The applications and advantages of nanopore sequencing in bacterial antimicrobial resistance surveillance and research

This review paper examines how long-read nanopore sequencing technology is transforming bacterial antimicrobial resistance (AMR) research and surveillance. It highlights that nanopore devices deliver ultra-long DNA reads and real-time sequencing, enabling detailed assembly of whole bacterial genomes, rapid detection of antimicrobial resistance genes (ARGs), and analysis of their genomic context (e.g., mobile elements, plasmids). These advantages support quicker clinical diagnostics and more comprehensive tracking of ARG dissemination in bacteria and microbiomes. The article also discusses technical advancements, current limitations (like error rates and costs), and prospects for expanding the use of nanopore sequencing in AMR monitoring.