Establishment of a Novel Short Tandem Repeat Typing Method for Exophiala dermatitidis.

IF 3.6 3区生物学 Q2 MYCOLOGY

Mycopathologia Pub Date : 2024-01-17 DOI:10.1007/s11046-023-00825-y

Hamide Zoqi, Dirk Schmidt, Ludwig Sedlacek, Peter-Michael Rath, Joerg Steinmann, Lisa Kirchhoff

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Abstract

The opportunistic black yeast-like fungus Exophiala dermatitidis frequently colonizes the respiratory tract of cystic fibroses (CF) patients. Additionally, it can cause superficial, systemic, and cerebral forms of phaeohyphomycoses. The objective of this study was to develop and apply a microsatellite or short tandem repeat (STR) genotyping scheme for E. dermatitidis. In total, 82 E. dermatitidis isolates from various geographic origins (environmental = 9, CF = 63, invasive isolates = 9, melanin-deficient mutant = 1) were included in this study. After next-generation sequencing of a reference strain and sequence filtering for microsatellites, six STR markers were selected and amplified in two multiplex PCR reactions. The included isolates were discriminated in a genetic cluster analysis using the Pearson algorithm to reveal the relatedness of the isolates. The E. dermatitidis isolates clustered on basis of both, their source and their origin. The invasive isolates from Asia were unrelated to isolates from CF. Nearly all environmental isolates were grouped separately from patients' isolates. The Simpson index was 0.94. In conclusion, we were able to establish a STR genotyping scheme for investigating population genomics of E. dermatitidis.

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建立皮炎嗜血杆菌的新型短串联重复分型方法

皮炎外酵母菌（Exophiala dermatitidis）是一种机会性黑色酵母样真菌，经常在囊性纤维化（CF）患者的呼吸道中定植。此外，它还能引起表皮、全身和脑部的噬菌体病。本研究的目的是开发并应用皮炎双球菌的微卫星或短串联重复（STR）基因分型方案。本研究共纳入了82株来自不同地域的皮炎双球菌分离株（环境分离株=9株、CF分离株=63株、入侵分离株=9株、黑色素缺失突变株=1株）。在对参考菌株进行下一代测序并对微卫星进行序列筛选后，选择了六个 STR 标记，并在两个多重 PCR 反应中进行扩增。利用皮尔逊算法对所包含的分离株进行了遗传聚类分析，以揭示分离株之间的亲缘关系。皮炎埃希氏菌分离物根据其来源和原产地进行了聚类。来自亚洲的入侵分离株与来自 CF 的分离株没有亲缘关系。几乎所有环境分离株都与患者分离株分开分组。辛普森指数为 0.94。总之，我们能够建立一种 STR 基因分型方案，用于研究皮炎埃希氏菌的群体基因组学。

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来源期刊

Mycopathologia 生物-真菌学

CiteScore

6.80

自引率

3.60%

发文量

审稿时长

3 months

期刊介绍： Mycopathologia is an official journal of the International Union of Microbiological Societies (IUMS). Mycopathologia was founded in 1938 with the mission to ‘diffuse the understanding of fungal diseases in man and animals among mycologists’. Many of the milestones discoveries in the field of medical mycology have been communicated through the pages of this journal. Mycopathologia covers a diverse, interdisciplinary range of topics that is unique in breadth and depth. The journal publishes peer-reviewed, original articles highlighting important developments concerning medically important fungi and fungal diseases. The journal highlights important developments in fungal systematics and taxonomy, laboratory diagnosis of fungal infections, antifungal drugs, clinical presentation and treatment, and epidemiology of fungal diseases globally. Timely opinion articles, mini-reviews, and other communications are usually invited at the discretion of the editorial board. Unique case reports highlighting unprecedented progress in the diagnosis and treatment of fungal infections, are published in every issue of the journal. MycopathologiaIMAGE is another regular feature for a brief clinical report of potential interest to a mixed audience of physicians and laboratory scientists. MycopathologiaGENOME is designed for the rapid publication of new genomes of human and animal pathogenic fungi using a checklist-based, standardized format.