Introduction to Pathogen Genomics for Public Health Webinar Series

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Webinar: Reporting considerations and processes for pathogen whole genome sequencing

Part one: Tuesday 12 September 2023 13:00 - 15:50 (AEST)

Part two: Thursday 14 September 2023 13:00 - 16:00 (AEST)

Overview

Are you a clinical scientist, medical microbiologist, genomic epidemiologist or trainee wanting to gain an understanding of the considerations when issuing microbial genomics reports? Epidemiologists at public health units, infectious diseases physicians and other recipients of genomic reports may also find this webinar informative.

Following on from the wet-lab and bioinformatics sessions held earlier in the year, this is third 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 third webinar in the Introduction to Pathogen Genomics for Public Health Webinar Series include:

• Interpretation and reporting of genomic results for identification and enhanced characterisation of pathogens.

• Approaches for interpretation and communication of typing data and phylogenetic relatedness for end users, including clinicians, epidemiologists, policy makers and government.

• Governance requirements and considerations for reporting and communication of genomic data.

Webinar facilitators

• Professor Sebastiaan Van Hal, Staff Specialist, Microbiology and Infectious Diseases, Royal Prince Alfred Hospital

• Associate Professor Norelle Sherry, Deputy Director, Microbiological Diagnostic Unit Public Health Laboratory

• Ms Taryn Crighton, Senior Scientist, NSW Health Pathology

• Dr Rikki Graham, Supervising Scientist, Forensic and Scientific Services, Queensland Health

• Dr John-Sebastian Eden, Senior Research Fellow, University of Sydney and Westmead Institute for Medical Research

• Dr Jen Kok, Senior Staff Specialist, Institute of Clinical Pathology and Medical Research Pathology, Westmead Hospital

• Dr Patiyan Andersson, Genomic Epidemiologist, Microbiological Diagnostic Unit Public Health Laboratory

• Ms Mathilda Wilmot, Genomic Epidemiologist, Microbiological Diagnostic Unit Public Health Laboratory & AusTrakka

• Dr Gillian Treloar, Assistant Director, National Health and Medical Research Council

• Associate Professor Amy Jennison, Chief Scientist, Forensic and Scientific Services, Queensland Health

Registration

Registrations have now closed.

Program

Part one: Tuesday 12 September 2023 13:00 - 15:50 (AEST)

Organism Identification - Prof Sebastiaan Van Hal

• Understanding challenges of taxonomic classification with WGS and impact of different bioinformatic approaches and database for identification.

• Harmonisation of bacterial identification for clinical reporting

• Requirements for NATA accreditation for reporting

Taming the AMR beast - Dr Norelle Sherry

• Understanding limitations and advantages of different bioinformatic tools used.

• Understanding the need of translating antimicrobial resistance gene identification into clinically relevant report and reporting acceptance criteria

• Considerations of information included in the report

• Requirements for NATA accreditation for reporting

MTS and WGS reporting - Ms (TBC) Taryn Crighton

• Understanding the complexities of TB phenotypic testing and its relationship to genotypic testing and reporting

• Understand the principles of confidence graded mutations (WHO catalogue) and the impact on reporting TB antibiotic susceptibility from AMR detection.

• Integrating comparative genomics into reporting Tb genomics (cgmlst and SNP analysis)

• Requirements for NATA accreditation for reporting

Session 1 wrap-up activity

Part two: Thursday 14 September 2023 13:00 - 16:00 (AEST)

Common/notifiable respiratory diseases - Dr Jen Kok

• Complexities associated with highly transmissible communicable viruses

• Reporting mutations associated or potentially associated with treatment failure, increased transmissibility, and severity of disease

• Complexities of phylogenetic interpretation and source attribution

• Communication to public health and infection control

• Monitoring for emergence of potential pandemic zoonotic influenza

Reporting and communication considerations for phylogenetic analysis - Dr Patiyan Andersson

• Application of genomic typing schemes and limitations. (including in silico MLST, cgMLST, wgMLST)

• Standardisation of nomenclatures nationally and internationally

• Criteria for relatedness/ phylogenetic interpretation and source attribution

• Caveats and limitations with phylogenetic analysis (e.g. masking regions, reference genome choice)

• Data visualisation

Square pegs and round holes: Phylogenetic analysis for public health - Ms Mathilda Wilmot

• Understanding the challenges of integrating WGS data into surveillance systems and public health operations

• Governance of reporting phylogeny: the national context

• Making the most of an integrated national surveillance system (benefits and opportunities)

Overview of NATA accreditation - Dr Gillian Treloar

• Overview of reporting requirements based on ISO15189 and other standards

• Governance of sequencing (NATA accreditation, staff competency)

• Introducing the complexities and components underpinning reporting

• Notification and high-risk result requirements

• LIMS report vs offline report

• Governance and structure

Governance of microbial genomics - A/Prof Amy Jennison

• Technical aspects – what an assessor is looking for when completing a NATA inspection

• How do NATA approach auditing and validation of in-house bioinformatic pipelines

• Pre-analytical, analytical and post-analytical considerations

Panel Discussion: Integration of reporting into practice and implications of the data