TY - DATA T1 - Identification of Clinically Relevant Fungi and Prototheca Species by rRNA Gene Sequencing and Multilocus PCR Coupled with Electrospray Ionization Mass Spectrometry PY - 2014/05/16 AU - Xuan Wang AU - Yong-Feng Fu AU - Rui-Ying Wang AU - Li Li AU - Ya-Hui Cao AU - Yan-Qiong Chen AU - Hua-Zhen Zhao AU - Qiang-Qiang Zhang AU - Ji-Qin Wu AU - Xin-Hua Weng AU - Xun-Jia Cheng AU - Li-Ping Zhu UR - https://plos.figshare.com/articles/dataset/Identification_of_Clinically_Relevant_Fungi_and_Prototheca_Species_by_rRNA_Gene_Sequencing_and_Multilocus_PCR_Coupled_with_Electrospray_Ionization_Mass_Spectrometry/1029651 DO - 10.1371/journal.pone.0098110 L4 - https://ndownloader.figshare.com/files/1501390 L4 - https://ndownloader.figshare.com/files/1501391 KW - Computational biology KW - microbiology KW - Medical microbiology KW - Microbial pathogens KW - molecular biology KW - Molecular biology techniques KW - Sequencing techniques KW - Sequence analysis KW - Mycology KW - organisms KW - fungi KW - yeast KW - Diagnostic medicine KW - Infectious diseases KW - Fungal diseases KW - clinically KW - rrna KW - sequencing KW - multilocus KW - pcr KW - coupled KW - electrospray KW - ionization KW - spectrometry N2 - BackgroundMultilocus PCR coupled with electrospray ionization mass spectrometry (PCR/ESI-MS) is a new strategy for pathogen identification, but information about its application in fungal identification remains sparse.MethodsOne-hundred and twelve strains and isolates of clinically important fungi and Prototheca species were subjected to both rRNA gene sequencing and PCR/ESI-MS. Three regions of the rRNA gene were used as targets for sequencing: the 5′ end of the large subunit rRNA gene (D1/D2 region), and the internal transcribed spacers 1 and 2 (ITS1 and ITS2 regions). Microbial identification (Micro ID), acquired by combining results of phenotypic methods and rRNA gene sequencing, was used to evaluate the results of PCR/ESI-MS.ResultsFor identification of yeasts and filamentous fungi, combined sequencing of the three regions had the best performance (species-level identification rate of 93.8% and 81.8% respectively). The highest species-level identification rate was achieved by sequencing of D1/D2 for yeasts (92.2%) and ITS2 for filamentous fungi (75.8%). The two Prototheca species could be identified to species level by D1/D2 sequencing but not by ITS1 or ITS2. For the 102 strains and isolates within the coverage of PCR/ESI-MS identification, 87.3% (89/102) achieved species-level identification, 100% (89/89) of which were concordant to Micro ID on species/complex level. The species-level identification rates for yeasts and filamentous fungi were 93.9% (62/66) and 75% (27/36) respectively.ConclusionsrRNA gene sequencing provides accurate identification information, with the best results obtained by a combination of ITS1, ITS2 and D1/D2 sequencing. Our preliminary data indicated that PCR/ESI-MS method also provides a rapid and accurate identification for many clinical relevant fungi. ER -