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研究生：	劉向寧 Leaw, Shiang-Ning
論文名稱：	以核糖體RNA基因內轉錄區序列及寡核苷酸陣列晶片鑑定臨床酵母菌 Identification of Medically Important Yeasts by Sequence Analysis of the Internal Transcribed Spacer Regions and by an Oligonucleotide Array
指導教授：	張憲彰 Chang, Hsien-Chang 張長泉 Chang, Tsung-Chain
學位類別：	博士 Doctor
系所名稱：	工學院 - 醫學工程研究所 Institute of Biomedical Engineering
論文出版年：	2007
畢業學年度：	95
語文別：	英文
論文頁數：	92
中文關鍵詞：	核糖體RNA基因內轉錄區、酵母菌、寡核苷酸晶片、序列分析
外文關鍵詞：	Internal transcribed spacer regions, oligonucleotide array, sequence analysis, yeast
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近年來因低免疫力病人的增加，由酵母菌所引起的感染有顯著增加的趨勢。除了一些較常分離到的菌外，不常見的菌種如Pichia, Rhodotorula, Trichosporon, 及Saccharomyces近年來也有被報導引起人類感染。因此正確且快速的菌種鑑定，對病人的治療有很大的幫助。本研究之目的，在評估以核糖體RNA基因內轉錄區(internal transcribed spacer regions, ITS)序列鑑定酵母菌之可行性，並發展一快速、可靠且可鑑定許多種酵母菌之寡核苷酸晶片(oligonucleotide array)。本研究第一部份主要評估以ITS序列鑑定臨床上引起感染之酵母菌的可行性。以PCR將373株(86種酵母菌)的ITS1及ITS2區域增殖並定序。這373菌株中總共包含299株參考菌株(reference strains)及74臨床分離株(clinical isolates)。將這些序列與GenBank基因資料庫裡的參考菌株以BLAST (Basic Local Alignment Search Tool)進行序列比對，以確定是否能以ITS序列鑑定酵母菌。結果顯示以ITS1及ITS2序列鑑定酵母菌的正確率(identification rate)分別為96.8% (361/373)及99.7% (372/373)。第二部分研究要探討以不同方式標誌的PCR產物與正向探針(sense probe)或反向探針(antisense probe)進行雜合反應時，對訊號強弱的影響，以供發展晶片的基礎。發現在雙股引子皆以毛地黃素標誌之PCR產物雜合反應所呈現的訊號最強。另外有時正向探針的雜合反應較強，有時則以反向探針較強，無法事先預測，只能由實驗得知，顯示目標基因與探針之間會因探針長度與序列的不同或二級結構之不同，而產生不同的雜合效率，來放大目標基因以進行雜合反應。第三部分研究是以ITS序列為基礎發展寡核苷酸晶片以鑑定77種(16屬)臨床相關的酵母菌。首先利用一對標誌有毛地黃素之真菌專一性引子(fungus-specific universal primers)將ITS區域增殖後，與固定在尼龍薄膜上的種專一性探針(species-specific probe)進行雜合反應，以鑑定菌種。本實驗測試了452株酵母菌 (419株目標菌株及33株非目標菌株)，晶片的靈敏度(sensitivity)及特異性(specificity)分別為100%及97%，而檢測極限(detection limit)為10 pg DNA。以此晶片直接檢測42個陽性血瓶，其鑑定率為100%。本研究顯示，以ITS序列及DNA晶片鑑定酵母菌兼具快速及正確之特性，是一個具有發展潛力的檢驗工具。不管是ITS定序或以晶片鑑定皆可在24小時內完成。

Infections caused by yeasts have increased in recent decades due to the increasing population of immunocompromised patients. In addition to Candida spp., infections caused by less common species such as Pichia, Rhodotorula, Trichosporon, and Saccharomyces have been widely reported. Accurate and rapid identification of yeast pathogens is important for appropriate treatment of patients with antifungal agents. The objectives of this study were to evaluate the feasibility of using the sequence of ribosomal DNA internal transcribed spacer (ITS) regions and an oligonucleotide array to identify clinically important yeasts. The first part of this thesis evaluated the feasibility of ITS sequencing for yeast identification. Both ITS1 and ITS2 regions of 373 strains (86 species) including 299 reference strains and 74 clinical isolates were amplified by PCR and sequenced. The sequences were compared to reference data available at the GenBank database using BLAST (Basic Local Alignment Search Tool) for species determination. The rates of correct identification by ITS1 and ITS2 sequence analysis were 96.8% (361/373) and 99.7% (372/373), respectively. The second part of this thesis was to evaluate primer labeling (one or both primers) and the use of sense or antisense probe on the hybridization signal. It was found that labeling of both primers produced, under most conditions, stronger hybridization signal. However, the effect of using sense or antisense probe on hybridization signal was not predictable. The third part of this thesis was to develop an oligonucleotide array to identify 77 species (16 genera) of clinically relevant yeasts based on the ITS sequence. The ITS regions were amplified by PCR with a pair of fungus-specific primers, followed by hybridization of the digoxigenin-labeled PCR product to a panel of oligonucleotide probes immobilized on nylon membrane for species identification. A collection of 452 yeast strains (419 target and 33 nontarget strains) was tested, and a sensitivity of 100% and a specificity of 97% were obtained by the array. The detection limit of the array was 10 pg of yeast genomic DNA per assay. In addition, 42 yeast-positive blood cultures were analyzed by the oligonucleotide array, and all specimens were correctly identified. In conclusion, yeast identification by both methods (sequence analysis and oligonucleotide array) is highly reliable and can be used as an alternative to the conventional identification methods. The whole procedure can be finished within 24 h starting from isolated colonies.

Abstract..............................I
Chinese abstract..............................III
Acknowledgement..............................V
Table of Contents..............................VII
List of Figures..............................XI
List of Tables..............................XII

Chapter 1 Introduction..............................1
1-1  Yeast infections..............................1
1-2  Internal transcribed spacer regions (ITS)..............................3
1-3  Identification of yeasts..............................5
1-4  Objectives..............................7

Chapter 2 Identification of yeasts by sequences analysis of the internal transcribed spacer regions..............................9
2-1  The aim of this study..............................9
2-2  Materials..............................9
2-2.1  Yeast strains..............................9
2-2.2  DNA preparation..............................10
2-2.3  Amplification and sequencing of the ITS regions..............................11
2-2.4  Identification of yeast by ITS sequencing..............................21
2-3 Results..............................22
2-3.1  Identification of reference strains by ITS sequence analysis..............................22
2-3.2  Identification of clinical isolates by ITS sequence analysis..............................27
2-4 Discussion..............................28

Chapter 3  Evaluation of the signal intensity produced by hybridization of various labeled PCR products to sense and antisense probes..............................31
3-1  The aim of this study..............................31
3-2  Materials..............................31
3-2.1  Yeast strains..............................31
3-2.2  DNA preparation..............................31
3-2.3  Amplification for array hybridization..............................32
3-2.4  Design of oligonucleotide probes..............................33
3-2.5  Fabrication of oligonucleotide arrays..............................34
3-2.6  Hybridization procedures..............................37
3-2.7  Data analysis..............................38
3-3 Results..............................39
3-3.1  ITS amplification by using primer set P1 (ITS1 + ITS4-dig)	..............................39
3-3.2  ITS amplification by using primer set P2 (ITS1-dig + ITS4)..............................39
3-3.3  ITS amplification by using primer set P3 (ITS1-dig + ITS4-dig)..............................40
3-3.4  ITS amplification by using primer set P4 (ITS1-P + ITS4-dig)	..............................40
3-3.5  ITS amplification by using primer set P5 (ITS1-dig + ITS4-P)..............................	40
3-4 Discussion..............................43
Chapter 4  Identification of yeasts by an oligonucleotide array..............................45
4-1  The aim of this study..............................45
4-2  Materials..............................45
4-2.1  Yeast strains..............................45
4-2.2  DNA preparation..............................56
4-2.3  Amplification for array hybridization..............................56
4-2.4  Design of oligonucleotide probes..............................56
4-2.5  Fabrication of oligonucleotide arrays..............................64
4-2.6  Hybridization procedures..............................64
4-2.7  Analysis of discrepant strains..............................65
4-2.8  Limit of detection of the array..............................66
4-3 Results..............................67
4-3.1  Oligonucleotide probe development..............................67
4-3.2  Identification of reference strains by the array..............................68
4-3.3  Identification of clinical isolates by the array..............................71
4-3.4  Limit of detection of the array..............................72
4-4 Discussion..............................72

Chapter 5  Identification of clinical specimens by an oligonucleotide array..............................76
5-1  Blood specimens..............................76
5-2  Preparation of clinical specimens..............................76
5-2.1  DNA preparation from blood specimens..............................76
5-2.2  DNA preparation from nail specimen..............................77
5-3  Amplification of clinical specimens for array hybridization..............................78
5-4  Results..............................78
5-5  Discussion..............................80

Chapter 6  Conclusions..............................81

References..............................84

Publications..............................90
                                    

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