[ODP-044] Pythonを用いた薬剤耐性遺伝子媒介プラスミドの鳥瞰的表示とその系統解析
Plasmids carry multiple antimicrobial resistance (AMR) genes and confer a variety of genotypes and AMR phenotypes by transferring across bacteria. There are ready-to-use tools for classification of plasmids but no effective tools to analyze AMR plasmids phylogenetically have yet been established. Some software visualizes relationship of genes among some plasmids but similarity of multiple plasmids cannot be recognized well because of complicated visualization. To create a tool for phylogenic analysis of plasmids, we analyzed the similarity of multiple plasmids through mapping AMR genes on plasmids with Python.
We analyzed 274 plasmids carrying tunicamycin resistance gene (tmr) in this study. All of AMR genes were identified by BLASTn. In one spreadsheet, each gene of one plasmid was mapped onto each cell in one column and all plasmids were aligned side-by-side. When tmr of all plasmids was located in the middle of mapping, with bird’s-eye mapping and alignment using a new algorithm, we visualized similarities of types, positions, alignments and conformations of AMR genes among multiple plasmids in the spreadsheet. Incompatibility (Inc) groups of each plasmid were visualized in the spreadsheet and some plasmids possessing similar AMR genes were not always identified as the same Inc groups, suggesting that this method have a potential to be a new phylogenic analysis of plasmids.
We analyzed 274 plasmids carrying tunicamycin resistance gene (tmr) in this study. All of AMR genes were identified by BLASTn. In one spreadsheet, each gene of one plasmid was mapped onto each cell in one column and all plasmids were aligned side-by-side. When tmr of all plasmids was located in the middle of mapping, with bird’s-eye mapping and alignment using a new algorithm, we visualized similarities of types, positions, alignments and conformations of AMR genes among multiple plasmids in the spreadsheet. Incompatibility (Inc) groups of each plasmid were visualized in the spreadsheet and some plasmids possessing similar AMR genes were not always identified as the same Inc groups, suggesting that this method have a potential to be a new phylogenic analysis of plasmids.