Genotyping of Russian isolates of fungal pathogenTrichophyton 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 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

Time and cost‐efficient identification of Trichophyton indotineae

“…The finding of a genomic region, suitable for designing T. indotineae-specific primers, came as a by-product during the search for microsatellite loci for molecular typing of TMTISC isolates, as described for T. rubrum by Pchelin et al 20 Manual check of candidate locus C120-287 within arbitrary selected genomic coordinates QQSQ01000373.1:13198-13443 revealed two indel events in the sequences of available T. indotineae genomes. 21,22 The intergenic locus C120-287 is placed downstream the gene coding for tryptophan dimethyl allyltransferase H109_01622 and upstream the gene of hypothetical protein H109_01621.…”