Sequencer-Based Capillary Gel Electrophoresis (SCGE) Targeting the rDNA Internal Transcribed Spacer (ITS) Regions for Accurate Identification of Clinically Important Yeast Species.
Accurate species identification of Candida, Cryptococcus, Trichosporon and other yeast pathogens is important for clinical management. In the present study, we developed and evaluated a yeast species identification scheme by determining the rDNA internal transcribed spacer (ITS) region length types (LTs) using a sequencer-based capillary gel electrophoresis (SCGE) approach. A total of 156 yeast isolates encompassing 32 species were first used to establish a reference SCGE ITS LT database. Evaluation of the ITS LT database was then performed on (i) a separate set of (n = 97) clinical isolates by SCGE, and (ii) 41 isolates of 41 additional yeast species from GenBank by in silico analysis. Of 156 isolates used to build the reference database, 41 ITS LTs were identified, which correctly identified 29 of the 32 (90.6%) species, with the exception of Trichosporon asahii, Trichosporon japonicum and Trichosporon asteroides. In addition, eight of the 32 species revealed different electropherograms and were subtyped into 2-3 different ITS LTs each. Of the 97 test isolates used to evaluate the ITS LT scheme, 96 (99.0%) were correctly identified to species level, with the remaining isolate having a novel ITS LT. Of the additional 41 isolates for in silico analysis, none was misidentified by the ITS LT database except for Trichosporon mucoides whose ITS LT profile was identical to that of Trichosporon dermatis. In conclusion, yeast identification by the present SCGE ITS LT assay is a fast, reproducible and accurate alternative for the identification of clinically important yeasts with the exception of Trichosporon species.
Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.|Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
Xin
X
Hou
Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.|Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
Meng
M
Xiao
Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR- Pathology West, Westmead Hospital, University of Sydney, Darcy Road, Westmead, New South Wales, Australia.
Sharon C-A
SC
Chen
Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.|Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
He
H
Wang
Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.|Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
Li
L
Zhang
Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.|Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
Xin
X
Fan
Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.|Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
Zhi-Peng
ZP
Xu
Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.|Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
Jing-Wei
JW
Cheng
Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR- Pathology West, Westmead Hospital, University of Sydney, Darcy Road, Westmead, New South Wales, Australia.
Fanrong
F
Kong
Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.
Yu-Pei
YP
Zhao
Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.
Ying-Chun
YC
Xu
D002175:Candida / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D003454:Cryptococcus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D058893:DNA Barcoding, Taxonomic / Q000295:instrumentation / Q000379:methods*; D004271:DNA, Fungal / Q000235:genetics*; D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D019075:Electrophoresis, Capillary / Q000295:instrumentation / Q000379:methods; D005782:Gels; D006801:Humans; D060885:Multiplex Polymerase Chain Reaction / Q000295:instrumentation / Q000379:methods; D016533:Mycological Typing Techniques / Q000295:instrumentation / Q000379:methods*; D009181:Mycoses / Q000382:microbiology; D010802:Phylogeny; D014250:Trichosporon / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification
D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer; D005782:Gels