Genome sequences reveal cryptic speciation in the human pathogen Histoplasma capsulatum

Histoplasma capsulatum is a pathogenic fungus that causes life-threatening lung infections. About 500,000 people are exposed to H. capsulatum each year in the United States, and over 60% of the U.S. population has been exposed to the fungus at some point in their life. We performed genome-wide population genetics and phylogenetic analyses with 30 Histoplasma isolates representing four recognized areas where histoplasmosis is endemic and show that the Histoplasma genus is composed of at least four species that are genetically isolated and rarely interbreed. Therefore, we propose a taxonomic rearrangement of the genus. IMPORTANCE: The evolutionary processes that give rise to new pathogen lineages are critical to our understanding of how they adapt to new environments and how frequently they exchange genes with each other. The fungal pathogen Histoplasma capsulatum provides opportunities to precisely test hypotheses about the origin of new genetic variation. We find that H. capsulatum is composed of at least four different cryptic species that differ genetically and also in virulence. These results have implications for the epidemiology of histoplasmosis because not all Histoplasma species are equivalent in their geographic range and ability to cause disease.

荚膜组织胞浆菌（Histoplasma capsulatum）是一种可引发危及生命肺部感染的致病真菌。美国每年约有50万人接触该病原菌，且超过60%的美国人口在人生的某一阶段曾暴露于该真菌。我们对代表4个已知组织胞浆菌病流行区域的30株组织胞浆菌分离株开展了全基因组群体遗传学与系统发育分析，结果显示组织胞浆菌属（Histoplasma）至少包含4个遗传隔离且极少发生基因交流的物种。因此，我们建议对该属进行分类学重排。

研究意义：驱动新致病谱系形成的演化过程，对于理解病原体如何适应新环境、以及它们之间发生基因交换的频率至关重要。荚膜组织胞浆菌这一真菌病原体，为精准验证关于新遗传变异起源的假说提供了理想研究模型。本研究发现，荚膜组织胞浆菌复合体至少包含4个遗传特征与致病力均存在差异的隐秘物种。上述结果对组织胞浆菌病的流行病学具有重要启示：不同组织胞浆菌属物种的地理分布范围与致病能力并不相同。