Nanopore Long Read Sequencing Methods Development for Environmental Priorities and Microbial Identification

Funding period: 2024-2029
Lead: Derek Smith
Total GRDI funding: $205,374

This research builds upon prior STAGE NGS methods development for pathogen detection and microbial community characterization. The proposed work incorporates emerging approaches to address One Health priorities including the impacts of pollutants on microbial communities and the potential to co-select for pathogens and antimicrobial resistance (AMR). Adaptation of long-read sequencing technologies to a low-cost bait capture protocol allows for detection of AMR genes with flanking sequences used for microbial identification. These flanking sequences can also identify co-selection with pollution associated genes. Development of quasimetagenomic and metagenomic approaches also enhances the ability to characterize microbial communities and assess environmental impacts. The work supported under STAGE does not necessarily focus on gender, underrepresented groups, or vulnerable populations but genomics capacity and methods development could have benefits for these areas of focus in the future. For example, individuals with underlying health conditions may be disproportionality impacted through exposure to unintended pathogens in microbial products as well as the dissemination and enhancement of AMR.