How bioinformatics, genomics, and open data is transforming public health and clinical microbiology
Public health and clinical microbiology exist to protect society from infectious diseases, contaminated food and other important pathogens. It does this by continuous surveillance of microbial pathogens in our community and hospitals to identify potential threats. If an outbreak does occur, the goal is to track the source and accordingly shut down factories, recall food, or quarantine patients. Originally this was achieved solely by “show leather” epidemiology such as tracking history and movement. This was soon augmented with cellular and molecular assays which were applied to each isolate, but they varied in their ability to discriminate isolates. The advent of whole genomes sequencing offered the promise of the “one stop shop” by providing complete nucleotide level information for comparing isolates at the highest possible resolution. In this talk I will describe the data and bioinformatics methods used in genomic epidemiology and how they are transforming our ability to detect outbreaks earlier, shorten their duration, and improve public health and patient care, both locally and internationally.
Workshop: Introduction to genome assembly and annotation
A/Prof Torsten Seemann
The University of Melbourne
A/Prof Torsten Seemann is a lead bioinformatician at Melbourne Bioinformatics and Doherty Applied Microbial Genomics, both at the University of Melbourne. His work uses bioinformatics and genomics to better understand the spread and evolution of bacterial pathogens and antimicrobial resistance. He is best known for his software tools which are used internationally, and he is a strong supporter of open science and online communities to bring all scientists together.