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

Abstract

The Trichophyton rubrum species group consists of prevalent causative agents of human skin, nail and hair infections, including Trubrum sensu stricto and Tviolaceum, as well as other less well-established or debatable taxa like Tsoudanense, Tkuryangei and Tmegninii. Our previous study provided limited evidence in favour of the existence of two genetic lineages in the Russian Trubrum sensu stricto population. We aimed to study the genetic structure of the Russian population of Trubrum and to identify factors shaping this structure. We analysed the polymorphism of 12 simple sequence repeat (SSR or microsatellite) markers and single nucleotide polymorphism in the TERG_02941 protein-coding gene in 70 Trubrum isolates and performed a phylogenomic reconstruction. All three types of data provided conclusive evidence that the population consists of two genetic lineages. Clustering, performed by means of microsatellite length polymorphism analysis, was strongly dependent on the number of nucleotide repeats in the 5'-area of the fructose-1,6-bisphosphate aldolase gene. Analysis of molecular variance (AMOVA) on the basis of SSR typing data indicated that 22%-48% of the variability was among groups within Trubrum. There was no clear connection of population structure with types of infection, places of geographic origin, aldolase gene expression or urease activity. Our results suggest that the Russian population of Trubrum consists of two cosmopolitan genetic lineages.