RRR2 rapid respiratory response in rural and remote regions | LC26

Abstract
Dynamic microbial ecosystems drive chronic and acute respiratory infections, yet current culture-based diagnostics detect pathogens only after clinical deterioration has occurred and often miss key contributors, such as viruses and fungi, as well as emerging antimicrobial resistance. We present an integrated microbiome framework that spans early ecological warning of disease progression through to rapid, near-bedside pathogen detection enabled by Oxford Nanopore sequencing. In a longitudinal cohort of people with cystic fibrosis (CF), we analysed 127 airway metagenomes from sputum and bronchoalveolar lavage samples, sequenced with MinION and PromethION devices. We defined reproducible microbiome states that capture transitions from health-associated communities to pathogen-dominated ecosystems. These microbiome states predicted Pseudomonas aeruginosa colonisation, multidrug resistance, and impending infection up to one year before clinical detection, outperforming read-based and genome-resolved approaches and generalising across more than 1,000 external CF metagenomes from diverse sequencing platforms and geographic regions. Building on these ecological insights, we are deploying an Oxford Nanopore-based rapid response pipeline for paediatric respiratory infections in regional, rural, and remote Australian communities, where delayed diagnostics disproportionately impact Indigenous children. This pipeline delivers comprehensive bacterial and viral profiling within 24–48 hours, enabling clinicians to move beyond empirical therapy and implement targeted treatment during a single clinical encounter. By combining real-time sequencing with microbiome-informed interpretation, our approach addresses both chronic disease surveillance and acute infection management.

Biography
Robert (Rob) Edwards is a microbiologist, bioinformatician, and pioneer in metagenomics. After 25 years in the US developing metagenomics analysis tools and exploring environmental microbial communities, he moved to Australia. His Australian Research Council (ARC) Laureate Fellowship focuses on developing synthetic biology approaches for bacteriophages, and he is funded to use nanopore sequencing in rural and remote regions to understand the microbial causes of lung diseases. Rob has been a nanopore user since the Early Access Programme (EAP) and has taught sequencing and bioinformatics on five continents.