Evaluation of nucleic acid sequencing of the D1/D2 region of the large subunit of the 28S rDNA and the internal transcribed spacer region using SmartGene IDNS [corrected] software for identification of filamentous fungi in a clinical laboratory

The Journal of Molecular Diagnostics : JMD
Nicole P KwiatkowskiSean X Zhang

Abstract

Filamentous fungal infections have recently increased because of the increasing numbers of immunocompromised hosts. In this study, we evaluated DNA sequencing of the D1/D2 region of the large subunit of the 28S ribosomal RNA gene and the internal transcribed spacer (ITS) region using SmartGene (SG; SmartGene Inc., Raleigh, NC) for the identification of a broad range of commonly encountered filamentous fungi. The SG proofreaders were used to upload, align, and edit fragments, and the resultant sequences were interpreted using the quality-controlled SG database. The results were compared with reference identifications using conventional phenotypic methods or ITS DNA sequences obtained from GenBank if phenotypic identifications were inconclusive. A total of 146 clinical isolates were included in this study, representing 49 different genera. The overall agreements of the D1/D2 and the ITS sequencing methods to reference identification were 97.2% (95% CI, 93.1% to 98.9%) and 97.7% (95% CI, 92.8% to 99.4%), respectively. Of the 146 isolates, 18 (12.3%) did not amplify using the ITS universal primers after repeated attempts and, therefore, could not be sequenced using this target. Correct identification was achieved for 100% (95% CI, ...Continue Reading

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Citations

Oct 28, 2015·International Journal of Molecular Sciences·Ying ZhaoPatrick C Y Woo
Nov 26, 2015·PloS One·Mateus Laguardia-NascimentoEdel Figueiredo Barbosa-Stancioli
Sep 7, 2014·Journal of Microbiological Methods·Guillaume DesoubeauxPhilippe Lanotte
Feb 6, 2017·Journal of Infection and Chemotherapy : Official Journal of the Japan Society of Chemotherapy·Hiram Villanueva-LozanoGloria M González
Aug 31, 2019·Brazilian Journal of Microbiology : [publication of the Brazilian Society for Microbiology]·Silvia Giannattasio-FerrazEdel Figueiredo Barbosa-Stancioli
May 30, 2017·Antonie van Leeuwenhoek·Romina Daiana FernandezRoxana Aragón
May 1, 2021·Pathogens·Kamila KuleszaŁukasz Stępień
Oct 12, 2016·Microbiology Spectrum·Sean X Zhang, Nathan P Wiederhold

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