Issue #1
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Issue #1
Tuesday, 29 November 2022
Dear Stakeholder,
Welcome to the inaugural issue of the Australian Pathogen Genomics (AusPathoGen) 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.
This first edition will aim to set the scene with brief overviews of our foundational projects and cross-cutting themes, with future issues providing further in-depth information on a rotating basis . We’ll also share any additional highlights from the past few months.
As we approach the conclusion of a successful year of the program, we would like to give our AusPathoGen community an insight into where we will be taking the program in Years Two and Three. In addition to advancing our cross-cutting themes and engaging more extensively with both new and existing stakeholders, we will look to integrate our research findings further into national surveillance and reporting systems. This ties in with expanding the AusTrakka platform and national analysis team, plus the diversification of our key focus areas to include new pathogens, such as Invasive Bacterial Vaccine-Preventable Diseases (IB-VPD), respiratory diseases and biothreats.
We look forward to engaging with you in 2023, and on behalf of the AusPathoGen team from around Australia wish you a happy festive season as we wrap up 2022.
Thank you,
Ben
Professor Benjamin P. Howden
AusPathoGen Program Lead
AusPathoGen in 2022
At a glance
Engagement
APG Symposium 2022
We were delighted to connect in person for our inaugural All Partners Symposium, hosted by the University of Sydney. The full-day schedule was packed with sessions covering the progress on each of our foundational projects, an introduction to the cross-cutting themes and concurrent workshops examining strategies for the implementation for public health pathogen genomics. Plans are already underway for the 2023 edition with further details to come!
Queensland visit
Our team members from Melbourne were fortunate to be hosted by representatives from Forensic and Scientific Services, Queensland Health, and the Queensland Mycobacterium Reference Laboratory earlier this year. It was an exciting opportunity to gain a broader understanding of genomic projects in Queensland and how the teams can work together in the national context. We look forward to further engagement in-person across the country moving forward.
Foundational Project Updates
Our upcoming newsletters will go in-depth on a rotating basis to each of these projects and what the latest progress has been. For this first issue of the newsletter, we want to provide a few key milestones for each pathogen, and direct you to our website where we will be looking to expand on our findings over time, though noting that newsletter subscribers will receive an exclusive preview of the latest information via these updates.
Salmonella WG
The aims are: 1) to describe the phylogeographical and antimicrobial resistance (AMR) patterns of Salmonella enterica, and; 2) to establish ongoing national genomic surveillance of Salmonella Typhi to monitor AMR dynamics relative to travel history.
A prospective 3-month snapshot during which all Salmonella enterica in Australia will be sequenced will commence in January 2023.
Shigella WG
The aims are: 1) to unravel the genomic epidemiology of Shigella species across Australia, and; 2) to implement a genomic surveillance system onto AusTrakka for identifying Shigella clusters and AMR importations into Australia from abroad.
A prospective 12-month snapshot commenced in October 2022 – whereby all Shigella in Australia will be sequenced.
Tuberculosis WG
The aims are: 1) to unravel the genomic epidemiology of Mycobacterium tuberculosis (MTB) across Australia, and; 2) to develop a harmonised national surveillance system for MTB onto AusTrakka for identifying cross-jurisdictional clusters and AMR.
The prospective 12-month snapshot commenced in October 2022 – whereby all MTB in Australia will be sequenced.
For each of the pathogens, analysis of retrospective data has commenced with the establishment of individual bioinformatic analysis teams, with the purpose of executing the endorsed data analysis plan.
Cross-Cutting Themes
Similar to the project updates, issues of the newsletter will alternate the cross-cutting themes we will expand upon. “One Health” will be the highlight of this edition, with “Aboriginal and Torres Strait Islander engagement”, “Novel data approaches” and “Teaching and Training” to follow.
The project for the One Health theme has had three primary aims: to perform a retrospective analysis of available E. coli sequences in current collections and in public repositories; to establish a framework for prospective analysis; and to perform a pilot prospective study for One Health E. coli surveillance.
There has been a retrospective analysis of close to 5,500 samples performed thus far, the interrelatedness of sequences cross sources highlighting the need to address pathogens from a One Health perspective. The samples were predominantly pathogenic ExPEC, with 52% of the collection exhibited genotypic MDR. The team have drafted an initial stakeholder map and outlined the engagement methods, and are currently in the progress of preparing a prospective study proposal.
The intended outcomes will involve exploring the available data on existing inter and intra-sectoral trends in E. coli, looking to understand stakeholder needs and requirements and how to shape prospective surveillance. Additionally, looking to examine data on feasibility and utility of routine sequencing of E. coli, and developing a One Health surveillance framework for future pathogens
Evaluation of Whole Genome Sequencing Utility and Cost-Effectiveness
A key aspect of the program focuses on evaluating the utility and cost-effectiveness of genomics-based public health responses.
To enable the long-term public health translation of this process, it is also required to investigate and optimise the end-user acceptability and interpretation of the results.
Key highlights of the past year for the Evaluation Team include: submission of the ethics application in mid-November after addressing concerns from the ANU Human Ethics Committee; near completion of a systematic review of "Economic evaluations of whole genome sequencing for public health surveillance”; and conducted the initial project reference group meeting on 14th November 2022, which brought together a multi-disciplinary team with representation across Australia and New Zealand. The implementation group plans to pilot questionnaires for the situation assessment of the current capacity of genomics-based public health response by public health laboratories across all jurisdictions. In the meantime, the Methodology of Expert Elicitation and Methodology/Data Analysis Plan for the economic analysis are being developed.
Upcoming Events
Webinar: Reporting considerations and processes for pathogen whole genome sequencing
Dates: Tuesday 29 Nov & Thursday 1 Dec
The third and final instalment of our "Introduction to Pathogen Genomics for Public Health" series, co-hosted with CDGN.
AusPathoGen Progam Partners
