Developing affordable phylodynamic surveillance workflows for under-resourced settings

Principal Investigator

This project will develop affordable, robust phylodynamic surveillance workflows for regional and resource-limited settings by combining low-cost portable sequencing with modelling approaches that can accommodate lower-quality data. Building on previous work estimating transmission dynamics in drug-resistant community-associated MRSA outbreaks in Papua New Guinea and Far North Queensland, the team will optimise DNA extraction and multiplexed Oxford Nanopore sequencing, benchmark results against existing Illumina data, and quantify how sequencing technology, variant-calling pipelines, pathogen species and Bayesian prior choices affect epidemiological estimates. The project will establish best-practice workflows and software for routine genomic surveillance, strengthen collaboration across northern Australia and Papua New Guinea, and support more accessible evidence-based outbreak control and antimicrobial-resistance decision-making.

23 Feb 2022 - 23 Feb 2023

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