Squiggles to the Rescue: Nanopore Sequencing and AI for Rapid One Health Surveillance

Nanopore sequencing holds the promise of integrating genomics in rapid One-Health frontline strategies at the intersection of environmental, animal, and global health. This talk will demonstrate how nanopore sequencing can empower our understanding of pathogens and antimicrobial resistance in the clinical and environmental setting. It will also highlight the extant major shortcomings for rapidly translating nanopore data into actual frontline strategies and how leveraging raw nanopore data, or squiggles, and AI-based analysis might help us tackle these shortcomings.

• While we and others have shown that nanopore sequencing can accurately profile pathogenic risk from bacterial isolates in the clinical setting—where comparisons with established diagnostics are available, we will discuss the challenges of implementing nanopore metagenomics for One Health surveillance.
• We will show how the nanopore raw data in combination with AI-based methodology can potentially solve these challenges, and will present a few exemplary projects.
• We will explore our very latest results on actually using these metagenomics advances in the clinical and food safety setting.

We will show how nanopore-driven metagenomic data can give us holistic and rapid insights into pathogens and resistances; we look forward to discussing how laboratory approaches can be adapted to allow for straightforward and on-site generation of such data.