Genotyping of Russian isolates of fungal pathogen Trichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism
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. Our previous study provided limited evidence in favor of the existence of two genetic lineages in Russian T. rubrum sensu stricto population. We aimed to study genetic structure of Russian population of T. rubrum, and to identify factors, shaping this structure. We analyzed polymorphism of 12 simple sequence repeat (SSR, or microsatellite) markers and single-nucleotide polymorphism in TERG_02941 protein-coding gene in 70 T. rubrum isolates and performed phylogenomic analysis. All three types of data provided evidence that the population consists of two genetic lineages. Clustering, performed by microsatellite length polymorphism, was strongly dependent on the number of nucleotide repeats in 5’-area of fructose 1,6-bisphosphate aldolase gene. 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. There was no clear connection of population structure with types of infection, places of geographic origin, aldolase gene expression and urease activity. Our results suggest that Russian population of T. rubrum consists of two cosmopolitan genetic lineages.