Phylogenetic classification and species identification of dermatophyte strains based on DNA sequences of nuclear ribosomal internal transcribed spacer 1 regions

Abstract

The mutual phylogenetic relationships of dermatophytes of the genera Trichophyton, Microsporum, and Epidermophyton were demonstrated by using internal transcribed spacer 1 (ITS1) region ribosomal DNA sequences. Trichophyton spp. and Microsporum spp. form a cluster in the phylogenetic tree with Epidermophyton floccosum as an outgroup, and within this cluster, all Trichophyton spp. except Trichophyton terrestre form a nested cluster (100% bootstrap support). Members of dermatophytes in the cluster of Trichophyton spp. were classified into three groups with ITS1 homologies, with each of them being a monophyletic cluster (100% bootstrap support). The Arthroderma vanbreuseghemii-Arthroderma simii group consists of A. vanbreuseghemii, A. simii, Trichophyton mentagrophytes isolates from humans, T. mentagrophytes var. quinckeanum, Trichophyton tonsurans, and Trichophyton schoenleinii. Arthroderma benhamiae, T. mentagrophytes var. erinacei, and Trichophyton verrucosum are members of the Arthroderma benhamiae group. Trichophyton rubrum and Trichophyton violaceum form the T. rubrum group. This suggests that these "species" of dermatophytes have been overclassified. The ITS1 sequences of 11 clinical isolates were also determined to identify the species, and all strains were successfully identified by comparison of their base sequences with those in the ITS1 DNA sequence database.

FIG. 1

NJ tree of dermatophytes on the basis of their ITS1 sequences. The NJ tree was constructed with data for standard strains of dermatophytes (see Table 1 and the text). The numbers above the branches indicate the percentage of bootstrap samplings. Branches without numbers have frequencies of less than 70%. A, cluster of Trichophyton spp. and Microsporum spp.; B, cluster of all Trichophyton spp. except T. terrestre; a, Arthroderma vanbreuseghemii-A. simii group; b, A. benhamiae group; c, T. rubrum group. K nuc, thousands of nucleotides.

FIG. 2

ML tree of dermatophytes on the basis of their ITS1 sequences. The ML tree was constructed with data for standard strains of dermatophytes (see Table 1 and the text). A, cluster of Trichophyton spp. and Microsporum spp.; B, cluster of all Trichophyton spp. except T. terrestre; a, A. vanbreuseghemii-A. simii group; b, A. benhamiae group; c, T. rubrum group. K nuc, thousands of nucleotides.

FIG. 3

Alignment of ITS1 sequences of dermatophytes. The sequences of 18 species of dermatophytes (see Table 1 and the text) were aligned by using the Clustal W (12) and GENETYX-MAC 10.1 (Software Development Co., Ltd.) computer programs. Hyphens designate gaps that were added to permit alignment. T. men. quinckeanum, T. mentagrophytes var. quinckeanum; T. men. erinacei, T. mentagrophytes var. erinacei; A. benhamiae A/E and Af, A. benhamiae Americano-European race and African race, respectively.