Phylogeny and taxonomy of the family Arthrodermataceae (dermatophytes) using sequence analysis of the ribosomal ITS region

Abstract

The internal transcribed spacer (ITS) region, covering the ITS1, ITS2 and 5·8S ribosomal DNA was used to evaluate phylogenetic relationships within the fungal family Arthrodermataceae. Sequences of variable length, ranging between 522 and 684 base pairs were aligned. An unrooted consensus tree based on parsimony analysis showed Trichophyton to be polyphyletic, and Microsporum to be paraphyletic. Non‐monophyly of these two genera is in conflict with traditional classification. But this relation is not strongly supported by bootstrap analysis. Phylogenetic analysis showed that the two known members of the genus Epidermophyton grouped widely apart from each other. Within Trichophyton, our results suggest a separation of human pathogenic species and primarily geophilic species. Bootstrap support for these two groups is fairly high and both groups are recognized by current taxonomy. Three lineages were revealed within the T. mentagrophytes species complex. Microsporum canis, M. audouinii and M. equinum were found to be closely related. The topology of the tree was robust to various methods of analysis (parsimony and distance) and a different weighting scheme. Weighting of transversions over transitions did not improve the status of poorly supported branches of the tree.

Phylogenetic analysis of Trichophyton mentagrophytes human and animal isolates based on MnSOD and ITS sequence comparison

“…1). Our results fitted well with the known predilection of dermatophyte species for certain body areas (De Hoog et al, 1998;Fumeaux et al, 2004;Graser et al, 1998Graser et al, , 1999aKardjeva et al, 2006;Ninet et al, 2003;Summerbell et al, 2002;Weitzman & Summerbell, 1995). Clade I human isolates Table 1) were isolated from tinea pedis, like the neotype of T.…”

“…Similar findings were made previously when other target genes were used: Ninet et al (2003) were able to distinguish three T. mentagrophytes genotypes on the basis of two 28S rDNA polymorphic sites, and Kano et al (1998Kano et al ( , 2003 were able to identify dermatophyte species with high sequence identity (99 %) between reference strains and clinical isolates using a chitin synthase 1 based PCR assay. Similarly to the previously described 15 % variation at the ITS region locus within the T. mentagrophytes complex (Graser et al, 1999a), ITS sequences from our isolates and standard strains reached up to 10.6 % divergence, and fell into two clades. Clade I was composed of two subclades (Fig.…”

“…Microscopic features were more contributive than macroscopic ones, making them useful as indicators for routine morphological identification. They included the shape of the microconidia, previously described as a criterion to distinguish A. vanbreuseghemii-and A. benhamiae-related isolates (Graser et al, 1999a). However, morphology was not always characteristic and stable, and, therefore, not totally reliable, as previously described (Nenoff et al, 2007).…”

“…For each PCR product, a consensus nucleotide sequence was determined using BioEdit software (Tippmann, 2004) and significant sequence identity with known fungal MnSOD gene or ITS region sequences was displayed by using the BLAST standard nucleotide-nucleotide local alignment search tool (NCBI; http:/ www.ncbi.nlm.nih.gov/BLAST/). T. rubrum isolate TR-104 showed complete sequence identity to T. rubrum CBS 392.58 at the ITS region locus (sequence accession number Z97993; Graser et al, 1999a).…”

“…These molecular approaches have been based primarily on the G+C content of chromosomal DNA (Davison et al, 1980), total DNA homology (Davison & Mackenzie, 1984), restriction fragment length polymorphism analysis of mitochondrial DNA (mtDNA) (Mochizuki et al, 1990(Mochizuki et al, , 1996, arbitrarily primed PCR (AP-PCR) (Liu et al, 2000), random amplification of polymorphic DNA (RAPD) analysis (Kac et al, 1999;Liu et al, 1997;Mochizuki et al, 1997) and PCR fingerprinting (Faggi et al, 2001;Graser et al, 1999b). More recently, sequence analysis of the rDNA regions (Graser et al, 1999a;Harmsen et al, 1995;Makimura et al, 1998Makimura et al, , 1999Mochizuki et al, 1999Mochizuki et al, , 2003 and, in particular, analysis of internal transcribed spacer (ITS) regions (Graser et al, 1999a;Makimura et al, 1998Makimura et al, , 1999Mochizuki et al, 1999), which appeared more suitable than the gene coding for the small-subunit rRNA (18S rRNA) (Harmsen et al, 1995), were used successfully to evaluate the phylogenetic relationships within the T. mentagrophytes complex. These accurate molecular studies emerged as a critical issue for comprehensive understanding of the clinical and epidemiological implications of the genetic heterogeneity of T. mentagrophytes and resulted in the re-establishment of three if not four species: Trichophyton interdigitale close to the teleomorph Arthroderma vanbreuseghemii, T. mentagrophytes close to the teleomorph A. simii, and T. erinacei, plus another Trichophyon anamorph, both close to the teleomorph A. benhamiae, which includes both European-American and African races (Graser et al 1999b;Probst et al, 2002;Takahashi et al, 2003;Nenoff et al, 2007).…”