Dip. Scienze Biomediche per la Salute, Università degli Studi di Milano, Milano, Italy.
Institut Pasteur, Molecular Mycology Unit, National Reference Center for Invasive Mycoses & Antifungal, CNRS UMR2000, Paris, France.
Fungal Genet Biol. 2019 Aug;129:16-29. doi: 10.1016/j.fgb.2019.04.001. Epub 2019 Apr 3.
A total of 476 European isolates (310 Cryptococcus neoformans var. grubii, 150 C. neoformans var. neoformans, and 16 C. gattii species complex) from both clinical and environmental sources were analyzed by multi-locus sequence typing. Phylogenetic and population genetic analyses were performed. Sequence analysis identified 74 sequence types among C. neoformans var. neoformans (VNIV), 65 among C. neoformans var. grubii (56 VNI, 8 VNII, 1 VNB), and 5 among the C. gattii species complex (4 VGI and 1 VGIV) isolates. ST23 was the most frequent genotype (22%) among VNI isolates which were mostly grouped in a large clonal cluster including 50% of isolates. Among VNIV isolates, a predominant genotype was not identified. A high percentage of autochthonous STs were identified in both VNI (71%) and VNIV (96%) group of isolates. The 16 European C. gattii species complex isolates analyzed in the present study originated all from the environment and all belonged to a large cluster endemic in the Mediterranean area. Population genetic analysis confirmed that VNI group of isolates were characterized by low variability and clonal expansion while VNIV by a higher variability and a number of recombination events. However, when VNI and VNIV environmental isolates were compared, they showed a similar population structure with a high percentage of shared mutations and the absence of fixed mutations. Also linkage disequilibrium analysis reveals differences between clinical and environmental isolates showing a key role of PLB1 allele combinations in host infection as well as the key role of LAC1 allele combinations for survival of the fungus in the environment. The present study shows that genetic comparison of clinical and environmental isolates represents a first step to understand the genetic characteristics that cause the shift of some genotypes from a saprophytic to a parasitic life style.
对来自临床和环境来源的 476 株欧洲分离株（310 株新型隐球菌 var. grubii、150 株新型隐球菌 var. neoformans 和 16 株假丝酵母复合种）进行了多位点序列分型分析。进行了系统发育和群体遗传学分析。序列分析在新型隐球菌 var. neoformans（VNIV）中鉴定出 74 种序列型，在新型隐球菌 var. grubii（56 种 VNI、8 种 VNII、1 种 VNB）中鉴定出 65 种，在假丝酵母复合种中鉴定出 5 种（4 种 VGI 和 1 种 VGIV）。ST23 是 VNI 分离株中最常见的基因型（22%），这些分离株主要聚集在一个大的克隆群中，包括 50%的分离株。在 VNIV 分离株中，没有确定主要基因型。在 VNI（71%）和 VNIV（96%）组的分离株中都发现了很高比例的本地 ST。本研究分析的 16 株欧洲假丝酵母复合种分离株均来自环境，均属于地中海地区特有的一个大的流行簇。群体遗传学分析证实，VNI 分离株组的特征是变异性低和克隆扩张，而 VNIV 组的特征是变异性高和多次重组事件。然而，当比较 VNI 和 VNIV 环境分离株时，它们表现出相似的种群结构，具有很高比例的共享突变和不存在固定突变。连锁不平衡分析也揭示了临床和环境分离株之间的差异，表明 PLB1 等位基因组合在宿主感染中的关键作用以及 LAC1 等位基因组合对真菌在环境中生存的关键作用。本研究表明，临床和环境分离株的遗传比较代表了理解导致某些基因型从腐生生活方式转变为寄生生活方式的遗传特征的第一步。
