Identification of medically relevant Trichosporon species based on sequences of internal transcribed spacer regions and construction of a database for Trichosporon identification

Abstract

The nucleotide sequences of the internal transcribed spacer (ITS) 1 and 2 regions in the rRNA gene were determined by directly sequencing PCR-amplified fragments for all of the species (17 species and five varieties) in the genus Trichosporon. Comparative sequence analysis suggests that six medically relevant species, T. asahii, T. asteroides, T. cutaneum, T. inkin, T. mucoides, and T. ovoides, can be readily identified by their ITS sequences. In addition, the sequence analysis showed that conspecific strains have fewer than 1% nucleotide differences in the ITS 1 and 2 regions overall. Molecular phylogenetic trees are also presented.

FIG. 1

Alignment of the Trichosporon ITS 1 sequences, including the 3′ end of 18S rDNA. Periods and asterisks are used when the nucleotide at a particular position is identical to that in T. cutaneum. Dashes represent deletions necessary for alignment. T. cut, T. cutaneum; T. jir, T. jirovecii; T. mnl, T. moniliiforme; T. mcd, T. mucoides; T. aqt, T. aquatile; T. a. ash, T. asahii var. asahii; T. a. cor, T. asahii var. coremiformis; T. a. fae, T. asahii var. faecalis; T. ast, T. asteroides; T. ink, T. inkin; T. ovd, T. ovoides; T. bra, T. brassicae; T. mot, T. montevideense; T. dom, T. domesticum; T. dul, T. dulcitum; T. gra, T. gracile; T. l. lob, T. loubieri var. loubieri; T. l. lab, T. loubieri var. laibachii; T. spt, T. sporotrichoides; M 9481, Trichosporon sp. strain M 9481.

FIG. 2

Alignment of the Trichosporon ITS 2 sequences. For symbols and abbreviations, see the legend to Fig. 1.

FIG. 3

Relationship between nuclear DNA relatedness value and similarities of ITS 1 and 2 sequences considered separately.

FIG. 4

Relationship between nuclear DNA relatedness value and similarity of combined ITS 1 and 2 sequences.

FIG. 5

Molecular phylogenetic trees based on the Trichosporon ITS 1 (A) and 2 (B) sequences. The trees were constructed by the neighbor-joining method. The numerals represent the confidence level from 1,000 replicate bootstrap samplings (frequencies less than 50% are not indicated). Knuc, Kimura’s parameter (15).

FIG. 6

Molecular phylogenetic trees based on the Trichosporon ITS 1 (A) and 2 (B) sequences. The trees were constructed by the maximum-likelihood method. The scale marker indicates the distance in relative units that equals 5% of the total branch length depicted.