[S1-1] Comprehensive analysis of plasmid-host interaction in natural environments
Antimicrobial resistance genes (ARGs) are often transferred among bacteria by plasmids and have spread over the world. Conventional molecular epidemiological analysis of antimicrobial-resistant bacteria is based on sequence analysis of isolates, however, there are limitations on individual characterization when analyzing meta-samples, such as animal feces and environmental waters. In this study, we aimed to perform comprehensive analysis of plasmid-host interaction in natural environments using bacteria from environmental water samples in Japan and Vietnam. To construct genomic structures that separate bacterial chromosomes and plasmids at the single-cell level, we utilized bioinformatics technologies combining data from high-throughput sequencing (short-read and/or long-read sequencing) and Hi-C (chromosome conformation capture), a method for detecting DNA interactions in the same cell, leading to link bacterial chromosome-plasmid-ARG. Furthermore, we constructed novel sequence libraries of ARGs and plasmids, and this enabled the single-cell genome analysis at unprecedented resolution and revealed previously unknown dynamics of plasmids and ARGs in environmental bacteria. Some of the relationships could be confirmed by analyzing antimicrobial-resistant isolates. Therefore, our approach would be promising for investigating bacterial antimicrobial resistance in the environment.