Whole genome sequencing of terbinafine-sensitive canine strains of Trichophyton indotineae isolated from India

IF 2.4 4区医学 Q3 MYCOLOGY

Journal de mycologie medicale Pub Date : 2025-12-01 Epub Date: 2025-10-09 DOI:10.1016/j.mycmed.2025.101584

Prasad Thomas , Sonu S. Nair , Mostafa Y. Abdel-Glil , Sudhir K. Prajapati , Subbaiyan Anbazhagan , Shubham Saini , Athira V , Bablu Kumar , Vinod K. Chaturvedi , Shivaprakash M Rudramurthy , G. Saikumar , Premanshu Dandapat , Abhishek

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引用次数: 0

Abstract

Background

Trichophyton indotineae (earlier Trichophyton mentagrophytes ITS genotype VIII) is a newly defined dermatophyte species frequently reported from India. The strains representing T. indotineae cause dermatophytosis in humans, and some strains exhibit resistance to terbinafine.

Objective

This study aims to characterize the animal strains of T. indotineae at the genomic level and compare them with human strains and other Trichophyton species.

Methods

In this study, we report the generation of de novo WGS data for two strains of T. indotineae isolated from canines of northern India. The genome sequence was subjected to functional and structural annotation, followed by comparative genomics and phylogeny.

Results

Genome assembly and annotation revealed a 22 Mb genome in both strains, comprising approximately 6800 protein-coding genes, and a 24 Kb contig representing the mitochondrion. Functional annotations revealed the presence of around 200 CAZymes and secretomes. The identified proteins include various proteolytic enzymes, such as keratinases, lyases, fungalysins, subtilisins, and chitinases. Orthologous cluster comparison among T. indotineae and T. rubrum identified a LysM effector virulence factor associated with the sequestration of chitin oligosaccharides unique to T. indotineae. Taxonomic inferences involving 69 species representing the Genus Trichophyton revealed similar clustering in genome ANI, mash distance, and core-genome phylogeny. Within all approaches, a total of 16 Indian strains represented T. indotineae. The SNP difference between any two T. indiotinae strains ranged from 8 to 257, indicating limited strain variation within the species. The core-genome phylogeny revealed two major clusters, with no cluster indicating a specific host association. Correlating their phenotypic susceptibility to the anti-fungal drug terbinafine (TRB), the coding sequences (CDS) maintained no amino acid substitutions at key positions 393 and 397. The comparative analysis of the squalene epoxidase gene across the 16 strains revealed a high frequency of SNPs at the 397th position in the squalene epoxidase genes in terbinafine-resistant strains.

Conclusion

To conclude, the study indicates similar genome composition in strains of T. indiotineae from canine and human origin, irrespective of the TRB resistance phenotype. The pathogen and genotypes circulating among humans and animals need to be continuously monitored to determine the exact role of animals in the transmission and endemicity of T. indotineae in India.

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印度印多毛癣菌特比萘芬敏感犬株全基因组测序。

背景：印度毛癣菌（Trichophyton indottineae，早期的毛癣菌ITS基因型VIII）是一种新定义的皮癣菌，经常在印度报道。代表indottineae的菌株引起人类皮肤癣病，一些菌株对特比萘芬具有抗性。目的：从基因组水平对印多毛癣菌动物菌株进行鉴定，并与人类和其他毛癣菌进行比较。方法：在本研究中，我们报道了从印度北部犬类中分离的两株印度乳杆菌的新生WGS数据。基因组序列进行了功能和结构注释，然后进行了比较基因组学和系统发育。结果：基因组组装和注释显示，两株菌株的基因组均为22 Mb，包括约6800个蛋白质编码基因和24 Kb代表线粒体的基因组。功能注释显示存在大约200个CAZymes和secretome。鉴定的蛋白质包括各种蛋白水解酶，如角化酶、裂解酶、真菌酶、枯草菌素和几丁质酶。通过对赤藓藓和红藓藓的同源聚类比较，鉴定出一个与赤藓藓特有的几丁质寡糖分离相关的LysM效应毒力因子。对代表毛藓属的69个物种的分类推断显示，在基因组ANI、mash distance和核心基因组系统发育上具有相似的聚类性。在所有的方法中，共有16个印度菌株代表了印蚊。两株不同的单核苷酸多态性（SNP）差异在8 ~ 257之间，表明该菌株在种内变异有限。核心基因组系统发育揭示了两个主要的集群，没有集群表明一个特定的宿主关联。与抗真菌药物特比萘芬（TRB）的表型敏感性相关，编码序列（CDS）在关键位置393和397保持无氨基酸取代。对16株耐特比萘芬菌株的角鲨烯环氧化酶基因进行比较分析，发现在397位角鲨烯环氧化酶基因snp频率较高。结论：综上所述，研究表明犬源和人类源的印蚊菌株的基因组组成相似，与TRB抗性表型无关。需要持续监测在人类和动物中传播的病原体和基因型，以确定动物在印度印蚊传播和流行中的确切作用。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal de mycologie medicale 医学-真菌学

CiteScore

5.10

自引率

2.80%

发文量

审稿时长

6-12 weeks

期刊介绍： The Journal de Mycologie Medicale / Journal of Medical Mycology (JMM) publishes in English works dealing with human and animal mycology. The subjects treated are focused in particular on clinical, diagnostic, epidemiological, immunological, medical, pathological, preventive or therapeutic aspects of mycoses. Also covered are basic aspects linked primarily with morphology (electronic and photonic microscopy), physiology, biochemistry, cellular and molecular biology, immunochemistry, genetics, taxonomy or phylogeny of pathogenic or opportunistic fungi and actinomycetes in humans or animals. Studies of natural products showing inhibitory activity against pathogenic fungi cannot be considered without chemical characterization and identification of the compounds responsible for the inhibitory activity. JMM publishes (guest) editorials, original articles, reviews (and minireviews), case reports, technical notes, letters to the editor and information. Only clinical cases with real originality (new species, new clinical present action, new geographical localization, etc.), and fully documented (identification methods, results, etc.), will be considered. Under no circumstances does the journal guarantee publication before the editorial board makes its final decision. The journal is indexed in the main international databases and is accessible worldwide through the ScienceDirect and ClinicalKey platforms.