10.1371/journal.pone.0098110 Xuan Wang Xuan Wang Yong-Feng Fu Yong-Feng Fu Rui-Ying Wang Rui-Ying Wang Li Li Li Li Ya-Hui Cao Ya-Hui Cao Yan-Qiong Chen Yan-Qiong Chen Hua-Zhen Zhao Hua-Zhen Zhao Qiang-Qiang Zhang Qiang-Qiang Zhang Ji-Qin Wu Ji-Qin Wu Xin-Hua Weng Xin-Hua Weng Xun-Jia Cheng Xun-Jia Cheng Li-Ping Zhu Li-Ping Zhu Identification of Clinically Relevant Fungi and <i>Prototheca</i> Species by rRNA Gene Sequencing and Multilocus PCR Coupled with Electrospray Ionization Mass Spectrometry Public Library of Science 2014 Computational biology microbiology Medical microbiology Microbial pathogens molecular biology Molecular biology techniques Sequencing techniques Sequence analysis Mycology organisms fungi yeast Diagnostic medicine Infectious diseases Fungal diseases clinically rrna sequencing multilocus pcr coupled electrospray ionization spectrometry 2014-05-16 02:54:32 Dataset 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 <div><p>Background</p><p>Multilocus 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.</p><p>Methods</p><p>One-hundred and twelve strains and isolates of clinically important fungi and <i>Prototheca</i> 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.</p><p>Results</p><p>For 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 <i>Prototheca</i> 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.</p><p>Conclusions</p><p>rRNA 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.</p></div>