表水还含有高度多样性的非致病性钩端螺旋体和毒力状态尚未明确确定的物种。目前，钩端螺旋体属分为35个物种，分为三个系统发育簇，推测与该细菌的毒力有关。在这项研究中，从世界各地包括日本、马来西亚、新喀里多尼亚、阿尔及利亚、法国大陆和印度洋马约特岛分离的90株钩端螺旋体菌株被测序。将90株钩端螺旋体的基因组与已知物种的代表性基因组的平均核苷酸同源性(ANI)值进行比较，发现30个钩端螺旋体新种。这些数据还支持存在两个支系和4个亚支。为了避免对毒力状态的假设进行分类，我们将它们命名为P1、P2、S1、S2。其中一个亚枝尚未被描述，由伊顿钩端螺旋体和4个新种组成，这些新种与腐生植物有亲缘关系。然后，我们通过研究盘根组和核心基因组，研究了钩端螺旋体属成员之间的基因组多样性和进化关系。我们的数据使我们能够识别对每个亚纲重要的基因组特征、基因和结构域，从而为完善这一复杂细菌属的分类奠定了基础。我们还阐明了一组物种的非典型基因组特征，其中包括经常与人类感染相关的物种，这表明这一组物种的特定和正在进行的进化将需要更多关注。总而言之，我们发现了大量的物种多样性，并在世界各地收集的环境样本中发现了一个新的亚类，我们重新定义了该属的物种分类。几个新的潜在传染性钩端螺旋体物种对人类和动物健康的影响仍有待确定，但我们的数据也为这些致病物种出现毒力提供了新的见解。钩端螺旋体病是一种全球新出现的人畜共患疾病，通过接触土壤或被水库动物尿液污染的表面水传播给人类。钩端螺旋体的种类，包括传染性和非传染性的菌株，在环境中无处不在。在这项研究中，我们对从世界各地的几个环境来源分离的钩端螺旋体菌株的基因组进行了测序。将这些基因组与钩端螺旋体属的其他成员进行比较，发现存在30个新的钩端螺旋体种。对该属物种的比较基因组分析使我们能够识别感染物种特有的基因或基因组特征，为这些非典型细菌的毒力进化提供洞察，也允许完善钩端螺旋体的分类。
The causative agents of leptospirosis are responsible for an emerging zoonotic disease worldwide. One of the major routes of transmission for leptospirosis is the natural environment contaminated with the urine of a wide range of reservoir animals. Soils and surface waters also host a high diversity of non-pathogenic Leptospira and species for which the virulence status is not clearly established. The genus Leptospira is currently divided into 35 species classified into three phylogenetic clusters, which supposedly correlate with the virulence of the bacteria. In this study, a total of 90 Leptospira strains isolated from different environments worldwide including Japan, Malaysia, New Caledonia, Algeria, mainland France, and the island of Mayotte in the Indian Ocean were sequenced. A comparison of average nucleotide identity (ANI) values of genomes of the 90 isolates and representative genomes of known species revealed 30 new Leptospira species. These data also supported the existence of two clades and 4 subclades. To avoid classification that strongly implies assumption on the virulence status of the lineages, we called them P1, P2, S1, S2. One of these subclades has not yet been described and is composed of Leptospira idonii and 4 novel species that are phylogenetically related to the saprophytes. We then investigated genome diversity and evolutionary relationships among members of the genus Leptospira by studying the pangenome and core gene sets. Our data enable the identification of genome features, genes and domains that are important for each subclade, thereby laying the foundation for refining the classification of this complex bacterial genus. We also shed light on atypical genomic features of a group of species that includes the species often associated with human infection, suggesting a specific and ongoing evolution of this group of species that will require more attention. In conclusion, we have uncovered a massive species diversity and revealed a novel subclade in environmental samples collected worldwide and we have redefined the classification of species in the genus. The implication of several new potentially infectious Leptospira species for human and animal health remains to be determined but our data also provide new insights into the emergence of virulence in the pathogenic species.Author summary Leptospirosis which is an emerging zoonotic disease worldwide, is transmitted to humans through contact with soils or surface waters contaminated with the urine of reservoir animals. Species of Leptospira, which include infectious and non-infectious strains, are ubiquitous in the environment. In this study we have sequenced the genomes of strains of Leptospira isolated from several environmental sources worldwide. Comparison of these genomes with other members of the Leptospira genus revealed the existence of 30 novel Leptospira species. A comparative genomic analysis of species of the genus allowed us to identify genes or genome features that are specific of infectious species, providing insights into virulence evolution in these atypical bacteria but also allow refinement of the Leptospira classification.