Internal transcribed spacer sequencing versus biochemical profiling for identification of medically important yeasts

Abstract

In this study, we established an in-house database of yeast internal transcribed spacer (ITS) sequences. This database includes medically important as well as colonizing yeasts that frequently occur in the diagnostic laboratory. In a prospective study, we compared molecular identification with phenotypic identification by using the ID32C system (bioMérieux) for yeast strains that could not be identified by a combination of CHROMagar Candida and morphology on rice agar. In total, 113 yeast strains were included in the study. By sequence analysis, 98% of all strains were identified correctly to the species level. With the ID32C, 87% of all strains were identified correctly to the species or genus level, 7% of the isolates could not be identified, and 6% of the isolates were misidentified, most of them as Candida rugosa or Candida utilis. For a diagnostic algorithm, we suggest a three-step procedure which integrates morphological criteria, biochemical investigation, and sequence analysis of the ITS region.

FIG. 1.

Similarity tree calculated from the alignment of yeast species included in the ITS database (one ITS sequence per species), using SeqWeb version 2.1.0.

FIG. 2.

Similarity tree calculated from the alignment of Cryptococcus ITS sequences using SeqWeb version 2.1.0. The sequences of Cryptococcus laurentii cluster in three genogroups called group Ia, group Ib, and group II. Sequences with the prefix AB or AF were extracted from GenBank (NCBI); sequences with the prefix IMM and marked with a star were obtained from the strain collection in-house.

FIG. 3.

Similarity tree calculated from the alignment of Trichosporon ITS sequences using SeqWeb version 2.1.0. The sequences of Trichosporon asahii, T. asteroides, T. inkin and T. ovoides cannot be clearly distinguished from each other, thus, they are combined in the Trichosporon group A. Sequences with the prefix AB or AF were extracted from GenBank (NCBI); sequences with the prefix IMM and marked with a star were obtained from the strain collection in-house.

FIG. 4.

Diagnostic algorithm. The numbers in bracket are based on applying this algorithm to the study isolates. a, combination of chromogenic agar and rice agar.