Population differentiation and genetic diversity of Trichophyton rubrum as revealed by highly discriminatory microsatellites

Gong, Jie; Wu, Weiwei; Ran, Menglong; Wang, Xiaowen; Liu, Wei; Wan, Zhe; Yao, Limin; Li, Ruoyu

doi:10.1016/j.fgb.2016.08.002

Cited by 8 publications

(13 citation statements)

References 24 publications

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“…There were two exceptions, the isolate D15P139 had 247insC mutation, and another isolate had additional TA element in the microsatellite near the 3'-end of the sequence. Our preliminary study showed discrepancies between the results of strain typing by TERG_02941 locus polymorphism and the microsatellite typing assay of Gong et al, 8 based on eight loci. 40 We hypothesised that this discrepancy was due to insufficient informativeness of the assay and used four additional Our first approach for calculating microsatellite polymorphism-based genetic distances employed the probability of mutation events, described with the use of stepwise mutation model.…”

Section: Resultscontrasting

confidence: 79%

“…Secondly, we performed microsatellite typing. We used eight microsatellite loci from the papers by Gräser et al 7 and Gong et al 8 and developed four additional loci ( performed using the MiSeq sequencer (Illumina, USA). The reads obtained were prepared for the analyses as described earlier.…”

Section: Species Identificationmentioning

confidence: 99%

“…[2][3][4][5][6] Statistical analysis of genetic polymorphism in simple sequence repeats (SSR, or microsatellites) revealed clonal mode of reproduction in the species. [7][8] It is expectedly accompanied by low genetic polymorphism. [9][10][11] Several studies of mating type locus idiomorphs distribution in T. rubrum population found a single mating type locus variant, out of two, which are necessary for mating.…”

Section: Introductionmentioning

confidence: 99%

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Genotyping of Russian isolates of fungal pathogenTrichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism

Pchelin

Mochalov

Azarov

et al. 2020

Preprint

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The Trichophyton rubrum species group consists of prevalent causative agents of human skin, nail and hair infections, including T. rubrum sensu stricto and T. violaceum, as well as other less well established or debatable taxa like T. soudanense, T. kuryangei and T. megninii. We aimed to describe genetic lineages in Russian T. rubrum sensu stricto, to find whether these lineages possess specific characteristics and to identify factors, shaping the population structure. We assessed polymorphism of 12 simple sequence repeat (SSR, or microsatellite) loci and TERG_02941 protein-coding gene in 70 T. rubrum isolates and also performed phylogenomic analysis. In both cases, two genetic lineages were found. The analysis of molecular variance (AMOVA) on the basis of SSR typing data indicated that 22-48% of the variability was between groups within T. rubrum. The pattern of phylogenetic changes in polymorphic protein-coding loci and SSR typing results revealed the pressure of strong directional selection, but its sources remained elusive. Our results suggest that Russian population of T. rubrum consists of two cosmopolitan genetic lineages, with no clear connection of population structure with types of infection, places of geographic origin, aldolase gene expression and urease activity.HighlightsRussian population of fungal pathogen Trichophyton rubrum is formed by two global genetic lineagesPopulation structure in T. rubrum can be studied by improved microsatellite typing assay along with SNP typing and whole genome sequencingIn T. rubrum, there is seemingly no association between genetic lineages and types of infection, places of geographic origin, aldolase gene expression and urease activityIn T. rubrum, microevolution is driven by strong directional selection of yet unknown nature

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Section: Resultscontrasting

confidence: 79%

Section: Species Identificationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genotyping of Russian isolates of fungal pathogenTrichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism

Pchelin

Mochalov

Azarov

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

Section: Discussionmentioning

confidence: 99%

“…The speculation for this shift included environmental factors, humidity, temperature, trauma and internal factors such as host‐parasite relationship, host susceptibility and immunological factors . Gong et al were able to show that population differentiation and genetic diversity of T rubrum are correlated to highly discriminatory microsatellites. They were the first to reveal population information of T rubrum using highly discriminatory molecular markers, suggesting that T rubrum populations in densely populated cities may have better adaptability due to higher genetic diversity under selective pressures (such as antifungal agents).…”

Section: Discussionmentioning

confidence: 99%

The current Indian epidemic of superficial dermatophytosis due toTrichophyton mentagrophytes—A molecular study

Nenoff¹,

Verma²,

Vasani³

et al. 2019

Mycoses

199

216

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Summary The disease burden of chronic‐relapsing and therapy‐refractory superficial dermatophytosis dramatically increased in India within the past 5‐6 years. In order to evaluate the prevalence of this trend, 201 skin scrapings were collected from patients from all parts of India and were tested for dermatophytes using both fungal culture and a PCR‐ELISA directly performed with native skin scrapings. Fungal culture material was identified by genomic Sanger sequencing of the internal transcribed spacer (ITS) region and the translation elongation factor (TEF)‐1α gene. In total, 149 (74.13%) out of the 201 samples showed a dermatophyte‐positive culture result. Out of this, 138 (92.62%) samples were identified as Trichophyton (T.) mentagrophytes and 11 (7.38%) as Trichophyton rubrum. The PCR‐ELISA revealed similar results: 162 out of 201 (80.56%) samples were dermatophyte‐positive showing 151 (93.21%) T mentagrophytes‐ and 11 (6.79%) T rubrum‐positive samples. In this study, we show for the first time a dramatic Indian‐wide switch from T rubrum to T mentagrophytes. Additionally, sequencing revealed a solely occurring T mentagrophytes “Indian ITS genotype” that might be disseminated Indian‐wide due to the widespread abuse of topical clobetasol and other steroid molecules mixed with antifungal and antibacterial agents.

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Whole-genome resequencing of Trichophyton rubrum provides insights into population differentiation and drug resistance

et al. 2019

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Population differentiation and genetic diversity of Trichophyton rubrum as revealed by highly discriminatory microsatellites

Cited by 8 publications

References 24 publications

Genotyping of Russian isolates of fungal pathogenTrichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism

Genotyping of Russian isolates of fungal pathogenTrichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism

The current Indian epidemic of superficial dermatophytosis due toTrichophyton mentagrophytes—A molecular study

Whole-genome resequencing of Trichophyton rubrum provides insights into population differentiation and drug resistance

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