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A Short-Tandem-Repeat Assay (MmySTR) for Studying Genetic Variation in Madurella mycetomatis
Journal of Clinical Microbiology ( IF 9.4 ) Pub Date : 2021-02-18 , DOI: 10.1128/jcm.02331-20
Bertrand Nyuykonge 1 , Kimberly Eadie 1 , Willemien H A Zandijk 1 , Sarah A Ahmed 2, 3 , Marie Desnos-Ollivier 4 , Ahmed H Fahal 5 , Sybren de Hoog 2 , Annelies Verbon 1 , Wendy W J van de Sande 1 , Corné H W Klaassen 6
Affiliation  

Madurella mycetomatis is the major causative agent of eumycetoma, a neglected tropical infection characterized by painless subcutaneous lesions, inflammation, and grains draining from multiple sinuses. To study the epidemiology of mycetoma, a robust discriminatory typing technique is needed. We describe the use of a short-tandem-repeat assay (MmySTR) for genotyping of M. mycetomatis isolates predominantly from Sudan. Eleven microsatellite markers (3 dinucleotides, 4 trinucleotide repeats, and 4 tetranucleotide repeats) were selected from the M. mycetomatis MM55 genome using the Tandem Repeats Finder software. PCR amplification primers were designed for each microsatellite marker using primer3 software and amplified in a multicolor multiplex PCR approach. To establish the extent of genetic variation within the population, a collection of 120 clinical isolates from different regions was genotyped with this assay. The 11 selected MmySTR markers showed a large genotypic heterogeneity. From a collection of 120 isolates, 108 different genotypes were obtained. Simpson’s diversity index (D) value for individual markers ranged from 0.081 to 0.881, and the combined panel displayed an overall D value of 0.997. The MmySTR assay demonstrated high stability, reproducibility, and specificity. The MmySTR assay is a promising new typing technique that can be used to genotype isolates of M. mycetomatis. Apart from the possible contribution of host factors, the genetic diversity observed among this group of isolates might contribute to the different clinical manifestations of mycetoma. We recommend that the MmySTR assay be used to establish a global reference database for future study of M. mycetomatis isolates.

中文翻译:

用于研究 Madurella mycetomatis 遗传变异的短串联重复测定 (MmySTR)

Madurella mycetomatis真菌瘤的主要病原体,真菌是一种被忽视的热带感染,其特征是无痛的皮下病变、炎症和从多个鼻窦排出的颗粒。为了研究足菌肿的流行病学,需要一种强大的判别分型技术。我们描述了使用短串联重复检测(的MMY STR),用于基因分型M. mycetomatis从苏丹主要分离物。从M. mycetomatis中选择了 11 个微卫星标记(3 个二核苷酸、4 个三核苷酸重复和 4 个四核苷酸重复)MM55 基因组使用 Tandem Repeats Finder 软件。使用primer3 软件为每个微卫星标记设计PCR 扩增引物,并在多色多重PCR 方法中扩增。为了确定群体内遗传变异的程度,使用该测定对来自不同地区的 120 个临床分离株进行了基因分型。11 个选定的Mmy STR 标记显示出很大的基因型异质性。从 120 个分离株的集合中,获得了 108 个不同的基因型。单个标记的辛普森多样性指数 (D) 值范围从 0.081 到 0.881,组合面板显示的整体 D 值为 0.997。所述MMY STR测定证明稳定性高,重现性和特异性。该MMYSTR 分析是一种很有前途的新分型技术,可用于对分枝杆菌分离株进行基因分型。除了宿主因素的可能贡献外,在这组分离株中观察到的遗传多样性可能导致足菌肿的不同临床表现。我们建议MMY STR测定中,建立对未来研究的一个全球参考数据库M. mycetomatis分离。
更新日期:2021-02-18
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