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研究生:李美鳳
研究生(外文):Mei-Feng Lee
論文名稱:革蘭氏陰性桿菌第一類型integron之研究
論文名稱(外文):Study on class 1 integron among Gram-negative bacteria
指導教授:彭健芳
指導教授(外文):Chien-Fang Peng
學位類別:博士
校院名稱:高雄醫學大學
系所名稱:醫學研究所
學門:醫藥衛生學門
學類:醫學學類
論文種類:學術論文
論文出版年:2009
畢業學年度:97
語文別:中文
論文頁數:222
中文關鍵詞:第一類型integron基因卡匣革蘭氏陰性桿菌
外文關鍵詞:class 1 integrongene cassetteGram-negative bacteria
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Integron基因體是抗藥性菌株獲得、散佈和保存抗藥基因重要的機制之一。革蘭氏陰性菌常藉著可移動的DNA元素從外界獲得抗藥基因用以對抗抗生素的作用。為避免因抗生素過度使用而造成抗藥菌株增加及抗藥基因散佈,抗藥性integron基因體在不同菌種間分佈的研究及了解抗藥基因的特性是刻不容緩。本研究選擇具有伺機致病及人畜共通感染特性的革蘭氏陰性桿菌進行抗藥性integron基因體的篩檢以及基因卡匣的分析,以了解存在這些革蘭氏陰性桿菌中integron基因體所帶的抗藥基因之特性。
於1997-2006年間,依據研究項目,本研究分別收集自南台灣地區醫學中心歸屬於人畜共通感染的革蘭氏陰性菌以Serratia marcescens、Salmonella enterica serovar Choleraesuis (S. Choleraesuis)、Aeromonas spp. (包含Aeromonas hydrophila、Aeromonas sobria、Aeromonas caviae 及Aeromonas veronii)、Pseudomonas spp.(包括Pseudomonas aeruginosa及Pseudomonas putida) 和Acinetobacter spp.(包括Acinetobacter baumannii及Acinetobacter haemolyticus)為主軸,再配合其他致病菌如Stenotrophomonas maltophilia 、Chryseobacterium spp.、Burkholderia cepacia、Enterobacter cloacae、Escherichia coli 、Klebsiella pneumoniae、Sphingobacterium spiritivorum等為研究的材料。試驗的菌株分別來自人體血液、尿液、痰液、糞便及部分動物血液等臨床檢體。其中,S. Choleraesuis 包括人體和動物的菌株。
首先利用PCR技術檢測試驗菌株帶有class 1、2和3 integron的基因體的盛行率。由於沒有發現class 2和3 integron存在,所以針對class 1 integron基因體陽性的菌株進一步利用基因卡匣增幅引子對5’-CS和3’-CS,分析class 1 integron中的基因卡匣及其抗藥基因序列組合特性。而藥物敏感性試驗的結果顯示試驗菌株具有class 1 integron,其抗藥比例比不具class 1 integron的試驗菌株偏高。質體DNA抽取、脈衝式電泳分別與南方雜交技術分析的結果,得知class 1 integron可存在質體或染色體,且抗藥基因卡匣可與class 1 integron同時存在質體或染色體。根據conjugation experiments的分析,位在質體上的class 1 integron基因體的抗藥基因隨著質體轉移的能力與菌種的差異有關。Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR)技術,用於分析具有相同基因卡匣排列的菌種其遺傳同源相關性。利用inverse PCR技術,用於分析具有奇特3’-CS端的class 1 integron和複雜型class 1 integron。
在本研究中,發現許多新型且具臨床重要意義的基因卡匣,包括aminoglycosides、trimethoprim、sulfamethoxazole、β-lactam antibiotics、chloramphenicol、rifampin、quarternary compounds及erythromycin等藥物的抗藥型基因卡匣和一些未知功能的開放性讀碼區ORFs (open reading frames),依其基因排列可有30種不同的組合變化。其中,dfrA12-orfF -aadA2之基因卡匣排列,最常見於分析的菌株。尤其是來自動物所分離出之S. Choleraesuis菌株所攜帶的比例高達71.4%,即使人類分離株也有69.4%。 A. hydrophila菌株有17.9% 呈現dfrA12- orfF -aadA2基因卡匣排列組合。而在S. marcescens (36.6%)則是出現頻率第二多的基因卡匣組合。經由質體DNA分析、接合生殖實驗與南方雜交技術,基因卡匣排列組合為dfrA12- orfF -aadA2之基因卡匣不僅可以位在染色體上,也可以位在接合性質體上,這也許說明了這類基因卡匣迅速散佈之原因。基因卡匣排列為aacA4-catB8-aadA1之組合在A. baumannii與P. aeruginosa和P. putida菌株最為常見。Acinetobacter spp.和Pseudomonas spp.中的基因卡匣大部分都位在染色體上,這些菌株不具有接合性質體。基因卡匣排列為dfrA1-UN 之組合,只出現於S. marcescens及S. Choleraesuis菌株。基因卡匣排列組合為dfr2d-catB3-aadA1(GenBank accession number AY751518)則只在A. hydrophila及A. sobria菌株中找到。aac(6'')-II-blaOXA-21-catB3 (GenBank accession number DQ993182)基因卡匣排列組合,在A. hydrophila及A. veronii菌株中出現。基因卡匣排列為arr-3-aacA4(GenBank accession number DQ174291)組合首次在A. haemolyticus找到。另外,未知功能的讀碼區orfUN1及orfUN2和基因卡匣排列組合arr-2-aacA4-dfrA1-orfC及 aadA1-aac(6'')-II(GenBank accession number DQ402099)只出現在A. hydrophila。 dfrA5-ereA2(GenBank accession number EU085376)在A. sobria找到,而blaOXA-31-aadA5(GenBank accession number EF067840)和blaIMP-8-aadB-cmlA(GenBank accession number EF394441)則在S. marcescens發現。此外,分別在S. Choleraesuis和A. hydrophlila發現三個新型的基因卡匣如aadA1-like(GenBank accession number EU834941)、aadA22(GenBank accession number AY550883)和aadA4a(GenBank accession number DQ536502)基因。其中,aadA22為一抗藥型的基因卡匣,而addA1-like及aadA4a則不表現其抗藥性的特徵。再者,基因卡匣 aadA2、aadB、catB、dfrA12和orfF大都位在接合性質體上,可以水平轉移至E. coli接受菌株中。
同時,本研究也首次從南台灣所分離具imipenem抗藥性的P. aeruginosa 、A. baumanni 、A. hemolyticus和S. marcescens中發現metallo-ß-lactamases (MBLs)基因blaVIM-3 (GenBank accession number EU090799)、blaVIM-11(GenBank accession number DQ022682 和 DQ835309)、blaIMP-8 (GenBank accession number EF394441)及blaIMP-24(GenBank accession number EF192154)基因,其中blaVIM-3 、blaVIM-11和blaIMP-8更是以基因卡匣之形式呈現。blaVIM-11基因卡匣不只存在P. aeruginosa 與A. baumanni ,更首次在A. hemolyticus中找到,說明blaVIM-11 (屬於blaVIM-11-a)基因是南台灣地區carbapenem抗藥性臨床菌株間散佈的重要因子。
另外,經由inverse PCR技術及序列分析13株具有與sul3基因相關之S. Choleraesuis和兩株基因卡匣增幅陰性的P. aeruginosa,得到基因卡匣排列組合分別為sat-psp-aadA2-cml1-aadA1-like-qacH-tnp-sul3 (GenBank accession number EU834941) 變異型class 1 integron 和intI1-sul3-orf5 (GenBank accession number EU930362) 缺陷型class 1 integron架構,這兩種都是屬於奇特3’-CS端的class 1 integron。同時發現以dfrA19基因串聯兩個class 1 integron而形成的complex class 1 integron存在S. marcescens中,而complex class 1 integron 的確可以擴增細菌的抗藥性種類。特殊的integron基因體架構存在是細菌產生抗藥性擴增的重要機制之一。
總之,就本研究所分析之革蘭氏陰性菌中,找到許多新型且重要的基因卡匣,也發現基因卡匣組合具有多變性,更發現抗藥型基因以基因卡匣或基因卡匣排列組合型式的如blaVIM-3 、blaVIM-11和dfrA12-orfF -aadA2等可重複出現在不同菌種中。可見基因卡匣的獲得或移出,不因菌種不同而有差異。依據本研究的實驗結果,推論環境中存在著特異交換重組性的基因卡匣共通資源庫,透過integron系統讓不同的菌種,在適當的抗生素選擇壓力下,擷取所需使之生存的基因卡匣。未來,應更深入瞭解特殊的integron基因體架構形成的機轉與抗藥型基因卡匣的相關性,除提供臨床用藥參考外,發展拮抗integron系統的計畫也需一併進行。
目次 頁次

中文摘要 5

英文摘要 10

背景說明

一、 前言 15

二、 Integron之種類與構造 17

三、 基因卡匣之構造及種類 20

四、 抗藥基因水平轉移機制 21

五、 台灣地區相關研究 21

研究目的 25

研究工作項目 27

一、 Class 1 integron相關之基因卡匣分析
(Class 1 integron-associated gene cassettes analysis)
(一) 前言 27

(二) 材料與方法 32
1. 菌種收集及鑑定
2. 藥物敏感性試驗
3. Integron的篩檢及Class 1 integron基因卡匣的偵測與定序分析
4. Class 1 integron基因體所在位置分析
5. 抗藥基因卡匣之抗藥性表現分析
6. 攜帶增幅片段之轉型菌株抗藥性之表現分析
7. 新型基因卡匣之分析
(三) 結果 51

(四) 討論 57

二、 基因卡匣排列之分子多變性
(Molecular diversity of gene cassette array)

(一) 前言 66

(二) 材料與方法 66
1. 基因卡匣的PCR增幅及定序分析
2. Class 1 integron基因體所在位置分析
3. 抗藥基因卡匣之抗藥性表現分析
4. 攜帶增幅片段之轉型菌株抗藥性之表現分析
5. 新型基因卡匣排列組合之分析
6. Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR)

(三) 結果 69

(四) 討論 73

三、 Class 1 integron相關之MBLs基因卡匣分析
(Analysis of class 1 integron-associated MBLs)

(一) 前言 77

(二) 材料與方法 84
1. 菌株之分離與鑑定
2. 藥物敏感性試驗
3. 偵測Metallo-β-lactamases (MBLs)之表現
4. Class 1 integron 和 MBLs 基因之PCR增幅與定序分析
5. Class 1 integron 及MBLs基因所在位置分析
6. Enterobacterial repetitive intergenic consensus PCR(ERIC-PCR)
7. 抗藥基因卡匣之抗藥性表現分析
8. 攜帶增幅片段之轉型菌株抗藥性之表現分析

(三) 結果 88

(四) 討論
91
四、 奇特3’端的class 1 integron 之分析
(Analysis of class 1 integron with unusual 3’- end)

(一) 前言 95

(二) 材料與方法 97
1. 菌株收集
2. 藥物敏感性試驗
3. Genomic DNA之製備
4. Class 1 integron之3’CS端變異分析
5. PCR及inverse PCR產物的純化
6. 核酸自動定序分析
7. 基因序列之電腦分析
8. Class 1 integron 基因所在位置分析
9. Nucleotide sequence accession number

(三) 結果 105

(四) 討論
107
五、 複雜型之 class 1 integron 分析
(Analysis of complex class 1 integron)

(一) 前言 109

(二) 材料與方法 110
1. 具CTX抗藥性之Serratia marcescens菌株的分離
2. 藥物敏感性試驗
3. Serratia marcescens 菌株內class 1 integron與CTX-M基因結構鄰近周邊之分子序列分析
4. Class 1 integron 和blaCTX-M-3基因所在位置分析
5. PCR產物之選殖
(三) 結果 120

(四) 討論 122

總結 125

本論文對學術及臨床的展望 128

參考文獻 129

附錄

一、附表 149

二、附圖 164

三、 Publications 181
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