NCM 2023 Houston: Nanopore sequencing for enhanced antimicrobial resistance gene surveillance

Antimicrobial resistance (AMR) remains a critical public health concern, particularly among bacteria such  as Citrobacter freundii and Acinetobacter baumannii. Addressing this issue necessitates identifying genes  associated with AMR, which in turn aids in understanding and mitigating outbreaks. However, conventional  short-read sequencing technologies often yield truncated gene sequences and limited plasmid  identification capabilities. To assess the potential of nanopore sequencing for AMR gene surveillance, we  conducted a comprehensive analysis of 178 bacterial isolates from 12 distinct organisms within a public  health context. Our findings demonstrate that nanopore sequencing exhibits a higher likelihood of  completing partial gene matches and offers a more comprehensive depiction of plasmid content within the  isolates. These promising results underscore the utility of nanopore sequencing as a valuable tool for  advancing AMR surveillance and management strategies.