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. 

This quarter saw cgMLST and AMR profiling finalised for the datasets submitted to date. With this pathogen project nearing completion, the WG primarily focused on the data analysis, conducting phylogenetic analysis on key serovars. A June meeting will update members on latest findings. NTS manuscript drafts are underway as jurisdictions confirm finalisation of submissions for the second prospective snapshot (Jan-Mar 2024).

Analysis of ~5,000 sequences contributed by all Australian jurisdictions  revealed emergent multi-drug resistant and extensively drug resistant (XDR) Shigella – with 37% and 2.6% of the sequences genotypically MDR or XDR respectively.  Genomics revealed the presence of previously unknown multi-jurisdictional genomic clusters – identifying seven dominant clusters in Australia with distinct population groups, AMR and geographical patterns Re-engaging the national WG to present these new findings is a key priority for the project in the coming months. Collaboration with experts in the WG is crucial as we finalise our analysis and move towards publication of our findings.

Analysis of all sequences submitted up to April 8th, 2024 has yielded valuable insights into Mycobacterium tuberculosis strains circulating in Australia. The analysis confirms our previous observations of low rates of multidrug-resistant tuberculosis (MDR-TB) based on genetic markers. Additionally, the data suggests the presence of genomic signatures that may indicate clusters spanning multiple jurisdictions and lengthy time frames. Preliminary trees for the four major lineages of Mycobacterium tuberculosis have been uploaded to AusTrakka. We are prioritising re-engagement with the WG to progress manuscript preparation with a target submission by the end of the year.

The One Health E. coli  project is moving forward on multiple fronts. Writing for the retrospective study is progressing well, with two manuscripts currently undergoing internal review. Productive discussions with WG members have facilitated developments in the prospective study, particularly regarding collaboration with external stakeholders to acquire environmental samples. Upcoming priorities include the publication of the retrospective studies and initiating sequencing for isolates collected during the prospective study.

While data collection is ongoing, with six jurisdictions having contributed sequences to date, the project has made significant progress in laying the groundwork for robust data analysis. A dedicated bioinformatics WG convened in May to discuss the details of the data analysis. This critical meeting focused on the optimal utilisation of AusTrakka and the APG server, ensuring efficient data storage and accessibility. Additionally, the group reviewed data analysis guidelines and finalised a plan for analysing the collected sequences.

We are pleased to announce that three jurisdictions (VIC, SA, QLD) have submitted sequence data for the IPD project, totalling 2,327 samples. Progress has been made over several working group meetings towards finalising the specific vaccine-related metadata variables. These proposed variables have been submitted for ethics approval.  Discussions with the project members are ongoing to identify the most appropriate antimicrobial susceptibility testing variables to include in the metadata pro forma that ensures compatibility with the laboratory methods used by all jurisdictions. Pilot quality control and data analysis has began on the uploaded samples to test bioinformatic tools and ensure a streamlined analysis process for the entire dataset. The project continues to encourage timely data and metadata contributions from all partner jurisdictions for both retrospective and prospective periods.

The project recently held its first bioinformatics WG meeting, which served as a platform for establishing the groundwork for crucial data analysis pipelines and methods specifically tailored to C. auris. These pipelines will be instrumental in efficiently processing and assembling the complex genetic data of isolates. Looking ahead, the team anticipates receiving sequences for the retrospective study in the next quarter. Upon receiving this data, the finalised genome assembly pipeline will be implemented, and in-depth analysis of the C. auris genomes will commence.

The Situation Assessment project has successfully concluded its survey, receiving responses from nine out of eleven participating laboratories. Initial analysis reveals a diverse landscape, with larger labs demonstrating greater capacity for pathogen sequencing compared to their smaller counterparts.  Encouragingly, the preliminary findings also suggest a unified direction towards the implementation of pathogen genomics in public health across all labs, regardless of size.

Discussions during meetings centred on refining the presentation of these findings for individual laboratories and potential publications.  The project team will summarise the situation assessment data and provide reports back to labs for verification and to address any discrepancies.  The primary focus for the upcoming quarter is finalising and publishing the situation assessment results, aiming for publication by year-end.

The Cost Effectiveness project is nearing completion of a paper analysing the impact of WGS on Salmonella surveillance costs.  This analysis, utilising a two-stage difference-in-difference (2sDiD) approach, suggests WGS is associated with a 17-19% reduction in Salmonella cases. This translates to potential cost savings due to earlier detection and intervention.

Recent discussions addressed concerns about the 2sDiD method's ability to account for confounding factors. The team clarified that the 2sDiD design helps isolate the effect of WGS by comparing changes in Salmonella cases between groups that transitioned to WGS and those that didn't, while controlling for overall trends. The top priority for the coming quarter is finalising data collection and analysis for the Salmonella WGS cost-effectiveness paper. This will involve incorporating cost data from remaining laboratory surveys to provide a more comprehensive economic evaluation.

The Expert Elicitation project has wrapped up round two of the quantitative analysis.  Preliminary findings, presented at the CDIC conference on June 11th, 2024, suggest a collaborative approach to pathogen prioritisation for sequencing is favoured by experts.  This includes stakeholders at national and jurisdictional levels, encompassing public health departments, laboratories, and units.

The upcoming quarter prioritises finalising the analysis of results and translating them into a framework or guidelines for pathogen sequencing prioritisation.  Additionally, publication in a peer-reviewed journal is a key objective for the coming months.