You can see the inclusion of an infographic associated with each pathogen to allow for viewing the progress at a glance, in addition to the written update from the relevant working groups (WGs). The key for how this can be read can be seen to the side, with the progress bar indicating the stage of the project for each pathogen. 

Over the past three months, the remaining jurisdictions have finalised their governance approvals. This has allowed the outstanding data to be contributed for the retrospective period and the 2023 snapshot. As such, it has been possible to recommence the analysis phase. During this stage, updates across the working group members have been shared primarily via email. The upcoming quarter is expected to see the completion of the analysis of the existing data, which will be used to prepare the manuscript drafts. Additionally, the second prospective snapshot will be completed.

This quarter has focused on the collation and integration of data, specifically sequences and metadata, from New South Wales (NSW) to the project. This will enable the analysis team to include NSW data in the overall analysis. Following the approval of the ethics and data governance application, PHLs have commenced the contribution of enhanced metadata. The upcoming quarter will see Western Australia commencing the contribution of their jurisdictional data. Additionally, it is expected that the data analysis will be finalised and the manuscript preparation process will continue.   

The first quarter has seen the inclusion of genomes from Western Australia, allowing the dataset to be representative at the national level and encapsulating 62% of all notified cases during the study period. WG discussions have led to the conceptualisation of a spin-off genomic investigation, focusing on cross-jurisdictional cluster identification with the National Tuberculosis Advisory Committee. The upcoming months will focus on completion of the genomic analysis with the new data, and the preparation of two manuscripts looking at the genomic epidemiology and the national genomic AMR workflow respectively.

The first WG meeting of the year was held on March 13, which included a sample update for the prospective study. To date, 681 samples have been obtained from a variety of sectors including human, clinical, wildlife, livestock, and retail food. For the retrospective study, two manuscript drafts are currently under internal review – the first detailing cross-sectoral core genomic overlap and considerations relating to methodologies relating to phylogenetic distance measurements, and the second detailing advanced plasmid typing and cross-source mobilisation. The next quarter will focus on the submission of the two retrospective study manuscripts, and engaging with both veterinary pathology laboratories and the environmental sector to ensure comprehensive sampling for the prospective study.

Similar to the other pathogens, the outstanding jurisdictions have been able to finalise the governance approvals allowing for the contribution of their data towards the iGAS project.  The project is currently in the data collation phase, with a strong focus on working with stakeholders to contribute both retrospective and prospective snapshot data. Over the next few months, the dedicated implementers and advisors in the working group will meet to commence the optimisation of analysis approaches.

Given the early stage of the IPD project, the current priority is on encouraging the timely upload of IPD sequences by all jurisdictions to adhere to the planned project timeline. Discussions in recent WG meetings have focused on obtaining endorsement of the IPD metadata proforma, including: modification of antimicrobial therapies; addition of minimum inhibitory concentration (MIC) values and interpretation fields; and complexities of capturing appropriate vaccine metadata. Key next steps include determining the optimal strategy for sourcing relevant vaccine metadata, whether at the Commonwealth or jurisdictional level, to achieve project objectives, and providing server access to the implementor team to ensure timely data collation and analysis.

The most recent WG meeting in February focused on the enhanced metadata considerations specific to this project. Questionnaires capturing jurisdiction’s capacity for data contribution to both the retrospective and prospective snapshot studies have been completed. Additionally, expressions of interest for the bioinformatics WG have been sought, with the first meeting to focus on pipeline development for genome assembly. The Candida auris project has been created within the AusTrakka platform, which will allow uploads to commence for the retrospective study.

This quarter saw significant progress across the Evaluation Theme, specifically the Expert Elicitation Survey, the Case Study and the Economic Evaluation projects. The summaries for each of these are as follows.