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Identification of clinically relevant fungi and prototheca species by rRNA gene sequencing and multilocus PCR coupled with electrospray ionization mass spectrometry
- Source :
- PLoS ONE, Vol 9, Iss 5, p e98110 (2014), PLoS ONE
- Publication Year :
- 2014
- Publisher :
- Public Library of Science (PLoS), 2014.
-
Abstract
- Background 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. Methods One-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. Results 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 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. Conclusions 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.
- Subjects :
- Spectrometry, Mass, Electrospray Ionization
Sequence analysis
Electrospray ionization
Genes, Fungal
lcsh:Medicine
Mycology
Prototheca
Genes, Plant
Microbiology
Polymerase Chain Reaction
DNA sequencing
law.invention
Diagnostic Medicine
Aspergillus nidulans
law
Medicine and Health Sciences
Molecular Biology Techniques
Sequencing Techniques
lcsh:Science
Microbial Pathogens
Molecular Biology
Gene
Polymerase chain reaction
Genetics
Multidisciplinary
biology
lcsh:R
Organisms
Fungi
Fungal Diseases
Fungal genetics
Biology and Life Sciences
Computational Biology
Sequence Analysis, DNA
Ribosomal RNA
biology.organism_classification
Yeast
Infectious Diseases
Medical Microbiology
RNA, Ribosomal
lcsh:Q
Sequence Analysis
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 9
- Issue :
- 5
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....7ed49d3ff73bd85526c0679e4dd30e79