Identification of Medically Important Yeast Species by Sequence Analysis of the Internal Transcribed Spacer Regions

Leaw, Shiang Ning; Chang, Hsien Chang; Sun, Hsiao Fang; Barton, Richard; Bouchara, Jean Philippe; Chang, Tsung Chain

doi:10.1128/jcm.00078-07

Cited by 69 publications

(100 citation statements)

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“…It should be noted that the identity of isolate LMA 90603 was not resolved by sequencing of the D1-D2 region, although the strain was unambiguously identified as being M. fulvum by ITS sequencing. This indicates that the ITS region might be a more discriminative target than the D1-D2 region for fungal identification, as found in our previous study (26). It is not easy to differentiate M. gypseum from M. fulvum on the basis of morphological criteria (5).…”

Section: Discussionmentioning

confidence: 77%

Identification of Dermatophytes by an Oligonucleotide Array

Li¹,

Bouchara

Hsu

et al. 2007

J Clin Microbiol

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Species of dermatophytes are classified into three anamorphic (asexual) genera, Epidermophyton, Microsporum, and Trichophyton. Conventional methods used to identify dermatophytes are often lengthy and may be inconclusive because of atypical microscopic or colony morphology. Based on the internal transcribed spacer 1 (ITS-1) and ITS-2 sequences of the rRNA genes, an oligonucleotide array was developed to identify 17 dermatophyte species. The method consisted of PCR amplification of the ITS regions using universal primers, followed by hybridization of the digoxigenin-labeled PCR products to an array of oligonucleotides (17-to 30-mers) immobilized on a nylon membrane. Of 198 dermatophyte strains and 90 nontarget strains tested, the sensitivity and specificity of the array were 99.5% and 97.8%, respectively. The only strain not identified (Microsporum audouinii LMA 597) was found to have a nucleotide insertion at the ITS-2 region where the probe was designed. Two nontarget strains, Microsporum equinum LMA 40396666 and Trichophyton gourvilii var. intermedium CBS 170.65, were misidentified as Microsporum canis and Trichophyton soudanense, respectively. Sequence analysis of the ITS regions revealed that the two misidentified strains displayed high sequence homology with the probes designed for M. canis and T. soudanense, respectively. The present method can be used as a reliable alternative to conventional identification methods and can be completed with isolated colonies within 24 h.

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Section: Discussionmentioning

confidence: 77%

Identification of Dermatophytes by an Oligonucleotide Array

Li¹,

Bouchara

Hsu

et al. 2007

J Clin Microbiol

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“…The availability of conserved and highly variable regions within the rRNA and its presence in multiple copies in fungal cells ( Figure 1) allows high sensitivity as well as accurate molecular identification for most yeasts [10,12,13].…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Pyrosequencing® technology for the identification of clinically relevant non-dematiaceous yeasts and related species

Montero

Shea

Jones

et al. 2008

Eur J Clin Microbiol Infect Dis

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Pyrosequencing was used to identify 133 isolates of clinically relevant non-dematiaceous yeasts. These included 97 ATCC strains (42 type strains), 7 UAMH strains, and 29 clinical isolates. Isolates belonged to the following genera: Candida (18 species), Trichosporon (10), Cryptococcus (7), Malassezia (3), Rhodotorula (2), Geotrichum (1), Blastoschizomyces (1) and Kodamaea (1). Amplicons were obtained of a hypervariable ITS region and analyzed using Pyrosequencing technology. The data were evaluated by a BLAST search against the GenBank database and correlated with data obtained by conventional cycle sequencing of the ITS1-5.8S-ITS2 region. Cycle sequencing identified (78.9%) if the isolates to the species level. Pyrosequencing technology identified 69.1%. In 90.1% of all the strains tested, identification results of both sequencing methods were identical. Most Candida isolates can be identified to the species level by pyrosequencing. Trichosporon species and some Cryptococcus cannot be differentiated at the species level. Pyrosequencing can be used for the reliable identification of most commonly isolated nondematiaceous yeasts, with a reduction of cost per identification compared to conventional sequencing.

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“…As an identification tool, the sequencing of this region is relatively simple to apply and yields clear results (Kurtzman and Robnett, 1997;Leaw et al, 2006). Thus, all yeast isolates were identified as Yarrowia lipolytica and showed 99 % sequence identity with strain NRRL YB-423.…”

Section: Identification Of Microorganism Strainsmentioning

confidence: 99%