Events

Tuesday, 1 December - Thursday, 3 December

Online course hosted by the Doherty Institute, The University of Melbourne.

Genomics is revolutionising the practice of public health microbiology and epidemiology globally, however capacity in genomic data analysis is a key limiting factor in implementation of the technology. This course, designed for public health microbiologists and epidemiologists, will introduce concepts and provide practical experience in the analysis and interpretation of microbial genome data for public health action, with a focus on antimicrobial resistance and the application of genomics to the COVID-19 response.

HOW TO APPLY

Cost

Standard fee: AUD $660

Low and middle income country subsidised fee: AUD $110

Applications close on Friday, 30 October 2020. Successful applicants will be notified via email.

Course overview

DAY ONE: TUESDAY 1 DECEMBER 2020

Introduction to microbial genomics for public health 

The program for day one will take a look at the typical equipment used in a high-throughput bacterial/viral genomics laboratory and talk about the workflows that are used to take a bacterial isolate or viral swab sample through the laboratory and produce sequence data. Activities will be used to guide participant through the analysis of bacterial isolate sequence data to produce an annotated draft genome sequence. 

The program includes: 

• Introduction to the Galaxy Analysis Platform 
• A Virtual Laboratory Tour

DAY TWO: WEDNESDAY 2 DECEMBER 2020

Using genomics to investigate bacterial pathogens and antimicrobial resistance (AMR)  

The program for day two will be a combination of specialist lectures and activities that will look at methods of antimicrobial resistance gene detection. This will be followed by a run through the way genomic data can be summarised to provide overviews of the genome sequences of small sets of isolates and how these summaries are used in actual studies 

The program includes: 

• Activities using tools like Abricate and Kraken 
• Specialist lecture: using genomics to track AMR in hospitals

DAY THREE: THURSDAY 3 DECEMBER 202

Application of genomics to COVID-19 and the use of isolate genomics in epidemiology  

The rapid developments in COVID-19 genomics over 2020 provides a topical example of how viral genomics is performed in a public health context, following the process from sample through to genome sequence. Using Mycobacterium tuberculosis as an example, the use of genomics-based phylogenies in Epidemiology will be demonstrated. 

The program includes:

• Introduction to phylogeny and trees
• Introduction to read mapping methods

ORGANISING COMMITTEE

Microbiological Diagnostic Unit Public Health Laboratory 

Doherty Applied Microbial Genomics

Professor Tim Stinear, Professor Ben Howden, Dr Dieter Bulach, Associate Professor Torsten Seemann, Professor Deborah Williamson, Dr Andre Mu, Dr Susan Ballard, Dr Sarah Baines, Dr Danielle Ingle, Dr Claire Gorrie, Dr Jake Lacey, Dr Kristy Horan, Dr Clare Sloggett.