Applications of Oxford Nanopore Technology in the analysis of antibiotic resistance genes: A review.

Antibiotic misuse has led to the rapid expansion of the antibiotic resistance gene (ARGs) pool, making antimicrobial resistance (AMR) a major global health threat. The efficient identification of ARGs and the development of strategies to control AMR have become research hotspots. However, the Next-generation sequencing (NGS) has many limitations in ARGs identification, hindering our understanding of their genetic context. This review uses Oxford Nanopore Technology (ONT) as an example to summarize the advantages and application prospects of the third-generation sequencing technologies in the migration and transmission of ARGs. By analyzing 12 sets of NGS - ONT datasets, this review demonstrates the strengths and limitations of ONT from multiple perspectives, including the identification of ARGs, key pathogens, plasmids, viruses, and horizontal gene transfer events, and provides detailed analytical workflows. It offers comprehensive analytical approaches and application insights for ARGs research based on ONT, highlighting the importance and necessity of the third-generation sequencing technologies in studying the prevalence and transmission of ARGs in complex environments.