BACKGROUND Leptospirosis is a complex zoonotic disease mostly caused by a group of eight pathogenic species (L. interrogans, L. borgpetersenii, L. kirschneri, L. mayottensis, L. noguchii, L. santarosai, L. weilii, L. alexanderi), with a wide spectrum of animal reservoirs and patient outcomes. Leptospira interrogans is considered as the leading causative agent of leptospirosis worldwide and it is the most studied species. However, the genomic features and phylogeography of other Leptospira pathogenic species remain to be determined. METHODOLOGY/PRINCIPAL FINDINGS Here we investigated the genome diversity of the main pathogenic Leptospira species based on a collection of 914 genomes from strains isolated around the world. Genome analyses revealed species-specific genome size and GC content, and an open pangenome in the pathogenic species, except for L. mayottensis. Taking advantage of a new set of genomes of L. santarosai strains isolated from patients in Costa Rica, we took a closer look at this species. L. santarosai strains are largely distributed in America, including the Caribbean islands, with over 96% of the available genomes originating from this continent. Phylogenetic analysis showed high genetic diversity within L. santarosai, and the clonal groups identified by cgMLST were strongly associated with geographical areas. Serotype identification based on serogrouping and/or analysis of the O-antigen biosynthesis gene loci further confirmed the great diversity of strains within the species. CONCLUSIONS/SIGNIFICANCE In conclusion, we report a comprehensive genome analysis of pathogenic Leptospira species with a focus on L. santarosai. Our study sheds new light onto the genomic diversity, evolutionary history, and epidemiology of leptospirosis in America and globally. Our findings also expand our knowledge of the genes driving O-antigen diversity. In addition, our work provides a framework for understanding the virulence and spread of L. santarosai and for improving its surveillance in both humans and animals.

中文翻译：

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美洲流行的致病菌圣塔罗赛钩端螺旋体的系统发育学。

背景钩端螺旋体病是一种复杂的人畜共患疾病，主要由八种致病菌（问号钩端螺旋体、博格彼得森钩端螺旋体、基氏钩端螺旋体、马约滕西斯钩端螺旋体、野口钩端螺旋体、桑塔罗赛钩端螺旋体、韦利钩端螺旋体、亚历山大钩端螺旋体）引起。具有广泛的动物宿主和患者结果。问号钩端螺旋体被认为是全世界钩端螺旋体病的主要病原体，也是研究最多的物种。然而，其他钩端螺旋体致病物种的基因组特征和系统发育地理学仍有待确定。方法/主要发现 在此，我们基于来自世界各地分离的菌株的 914 个基因组集合，研究了主要致病性钩端螺旋体物种的基因组多样性。基因组分析揭示了物种特异性基因组大小和 GC 含量，以及除 L. mayottens 之外的致病物种中的开放全基因组。利用从哥斯达黎加患者体内分离出的一组新的 L. santarosai 菌株基因组，我们仔细研究了该物种。L. santarosai 菌株主要分布在美洲，包括加勒比岛屿，超过 96% 的可用基因组源自该大陆。系统发育分析显示 L. santarosai 具有高度遗传多样性，并且 cgMLST 鉴定的克隆群与地理区域密切相关。基于血清分型和/或 O 抗原生物合成基因座分析的血清型鉴定进一步证实了物种内菌株的巨大多样性。结论/意义 总之，我们报告了致病性钩端螺旋体物种的全面基因组分析，重点是圣塔罗赛钩端螺旋体。我们的研究为美国和全球钩端螺旋体病的基因组多样性、进化历史和流行病学提供了新的线索。我们的发现还扩展了我们对驱动 O 抗原多样性的基因的了解。此外，我们的工作为了解 L. santarosai 的毒力和传播以及改善其对人类和动物的监测提供了一个框架。