Webinar: Reporting considerations and processes for pathogen whole genome sequencing

Part one: Tuesday 29 November 2022 13:00 - 16:20 (AEDT)

Part two: Thursday 1 December 2022 13:00 - 16:00 (AEDT)

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 the final of a three-part webinar series co-hosted by the Communicable Diseases Genomics Network (CDGN) and the Australian Pathogen Genomics Program.

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

• Associate Professor Amy Jennison, Chief Scientist, Public Health Microbiology, Forensic and Scientific Services, Queensland Health
• Professor Sebastiaan Van Hal, Staff Specialist, Microbiology and Infectious Diseases, Royal Prince Alfred Hospital
• Dr Sanmarie Schlebusch Medical Director, Microbiology, Virology and Genomics, Forensic and Scientific Services, Queensland Health
• Professor Martyn Kirk, Professor of Applied Epidemiology, Australian National University
• Professor Vitali Sintchenko Director, Centre for Infectious Diseases and Microbiology – Public Health,  Institute Of Clinical Pathology And Medical Research
• Dr Norelle Sherry, Acting Deputy Director, Microbiological Diagnostic Unit Public Health Laboratory
• Dr Patiyan Andersson, Genomic Epidemiologist, Microbiological Diagnostic Unit Public Health Laboratory
• Dr Alicia Arnott, Genomic Epidemiologist, NSW Health Pathology
• Associate Professor Torsten Seemann, Lead Bioinformatician, Microbiological Diagnostic Unit Public Health Laboratory & AusTrakka
• Ms Tuyet Hoang Pathogen Genomics Portfolio Manager, Microbiological Diagnostic Unit Public Health Laboratory

Registration

Registrations are available via the link here.

Program

Part one: Tuesday 29 November 2022 13:00 - 16:20 (AEDT)

Overview of reporting requirements and governance - A/Prof Amy Jennison

• Overview of reporting requirements based on ISO15189 and other standards
• Governance of sequencing (NATA accreditation, staff competency)
• Introducing the complexities and components underpinning reporting

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 - Prof Vitali Sintchenko

• 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

Part two: Thursday 1 December 2022 13:00 - 16:00 (AEDT)

SARS-CoV-2 - Dr Alicia Arnott

• Reporting SARS-CoV-2 lineages and VOC status
• 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

Reporting and communication considerations for phylogenetic analysis - Dr Patiyan Andersson

• Criteria for relatedness/ phylogenetic interpretation and source attribution
• Caveats and limitations with phylogenetic analysis (e.g. masking regions, reference genome choice)
• Data visualisation
• Requirements for NATA accreditation for reporting

Swiss cheese and report authorisation - Dr Sanmarié Schlebusch

• Notification and high-risk result requirements
• LIMS report vs offline report
• Governance and structure

Towards Harmonised Typing Schemes - Prof Martyn Kirk

• Application of genomic typing schemes and limitations (including in silico MLST, cgMLST, wgMLST)
• Standardization of nomenclatures nationally and internationally

AusTrakka - Ms Tuyet Hoang and A/Prof Torsten Seemann

• Preparing the laboratory to be part of the AusTrakka system (ethics/governance/ data sharing workflow)
• 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)

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