NCM 2023 Houston: Improving bacterial disease public health testing with nanopore sequencing

Our laboratory has been developing testing and analysis tools focused on next generation sequencing (NGS) to improve bacterial disease public health work for the last 10 years. Nanopore sequencing has enhanced and improved our work in many ways. We have utilized long-read nanopore sequencing to investigate the relatedness of plasmids in antibiotic resistant bacteria and elucidate antimicrobial resistance mechanisms. Our targeted NGS approaches have benefited from nanopore sequencing which has provided rapid, accurate and cost-effective testing to identify drug-resistant Mycobacterium tuberculosis from patient specimens Additionally, testing to identify unknown bacteria to the species level by 16S and other conserved targets is being utilized. Future work will include exploring direct specimen NGS and continuing to optimize NGS testing approaches for public health action.