Infectious diseases and antimicrobial resistance (AMR) are the threat to public health. With sequencing technology and bioinformatics approaches, we can use them to combat with infectious disease more effectively. In this talk, I will show various bioinformatics approaches applied in infectious disease and AMR studies such as characterization and sub-typing of bacteria including determination of AMR and identification of single nucleotide polymorphisms for outbreak detection of bacteria. Additionally, I will talk about Bayesian evolutionary analysis to identify the most recent common ancestor in order to understand the dissemination of infectious diseases and population size of bacteria.
Utilizing metagenomics, it is feasible to identify pathogens and AMR genes directly from sewage samples using metagenomic read mapping. This approach has clearly demonstrated that the global emergence and abundances of AMR is not only driven by antimicrobial use (AMU), but the impact of AMU should be seen in an ecological context.
Lastly, I will show another bioinformatics approach applied in food safety by combining novel technologies including whole genome sequencing, and machine learning for measuring and understanding virulence level and disinfectant resistance of foodborne bacteria (Listeria monocytogenes) in food industry.