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postgraduate thesis: Internal transcribed spacer as the DNA barcode for pathogenic fungi

TitleInternal transcribed spacer as the DNA barcode for pathogenic fungi
Authors
Issue Date2014
PublisherThe University of Hong Kong (Pokfulam, Hong Kong)
Citation
Cheung, M. [張微]. (2014). Internal transcribed spacer as the DNA barcode for pathogenic fungi. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5303892
AbstractIdentification of pathogenic fungi isolated from clinical specimens in clinical microbiology laboratories is primarily based on observing fungal phenotypic structures under the microscope and performing biochemical tests for fungal cultures. This conventional method is very time-consuming and labor-dependent. It usually requires several weeks for the fungi to grow sufficiently on culture media, and the identification processes on fungal phenotypic structure rely very much on experienced staff. Therefore, a more accurate and rapid method for pathogenic fungal identification is necessary for clinical laboratories to get abreast of modern development. Gene sequencing and phylogenetic analysis targeting the internal transcribed spacer (ITS) region in the fungal genomes are the most commonly used molecular methods for fungal identification. Because of the optimal inter and intra-species variation property of the ITS region, it can act as the DNA barcode to identify fungi to the species level. In this study, 33 clinical fungal isolates were identified by both phenotypic method and ITS sequencing. The results showed that 23 isolates were successfully identified to thespecies level by both phenotypic and molecular methods. Moreover, five isolates were only identified to the genus level by phenotypic method, but they could be successfully identified to the species level by ITS sequencing. However, five isolates have not been differentiated because there were mismatched results from phenotypic and sequencing methods. It may be due to the limitation of sequencing method on some fungal species. Building up a more comprehensive database or setting up a standard platform to guide the molecular process may help improve the performance of molecular method. To conclude, molecular method is a rapid and reliable way for fungal identification because ITS region acts as the DNA barcode for pathogenic fungi.
DegreeMaster of Medical Sciences
SubjectPathogenic fungi - Identification
Dept/ProgramMedical Sciences
Persistent Identifierhttp://hdl.handle.net/10722/206495

 

DC FieldValueLanguage
dc.contributor.authorCheung, Mei-
dc.contributor.author張微-
dc.date.accessioned2014-11-03T23:14:50Z-
dc.date.available2014-11-03T23:14:50Z-
dc.date.issued2014-
dc.identifier.citationCheung, M. [張微]. (2014). Internal transcribed spacer as the DNA barcode for pathogenic fungi. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5303892-
dc.identifier.urihttp://hdl.handle.net/10722/206495-
dc.description.abstractIdentification of pathogenic fungi isolated from clinical specimens in clinical microbiology laboratories is primarily based on observing fungal phenotypic structures under the microscope and performing biochemical tests for fungal cultures. This conventional method is very time-consuming and labor-dependent. It usually requires several weeks for the fungi to grow sufficiently on culture media, and the identification processes on fungal phenotypic structure rely very much on experienced staff. Therefore, a more accurate and rapid method for pathogenic fungal identification is necessary for clinical laboratories to get abreast of modern development. Gene sequencing and phylogenetic analysis targeting the internal transcribed spacer (ITS) region in the fungal genomes are the most commonly used molecular methods for fungal identification. Because of the optimal inter and intra-species variation property of the ITS region, it can act as the DNA barcode to identify fungi to the species level. In this study, 33 clinical fungal isolates were identified by both phenotypic method and ITS sequencing. The results showed that 23 isolates were successfully identified to thespecies level by both phenotypic and molecular methods. Moreover, five isolates were only identified to the genus level by phenotypic method, but they could be successfully identified to the species level by ITS sequencing. However, five isolates have not been differentiated because there were mismatched results from phenotypic and sequencing methods. It may be due to the limitation of sequencing method on some fungal species. Building up a more comprehensive database or setting up a standard platform to guide the molecular process may help improve the performance of molecular method. To conclude, molecular method is a rapid and reliable way for fungal identification because ITS region acts as the DNA barcode for pathogenic fungi.-
dc.languageeng-
dc.publisherThe University of Hong Kong (Pokfulam, Hong Kong)-
dc.relation.ispartofHKU Theses Online (HKUTO)-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.rightsThe author retains all proprietary rights, (such as patent rights) and the right to use in future works.-
dc.subject.lcshPathogenic fungi - Identification-
dc.titleInternal transcribed spacer as the DNA barcode for pathogenic fungi-
dc.typePG_Thesis-
dc.identifier.hkulb5303892-
dc.description.thesisnameMaster of Medical Sciences-
dc.description.thesislevelMaster-
dc.description.thesisdisciplineMedical Sciences-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.5353/th_b5303892-

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