Webinar: Introduction to Metagenomic Sequencing

Part one: Thursday 9 November 2023 13:00 - 15:20 (AEDT)

Part two: Friday 10 November 2023 13:00 - 15:10 (AEDT)

Overview

Are you a clinical scientist, medical microbiologist, infectious diseases physician, or work in clinical and public health laboratories and are wanting to gain expertise in whole genome sequencing?

Following on from the wet-lab, bioinformatics and reporting sessions held earlier in the year, this is fourth and final part of the webinar series co-hosted by the Communicable Diseases Genomics Network (CDGN) and the Australian Pathogen Genomics Program (AusPathoGen).

Learning outcomes

Key learning outcomes of the fourth webinar in the Introduction to Pathogen Genomics for Public Health Webinar Series include:

• An understanding of the technical performance, limitations and quality control requirements when setting up a clinical metagenomics assay
• An understanding of the challenges and methods associated with bioinformatic analysis of complex samples
• Ethics, clinical governance and use cases for clinical metagenomics

Webinar facilitators

• Dr Susan Ballard, Principal Scientist, Microbiological Diagnostic Unit Public Health Laboratory
• Dr Sanmarié Schlebusch, Medical Director Microbiology, Virology, and Genomics, Forensic and Scientific Services, Queensland Health
• Dr Prashanth Ramachandran, Research Fellow, Department of Infectious Diseases, University of Melbourne
• Dr Rikki Graham, Supervising Scientist, Forensic and Scientific Services, Queensland Health
• Dr Eike Steinig, Bioinformatician, Department of Infectious Diseases, University of Melbourne
• Dr Mitchell Sullivan, Bioinformatics Analyst, Forensic and Scientific Services, Queensland Health
• Dr Annaleise Howard-Jones, Microbiology Registrar, Institute of Clinical Pathology Medicine and Research
• Dr. Chisha Sikazwe, Senior Scientist, PathWest Laboratory Medicine
• Prof Vitali Sintchenko, Director, Centre for Infectious Diseases and Microbiology - Public Health
• Associate Professor Amy Jennison, Chief Scientist, Forensic and Scientific Services, Queensland Health
• Associate Professor Leon Caly, Section Head - Translational Diagnostics, Victorian Infectious Diseases Reference Laboratory
• Associate Professor Jason Kwong, Director, Infection Prevention & Control, Austin Health
• Professor Tim Stinear, Co-Director, Centre for Pathogen Genomics

Registration

Registrations are available via this link.

Program

Part one: Thursday 9 November 2023, 13:00 - 17:20 (AEDT)

Introduction to metagenomics - Dr Susan Ballard

• Introduction to the terms that will be discussed during the webinar, and the various methods involved
• Microbiome vs pathogen discovery
• Pathogen discovery
• Clinical metagenomics
• Public health metagenomics
• Microbiome – 16S/18S

Case studies Part 1: Interesting applications of metagenomics - Dr Sanmarié Schlebusch and Dr Prashanth Ramachandran

• Overview of two case studies involving interesting applications of metagenomics

Wet-lab metagenomics - Dr Rikki Graham

• An understanding of the technical performance, limitations and quality issues with setting up a clinical metagenomics experiment
• Challenges with different sample types
• Shot-gun vs targeted amplicon vs hybrid capture
• Importance of extraction
• Depletion approaches for human nucleic acids
• Impact of low biomass samples

Overview of bioinformatics pipelines for metagenomics - Dr Eike Steinig

• Methods associated with pathogen agnostic species identification
• Bioinformatic workflows including viral metagenomics (i.e. teasing out viral genomes from a mixed metagenomics sample)

Microbial metagenomic characterisation - Dr Mitchell Sullivan

• Understand characterisation from metagenomics analysis and what each can tell us, e.g. AMR, typing
• Challenges associated with outputs from metagenomic sequencing/analysis
• Understand the importance of controls and how to use them for interpreting results

Part two: Friday 10 November 2023 13:00 - 17:10 (AEDT)

Clinical governance and reporting of microbial metagenomics - Dr Prashanth Ramachandran

• Clinical governance, interpretation and reporting of metagenomics
• Quality Control
• Ethics - sample collection through to data analysis and upload. An understanding of the ethical challenges with clinical metagenomics
• TGA Special Access Scheme

Case studies Part 2: Interesting applications of metagenomics - Dr Annaleise Howard-Jones and Dr Chisha Sikazwe

• Overview of two case studies involving interesting applications of metagenomics

Panel Discussion:  Implementation and accreditation

Where to next? Introduction to the Meta-GP Grant - Prof Tim Stinear

• Overview of grant aims
• Clinical and public health focuses
• Update to the program

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