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Nucleotide Sequence Database Comparison for Routine Dermatophyte Identification by Internal Transcribed Spacer 2 Genetic Region DNA Barcoding.
J Clin Microbiol. 2018 05; 56(5)JC

Abstract

Conventional dermatophyte identification is based on morphological features. However, recent studies have proposed to use the nucleotide sequences of the rRNA internal transcribed spacer (ITS) region as an identification barcode of all fungi, including dermatophytes. Several nucleotide databases are available to compare sequences and thus identify isolates; however, these databases often contain mislabeled sequences that impair sequence-based identification. We evaluated five of these databases on a clinical isolate panel. We selected 292 clinical dermatophyte strains that were prospectively subjected to an ITS2 nucleotide sequence analysis. Sequences were analyzed against the databases, and the results were compared to clusters obtained via DNA alignment of sequence segments. The DNA tree served as the identification standard throughout the study. According to the ITS2 sequence identification, the majority of strains (255/292) belonged to the genus Trichophyton, mainly T. rubrum complex (n = 184), T. interdigitale (n = 40), T. tonsurans (n = 26), and T. benhamiae (n = 5). Other genera included Microsporum (e.g., M. canis [n = 21], M. audouinii [n = 10], Nannizzia gypsea [n = 3], and Epidermophyton [n = 3]). Species-level identification of T. rubrum complex isolates was an issue. Overall, ITS DNA sequencing is a reliable tool to identify dermatophyte species given that a comprehensive and correctly labeled database is consulted. Since many inaccurate identification results exist in the DNA databases used for this study, reference databases must be verified frequently and amended in line with the current revisions of fungal taxonomy. Before describing a new species or adding a new DNA reference to the available databases, its position in the phylogenetic tree must be verified.

Authors+Show Affiliations

Service de Parasitologie/Mycologie, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France annececile.normand@aphp.fr.Mycology and Aerobiology, Scientific Institute of Public Health, Brussels, Belgium.Aix Marseille University, CNRS, IRD, INSERM, AP-HM, URMITE, IHU Méditerranée-Infection, Marseille, France.Mycology and Aerobiology, Scientific Institute of Public Health, Brussels, Belgium.Aix Marseille University, CNRS, IRD, INSERM, AP-HM, URMITE, IHU Méditerranée-Infection, Marseille, France.Service de Parasitologie/Mycologie, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France. Sorbonne Université, INSERM, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

29491019

Citation

Normand, A C., et al. "Nucleotide Sequence Database Comparison for Routine Dermatophyte Identification By Internal Transcribed Spacer 2 Genetic Region DNA Barcoding." Journal of Clinical Microbiology, vol. 56, no. 5, 2018.
Normand AC, Packeu A, Cassagne C, et al. Nucleotide Sequence Database Comparison for Routine Dermatophyte Identification by Internal Transcribed Spacer 2 Genetic Region DNA Barcoding. J Clin Microbiol. 2018;56(5).
Normand, A. C., Packeu, A., Cassagne, C., Hendrickx, M., Ranque, S., & Piarroux, R. (2018). Nucleotide Sequence Database Comparison for Routine Dermatophyte Identification by Internal Transcribed Spacer 2 Genetic Region DNA Barcoding. Journal of Clinical Microbiology, 56(5). https://doi.org/10.1128/JCM.00046-18
Normand AC, et al. Nucleotide Sequence Database Comparison for Routine Dermatophyte Identification By Internal Transcribed Spacer 2 Genetic Region DNA Barcoding. J Clin Microbiol. 2018;56(5) PubMed PMID: 29491019.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Nucleotide Sequence Database Comparison for Routine Dermatophyte Identification by Internal Transcribed Spacer 2 Genetic Region DNA Barcoding. AU - Normand,A C, AU - Packeu,A, AU - Cassagne,C, AU - Hendrickx,M, AU - Ranque,S, AU - Piarroux,R, Y1 - 2018/04/25/ PY - 2018/01/08/received PY - 2018/02/23/accepted PY - 2018/3/2/pubmed PY - 2019/2/9/medline PY - 2018/3/2/entrez KW - ITS KW - barcode KW - dermatophyte KW - fungi KW - hospital KW - sequencing JF - Journal of clinical microbiology JO - J. Clin. Microbiol. VL - 56 IS - 5 N2 - Conventional dermatophyte identification is based on morphological features. However, recent studies have proposed to use the nucleotide sequences of the rRNA internal transcribed spacer (ITS) region as an identification barcode of all fungi, including dermatophytes. Several nucleotide databases are available to compare sequences and thus identify isolates; however, these databases often contain mislabeled sequences that impair sequence-based identification. We evaluated five of these databases on a clinical isolate panel. We selected 292 clinical dermatophyte strains that were prospectively subjected to an ITS2 nucleotide sequence analysis. Sequences were analyzed against the databases, and the results were compared to clusters obtained via DNA alignment of sequence segments. The DNA tree served as the identification standard throughout the study. According to the ITS2 sequence identification, the majority of strains (255/292) belonged to the genus Trichophyton, mainly T. rubrum complex (n = 184), T. interdigitale (n = 40), T. tonsurans (n = 26), and T. benhamiae (n = 5). Other genera included Microsporum (e.g., M. canis [n = 21], M. audouinii [n = 10], Nannizzia gypsea [n = 3], and Epidermophyton [n = 3]). Species-level identification of T. rubrum complex isolates was an issue. Overall, ITS DNA sequencing is a reliable tool to identify dermatophyte species given that a comprehensive and correctly labeled database is consulted. Since many inaccurate identification results exist in the DNA databases used for this study, reference databases must be verified frequently and amended in line with the current revisions of fungal taxonomy. Before describing a new species or adding a new DNA reference to the available databases, its position in the phylogenetic tree must be verified. SN - 1098-660X UR - https://www.unboundmedicine.com/medline/citation/29491019/Nucleotide_Sequence_Database_Comparison_for_Routine_Dermatophyte_Identification_by_Internal_Transcribed_Spacer_2_Genetic_Region_DNA_Barcoding_ L2 - http://jcm.asm.org/cgi/pmidlookup?view=long&pmid=29491019 DB - PRIME DP - Unbound Medicine ER -