Trichophyton spp. are important causative agents of superficial mycoses. The phylogeny of the genus and accurate strain identification, based on the ribosomal ITS region sequencing, are still under development. The present work is aimed at (i) inferring the genus phylogeny from partial ITS, LSU and BT2 sequences (ii) description of ribosomal ITS region polymorphism in 15 strains of Trichophyton interdigitale. We performed DNA sequence-based species identification and phylogenetic analysis on 48 strains belonging to the genus Trichophyton. Phylogenetic relationships were inferred by maximum likelihood and Bayesian methods on concatenated ITS, LSU and BT2 sequences. Ribosomal ITS region polymorphisms were assessed directly on the alignment. By phylogenetic reconstruction, we reveal major anthropophilic and zoophilic species clusters in the genus Trichophyton. We describe several sequences of the ITS region of T. interdigitale, which do not fit in the traditional polymorphism scheme and propose emendations in this scheme for discrimination between ITS sequence types in T. interdigitale. The new polymorphism scheme will allow inclusion of a wider spectrum of isolates while retaining its explanatory power. This scheme was also found to be partially congruent with NTS typing technique.

Trichophyton rubrum is an important causative agent of superficial mycoses worldwide. To uncover a genetic composition of a local population of this fungus, we sequenced A7C99_6411 and A7C99_6714 loci, coding for hypothetical proteins and revealed two complex genotypes, differing by a single missense mutation in each locus. One of the two A7C99_6411/6714 genotypes was not found in tinea pedis cases and demonstrated mostly longer TRS-1 elements when compared to another genotype. Thus, we present a description of nucleotide polymorphism in protein-coding loci in T. rubrum and provide evidence for ecological preferences of T. rubrum genotypes at a local scale.

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

Trichophyton rubrum is an ascomycete from the order Onygenales. It is prevalent fungus of medical importance in most countries due to its major contribution to the aetiology of toenail onychomycosis and foot skin mycosis. 1 Trichophyton rubrum sensu stricto is a part of species group, which also includes T violaceum and T soudanense along with several forms, potentially deserving species status. All of these can be differentiated by ribosomal DNA internal transcribed spacer (ITS) region sequences. 2-6 Statistical analysis of genetic

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