Issue #3

Monday, 19 June 2023

Dear Stakeholder,

Welcome to the quarterly issue of the Australian Pathogen Genomics (AusPathoGen/APG) Program newsletter. As a reminder, 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 earlier issues are now available to view in the archive on our website for any that have recently joined this mailing list, accessible via the link below.

This edition of the newsletter will go a bit further in-depth to the Salmonella foundational project, as well as some key updates in the bioinformatics space. We will cover some recent activities abroad, and provide an update into the work of our Evaluation team. Finally, we’ll be highlighting some key changes to the website.  

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 Salmonella project, specifically with regards to the prospective snapshot and subsequent analysis. We would like to thank the Salmonella Working Group (WG) members for their collaboration on the project thus far and for their contribution to this issue of the newsletter.  

Prospective Snapshot

The three-month snapshot where all non-typhoidal Salmonella enterica in all jurisdictions were sequenced has now concluded. The snapshot covered the high-incidence summer period of January to March 2023. This represents the first completed prospective national dataset collected by the AusPathoGen program partners, and will provide an exciting insight into the current phylogeographical and antimicrobial resistance landscape of non-typhoidal Salmonella across Australia.

A second three-month national snapshot is planned for January to March 2024, with this set to provide further information of the dynamics of the Salmonella population.

Analysis

The multi-centre network of bioinformaticians have collaboratively commenced analysis of the non-typhoidal Salmonella retrospective and prospective datasets, using the AusPathoGen dedicated high-performance computer cluster.

The collection of Salmonella Typhi remains ongoing, with the first analysis planned for the end of 2023 to capture the dynamics of the first year.

Bioinformatics Working Groups

A series of Working Groups (WGs) have been established for Bioinformatics, each consisting of ~40 members, including many domain experts, senior academics and public health professionals. This is an extensive collection of expertise, with many having previously helped to develop the data analysis plans for the foundational projects.

The Bioinformatics Implementer Groups have also been established, consisting of 22 bioinformaticians from across the country volunteering their time and expertise to conduct the analysis for the three foundational projects. There has been great progress across Salmonella, Shigella, and M. tuberculosis, and the team is collecting expressions of interest for an iGAS Bioinformatics WG.

APG Server

Through this, it has been possible to share Conda installations of all commonly used tools, ensuring consistency and reproducibility of the outputs.

Additionally, the sequence data is synced to the APG server upon uploads of new data, which permits that the most current collections are available to the team. Please note that these are kept partitioned, meaning that only team members authorized to analyse the sequences can access them.

APG Abroad

Dr Patiyan Andersson recently attended ABPHM UK on behalf of AusPathoGen. His talk included an overview of AusPathoGen and the establishment of the foundational projects, in a session with examples of national initiatives from Sri Lanka, Argentina and the UK.

The Australian experience of national data sharing and application of pathogen genomics, both during the pandemic and over the first year of the program, is seen as a success story. There was great interest from the audience, with questions around the engagement through the multi-disciplinary WG, establishment of the nationally collaborative bioinformatic analysis network, and prioritisation and collation of representative harmonised datasets.

Evaluation of Whole Genome Sequencing Utility and Cost-Effectiveness

The first round is expected to be completed soon, with the team presenting the expert elicitation at the CDIC Conference in Perth in June. The second survey, “Situation assessment questionnaire of the Public Health Laboratories’ capacity for whole genome sequencing”, is scheduled to commence this month as well.

A master’s student from the University of Melbourne is focusing on an evaluation component for their final project, looking at “Qualitative comparative analysis to identify the factors that influence the use of pathogen genomics in Australia”. They are currently identifying case studies and will start the data collection in June.

"Economic evaluations of whole genome sequencing (WGS) for pathogen identification in public health surveillance: a systematic review" has been submitted and currently awaiting the decision on acceptance. The economic evaluation team are also conducting a mapping exercise for their study, consultations with key stakeholders.

Finally, this team have developed a model to estimate the cost effectiveness of genomic sequencing as compared to traditional testing, with the draft model available for testing via the link below.

Website updates

In addition to the newsletter archive mentioned above, the website has been updated to show the counter for 'Genomes Contributed' for each of the foundational projects, in addition to the COVID-19 'Genomes Sequenced' counter that was already represented on the home page. 

These counters are synced to the individual pathogen pages, and we can incorporate this feature to any new pages as required. 

AusPathoGen Progam Partners