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Comprehensive analysis of pathogenic bacteria in environmental samples using metagenomic approaches [an abstract of entire text]

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Title: Comprehensive analysis of pathogenic bacteria in environmental samples using metagenomic approaches [an abstract of entire text]
Other Titles: メタゲノム解析による環境中の病原性バクテリアの総合解析 [全文の要約]
Authors: BORTHONG, Jednipit Browse this author
Issue Date: 25-Sep-2018
Abstract: Waterborne diseases caused by pathogenic bacteria are a concern for public health worldwide. The lack of information of overall pathogens in aquatic environments makes it difficult to establish a strategy for the prevention of pathogen infections from water. Recently, metagenomic analysis combined with the ability of next generation sequencing technology can be used for the direct detection of pathogenic bacteria in water samples. One important process in metagenomic studies is the taxonomy classification of bacteria. Several database search methods have been used for taxonomy classification of bacteria using bioinformatics algorithms, such as blastn searches. In this thesis, the different database search methods for taxonomy classification of bacteria were compared for their diagnostic ability in detecting pathogens. By focusing on a specific bacterium species, L. pneumophila, the detection results of each search method were compared with the results from L. pneumophila-specific nested PCR. The results demonstrate that database search methods using complete genomes as reference sequences showed numerous false positives and had a potential problem with specificity. On the other hand, database search methods using long specific marker genes as reference sequences provided the best agreement of detection with L. pneumophila-specific PCR. Subsequently, database search methods using specific marker genes were selected to analyze pathogenic bacteria in environmental samples collected from urban and rural areas in Thailand. The results indicated that pathogenic species from the genera Aeromonas, Bordetella, Burkholderia, Mycobacterium, Pseudomonas, and Ralstonia were common in these samples; they were detected in all samples with high abundance. In addition, the profiles of antibiotic resistance genes (ARGs) in each sample group were analyzed using a blastn search against the ARG database which contains reference sequences of ARGs. The results showed that the abundance of reads identified as ARGs in samples collected from urban areas were higher than those in samples collected from rural areas; indicating that urban environments may serve as reservoirs for the circulation of antibiotic resistant bacteria in the environment. In conclusion, metagenomic analysis could be a useful tool to establish a strategy for the prevention of waterborne diseases.
Description: この博士論文全文の閲覧方法については、以下のサイトをご参照ください。
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Conffering University: 北海道大学
Degree Report Number: 甲第13294号
Degree Level: 博士
Degree Discipline: 獣医学
Examination Committee Members: (主査) 教授 大橋 和彦, 教授 鈴木 定彦, 准教授 中島 千絵, 准教授 中尾 亮, 特任准教授 大森 亮介
Degree Affiliation: 獣医学研究科(獣医学専攻)
Type: theses (doctoral - abstract of entire text)
Appears in Collections:課程博士 (Doctorate by way of Advanced Course) > 獣医学院(Graduate School of Veterinary Medicine)
学位論文 (Theses) > 博士 (獣医学)

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