結核病仍是全球疾病和死亡的主要原因。雖然人均新發結核病例自2003年以來一直下降，耐多藥（MDR）和廣泛耐藥（XDR）的結核病例的突然增加為全球疾病控制帶來了新的威脅。結核分枝杆菌（MTB）北京株在過去十年越来越受重視，皆因其席捲亞洲，前蘇聯，和包括美國在內的好幾個地方。北京株在動物實驗中也表現出高毒性和耐多藥的傾向。目前結核菌廣泛耐藥定義為至少對異煙肼和利福平耐藥，再加上任何氟喹諾酮類，和至少一個二線藥物。我們對這種病菌的生物知識仍然有限。在這研究，我們為來自香港和福建五株MTB北京株進行了基因組測序，其中兩株的耐藥性遠超XDR標準 - “全耐藥“（TDR）的表型。五個北京株的比較基因組學為我們提供了在北京株的毒力相關基因的啟示。一個約4 KB大小的片段被找出来了，此片段是所有已知MTB中都没有的。我們討論了此片段對MTB進化的含義。當我們研究在北京耐藥株的獨特基因變化時發現，DNA修復和香葉醇降解有關連。我們還觀察到大的缺失（D）和截斷（T）的事件，顯著高於框移位（F）的突變。此外，在TDR菌株出現的FDT事件更頻繁地涉及到最佳生長和麻風分枝杆菌的基因組中保留的基因。這方面的証據表明，MTB通過缩减進化發展極端耐藥性。適應度的顯著降低也許解釋了TDR菌株的稀缺 。 / Tuberculosis (TB) remains one of the major causes of illness and death globally. Although the number of new TB cases per capita has been falling since 2003, the emergence of multidrug resistant (MDR) and extensively drug resistant (XDR) cases of TB poses new threat to the successful worldwide control of the disease (WHO, 2008; Iseman, 2007). The Beijing lineage of Mycobacterium tuberculosis (MTB) has received much attention over the past decade due to its prevalence throughout Asia, parts of the former Soviet Union, and several other geographical locations including the United States. The strain also demonstrated hypervirulence in animal models and an increased likelihood to develop multidrug resistance. The current definition of XDR in TB is defined as resistance to at least isoniazid and rifampicin, any fluoroquinolone, and with at least one of the three second-line drugs. Here we show that our knowledge of the biology of this pathogen is still limited. We performed genome sequencing and reported the complete genomes of five Beijing isolates from Hong Kong and Fujian, of which two were shown to have drug resistance that is far beyond the current XDR standard - a "Totally Drug Resistance" (TDR) phenotype. Comparative genomics of the five Beijing isolates provided us insights into the virulence-related genes in the Beijing family. A distinct region of about 4 kb in size that are absent in all known complete genomes of MTB was also identified. The evolutionary implications of this region were discussed. When we investigated the unique genetic changes in drug resistant Beijing strains, a correlation to DNA repair and geraniol degradation was implicated. We have also observed that the big deletions (D) and truncations (T) events were significant higher when compare with frameshift (F) mutations. Moreover, the FDT events in TDR strains were more frequently found in genes that are involved in growth attenuation and retained in the genome of the Mycobacterium leprae. This evidence suggests that MTB develops its extreme drug resistance through the reductive evolution. The significant decrease in the fitness may explain the rareness of TDR strains. / Detailed summary in vernacular field only. / Leung, Ka Kit. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 93-108). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese. / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Epidemiology - a ubiquitous threat --- p.1 / Chapter 1.2 --- Surviving the Hell --- p.3 / Chapter 1.3 --- Relatives of M. tuberculosis --- p.4 / Chapter 1.4 --- The age of M. tuberculosis --- p.5 / Chapter 1.5 --- Characteristics of Beijing strains --- p.6 / Chapter 1.6 --- Drug resistance --- p.7 / Chapter 1.7 --- Genome sequencing --- p.9 / Chapter 1.7.1 --- Conventional sequencing --- p.9 / Chapter 1.7.2 --- High-throughput sequencing --- p.10 / Chapter 1.8 --- Sequence assembly --- p.11 / Chapter 1.8.1 --- De novo assembly --- p.11 / Chapter 1.8.2 --- Reference mapping --- p.12 / Chapter Chapter 2 --- Materials and Methods --- p.14 / Chapter 2.1 --- Sample preparation --- p.14 / Chapter 2.2 --- DNA extraction and genome sequencing --- p.18 / Chapter 2.3 --- Gap filling and finishing --- p.20 / Chapter 2.3.1 --- In silico gap verification --- p.20 / Chapter 2.3.2 --- Comparison among different reference mapped contigs --- p.24 / Chapter 2.3.3 --- Experimental work --- p.26 / Chapter 2.4 --- Bioinformatics analysis --- p.27 / Chapter 2.4.1 --- Genome annotation --- p.27 / Chapter 2.4.2 --- Phylogeny analysis --- p.27 / Chapter 2.4.3 --- Variation analysis --- p.28 / Chapter 2.4.4 --- In silico functionality analyses --- p.29 / Chapter Chapter 3 --- Results --- p.30 / Chapter 3.1 --- Genome features of M. tuberculosis Beijing genotype strains --- p.30 / Chapter 3.2 --- Phylogeny of M. tuberculosis Beijing genotype strains --- p.36 / Chapter 3.3 --- Evolutionary implications of a 4kb-insertion in Beijing strains --- p.40 / Chapter 3.4 --- Beijing family specific gene variations --- p.48 / Chapter 3.5 --- Drug resistance --- p.52 / Chapter Chapter 4 --- Discussions --- p.75 / Chapter 4.1 --- 4kb insertion, a potential bridge to our knowledge gap --- p.75 / Chapter 4.2 --- Beijing common and Beijing drug resistant specific variations --- p.77 / Chapter 4.3 --- Regions of deletion --- p.79 / Chapter Chapter 5 --- Conclusions --- p.82 / Chapter Chapter 6 --- Future Work --- p.84 / Chapter 6.1 --- Compensatory mutation study --- p.84 / Chapter 6.1.1 --- Database construction for drug resistance compensatory mutations --- p.85 / Chapter 6.2 --- Non-protein coding region study --- p.92
| Identifer | oai:union.ndltd.org:cuhk.edu.hk/oai:cuhk-dr:cuhk_328078 |
| Date | January 2012 |
| Contributors | Leung, Ka Kit, Chinese University of Hong Kong Graduate School. Division of Biomedical Sciences. |
| Source Sets | The Chinese University of Hong Kong |
| Language | English, Chinese |
| Detected Language | English |
| Type | Text, bibliography |
| Format | electronic resource, electronic resource, remote, 1 online resource ([8], 121 leaves) : ill. (chiefly col.), col. map |
| Rights | Use of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/) |
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