As such, you can see the inclusion of an infographic associated with each pathogen to allow for you to view 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 which stage of the project the respective pathogen is at. 

Initial examination of common serovars reveals clusters of closely related samples extending across various jurisdictions, and low antimicrobial resistance observed within the dataset. As of November 30, 2023, the datasets have been closed to allow for the bioinformatic analysis teams to finalise the analysis and commence manuscript preparation. Key priorities for the Salmonella enterica working group in the coming months include the second 3-month snapshot, commencing January 1 2024, and contributing toward the prospective collection of Typhi sequencing, with analysis planned for early 2024.

Changes in Shigella flexneri serotypes and Shigella sonnei types, both pre- and post-pandemic, have been noted. Shigella sonnei clusters were identified, some spanning multiple jurisdictions and others specific to certain jurisdictions. As with Salmonella enterica, the datasets were closed on November 30, 2023. Discussions within the WG meeting included the consideration of a potential definition for extensively drug-resistant (XDR) Shigella spp. to be applied in the AusPathoGen project. Further steps involve collaboration with stakeholders and end-users for the implementation of the findings.

The inclusion of supplementary retrospective sequences this quarter has allowed the genomic dataset to encapsulate 42% of all notified cases in Australia from 2015 to 2023. Discussions on the genomic prediction of Mycobacterium tuberculosis AMR have taken place, prompting the team to investigate further the current results. In the next quarter, the aim is to finalise the data analysis for the retrospective data with the advisory sub-working group. The team will also be actively seeking to engage further with PHUs and end-users involved in the project.

Identified across diverse hosts and environments, closely related Escherichia coli strains reveal intricate bacterial transmission networks between humans, pets, food, livestock, wildlife, and the environment. We have also identified shareable genetic elements ('plasmids') which promote their virulence capacity and AMR. WG meetings have been critical in shaping the prospective sampling regime, leveraging professional networks accessible to the AusPathoGen team. Retrospectively, two manuscripts are nearing submission, with two more in development. Ongoing prospective sampling remains a top priority.

The invasive group A streptococcal disease (iGAS) WG have now reviewed and endorsed the data analysis plan, which was developed collaboratively between the iGAS bioinformatic sub-WG. Priorities for the next quarter include completing the collation of retrospective datasets, continuing the 12-month national snapshot that commenced on 1 August 2023, and re-establishing the bioinformatic WG to commence the data analysis.

The inaugural meeting of the invasive pneumococcal disease (IPD) WG was held on October 27, 2023. The distribution of terms of reference and metadata proforma to WG members for review marked the initiation of the collaborative effort. Activities included the commencement of data contribution, encompassing both retrospective and prospective data, and discussion to guide the development of a comprehensive data analysis plan in the future. Furthermore, a bioinformatic analysis group will be established to enhance the analytical aspects of the IPD project.

The inaugural WG meeting on October 23rd fostered an engaging discussion on the distinctive laboratory and bioinformatics prerequisites for the project. Emphasising key priorities, the team aims to distribute a questionnaire, capturing laboratories' capacity for data contribution to both retrospective and snapshot studies. Simultaneously, efforts are underway to assemble the bioinformatics working group, ensuring a comprehensive approach to the project's laboratory and analytical needs.

In the current phase of data collection for the Expert Elicitation and Situation Assessment surveys, the team is actively engaged. Notably, two impactful studies are on track for a rollout in the initial quarter of 2024, promising insights into the ongoing research endeavours.