Developing phylodynamic methods and tools for bacterial pathogens in Far North Queensland

Transmission of drug-resistant infectious diseases presents a significant threat for Northern Australia, particularly through the critical interface between regional Far North Queensland (FNQ) and our nearest neighbour Papua New-Guinea (PNG). Indeed, the re-emergence of community associated methicillin-resistant Staphylococcus aureus (MRSA) strains in FNQ is a troubling development for the region (up to 73% carriage rates in some communities, the highest in Australia, in preparation Dr Simon Smith). These strains share an unusually high incidence of osteomyelitis and antibiograms with strains from Madang and Goroka in PNG (in preparation) suggesting transmission routes through Northern Australia already exist. To prevent further incursions and severe outbreaks among local communities, it is imperative that we investigate the scale and directionality of cross border transmission using all available genomic and epidemiological data.

To this end, population genomic analyses and phylodynamic methods are useful tools for reconstructing outbreak dynamics. By combining phylogenetic inferences generated from sequence data, and the predictions of transmission dynamic models informed by disease epidemiology, phylodynamic approaches can be used to identify transmission events, compute epidemiological parameters, and describe the evolution and demographics of disease outbreaks. Predominantly, phylodynamic analyses have focused on viral pathogens for which genetic variations can rapidly accumulate. However, the rise of whole-genome sequencing has led to unprecedented genetic resolution making similar inference possible for more slowly evolving bacterial pathogens such as MRSA. Despite this advance, existing phylodynamic models are unable to account for several key aspects of bacterial infection, such as prolonged carriages and variability in the duration of infection, among others.

In this project, we will address these shortcomings by employing an integrated genomics/transmission dynamic modelling approach that extends from the initial sequencing of collected samples through to the reconstruction of outbreak dynamics. In particular, we will utilize existing knowledge of bacterial disease epidemiology and modelling to develop phylodynamic models for MRSA in FNQ and PNG. These will be informed by previously collected sequence data of MRSA from PNG (ethics for this work already secured) and new data from FNQ (sample collection is a separately funded activity, ethics approved for sequencing and analysis).

This project will foster collaboration with researchers from Northern Australia and PNG and expand PRISM’s reach in the Asia-Pacific region, and provide a detailed analysis of the genomic epidemiology and circulation of MRSA in FNQ. Ultimately, these models will be used to enhance policy and decision making at a critical border interface in Northern Australia. Moreover, our project adresses two of the PRISM themes (characterising emerging diseases, new methods for simulation and modelling) and spans three of the five research themes of HOT North (emerging diseases, skin health, antimicrobial resistance).