This project will conduct a second time-limited intensive sampling project across different sectors of E. coli and extend this snapshot to Salmonella enterica and Vibrio parahaemolyticus. It will apply phylodynamic models, combining genomic evolutionary and epidemiological information to infer transmission dynamics between sectors using population-structured approaches. The work will also encompass design of methodologies specifically for One Health genomic data interrogation and establish cross-sectoral data governance framework.

Outcome:

Strengthened baseline data for cross-sectoral pathogen co-occurrence, tailored genomic surveillance guidance for each sector, and defined methodologies for One Health surveillance and outbreak response.

Develop and assess utility of a framework for integration of pathogen genomics from clinical practice.

This project will survey clinical laboratories to assess genomic literacy and capacity. It will explore integration models with national surveillance systems and identify clinical patient management use cases. The project will conduct a national genomic surveillance pilot for carbapenem-resistant organisms, including harmonisation of methodologies, establish data sharing protocols, and integrating clinical and public health laboratory data. The framework will be developed by the Clinical Microbiology Special Interest Group composed of more than 70 members from clinical and public health settings.

Outcome:

A national framework for clinical genomics application, integration of clinical laboratories into national surveillance, and evidence to support Medicare Benefits Schedule funding for clinical genomics.