Issue #2

Tuesday, 7 March 2023

Dear Stakeholder,

Welcome to the second issue of the Australian Pathogen Genomics (AusPathoGen/APG) Program newsletter. Our team will use these communications to keep you up to date on the latest news, as well as any events and opportunities that may be of interest to this community.

Our first issue last year contained brief overviews of our foundational projects and cross-cutting themes, along with some highlights and statistics from 2022 as a whole.

This edition of the newsletter will go a bit further in-depth to the Shigella foundational project, as well as introducing the work we will be doing on Invasive Group A Streptococcus. We’ll share some exciting news about AusTrakka, highlight details around our Teaching and Training cross-cutting theme and finish with an update from the Evaluation Team.

We hope you will find this newsletter informative, and if you have any colleagues that may be interested in receiving this too, please feel free to put them in touch with our team.

Foundational Project Updates

This quarterly update will go in-depth on the recent progress for the Shigella project, specifically with regards to the retrospective data analysis, the prospective snapshot and the draft of a paper. We would like to thank the Shigella Working Group (WG) members for their collaboration on the project thus far and for their contribution to this issue of the newsletter.

Data analysis on retrospective (2015-2021) and snapshot data

Genomic data analysis plans have been finalised thanks to a highly collaborative approach by the Shigella WG bioinformaticians, academic and genomic epidemiologists, with contributions from all Australian jurisdictions and New Zealand representation.

Bioinformatic Implementers have been identified, with the approved data analysis set to commence on the retrospective and snapshot data. This has been designed to align with one of the primary aims of the project - to unravel the genomic epidemiology of shigella via the establishment of a national genomic surveillance system and integration with AusTrakka.

Prospective Snapshot

We are halfway through the 12-month prospective snapshot, with 160 sequences and their corresponding metadata from across Australia contributed to the AusTrakka platform. This is an exciting mark of progress with the platform being able to accept data directly from jurisdictions, with the intention that members from the WG will soon be able to visualise the snapshot genomic data via AusTrakka itself.

The collection of time points to include details such as the date received at the PHL and the date the isolate was sequenced will provide valuable information about the sequence generation process, and suitability to inform public health response.

Draft paper outline

The WG have discussed how the results from the snapshot should be written up for publication, with ideas presented to and discussed with the APG Executive Group. The Shigella Lead Research Fellows have commenced drafting the outlines for this paper, and we will make sure to share any updates with the APG community.

Invasive Group A Streptococcus Working Group established

An APG Working Group (WG) has been established for invasive Group A Streptococcus (iGAS), bringing together the expertise and key public health stakeholders to collaboratively address emerging national needs. The WG has representation from all jurisdictions, with the first meeting held on Wednesday 8th February.

The aim of the APG iGAS WG is to develop a national surveillance framework for integration into AusTrakka, to be achieved via the implementation of harmonised national analysis methodologies; analysis of retrospective datasets contributed by WG members; and the execution of a comprehensive national 6-month snapshot during which all notified iGAS samples are sequenced in all jurisdictions.

As iGAS was only made a nationally notifiable pathogen in 2021, though notifiable for longer in certain jurisdictions, there is currently limited nationally representative genomic data available. A recent rise in numbers reported in Australia and internationally, combined with increasing AMR observed in high-income countries, has led to significant public health interest. Indeed, the international emergence of hyper-virulent iGAS lineages with a higher incidence of severe cases has been observed in multiple countries (such as M1UK), and you can read more about that below.

In the news

Cross-Cutting Themes

Similar to the project updates, issues of the newsletter will alternate the cross-cutting themes we will expand upon, with “Teaching and Training” being the highlight of this edition. The primary aim for this theme is looking to develop ways to expand the workforce in public health genomics based on the demand for disciplines in the field, such as genomic epidemiology and bioinformatics.

In partnership with the Communicable Diseases Genomics Network (CDGN) in 2022, we co-hosted the inaugural “Introduction to Pathogen Genomics for Public Health” webinar series. This was a series of three webinars spread across the latter half of the year, with dedicated sessions on wet-lab, bioinformatics and reporting and clinical governance processes. 

Many APG members contributed to the sessions and activities, sharing their expertise with the audiences as we trialled the online format. Given the strong attendance and positive feedback, we will be running a similar series this year, with details posted on the ‘Events’ section of the website. The first sessions will be covering topics related to "Wet-lab processes for pathogen whole genome sequencing" taking place on Tuesday 16 and Thursday 18 May, and you can find more details posted on the AusPathoGen website via the link below soon. 

Evaluation of Whole Genome Sequencing Utility and Cost-Effectiveness

These materials are focused on assessing the capacity of Public Health Laboratories; identifying the mechanisms to prioritise pathogens; identifying the most important pathogens for Whole Genome Sequencing; studying the ethical and social implications of pathogen genomics; evaluating the impact of genomic-based public health response; and conducting an economic evaluation.

The team has cleared the questionnaires for the situation assessment and Delphi survey internally, and will pilot them in two jurisdictions in early March 2023. This is to check the language, consistency and flow of the surveys, as well as to make sure that the necessary data are available. They will then roll out the surveys in all jurisdictions of Australia by the end of March 2023.

The team will also hold their first Project Reference Group (PRG) meeting for the year in early March, where they will update members on their progress and seek assistance in rolling out the surveys. The PRG is a multi-disciplinary group that meets quarterly to provide strategic feedback and input into the evaluation project activities and outputs.

Finally, the team have submitted a systematic review on “Economic evaluations of whole genome sequencing (WGS) for pathogen identification in public health surveillance” to Lancet.

AusPathoGen Progam Partners