The usefulness of Nanopore Sequencing in Whole-Genome Sequencing-Based Genotyping ofListeria monocytogenesandSalmonella entericaserovar Enteritidis

Abstract

ABSTRACTBacterial genotyping through whole-genome sequencing plays a crucial role in disease surveillance and outbreak investigations in public health laboratories. This study assessed the effectiveness of Nanopore Oxford Technologies (ONT) sequencing in the genotyping ofListeria monocytogenesandSalmonella entericaserovar Enteritidis. Our results indicated that ONT sequences, generated with the R10.4.1 flow cell and basecalled using the Dorado 0.5.0 Super Accurate 4.3 model, exhibited comparable accuracy to Illumina sequences, effectively discriminating among bacterial strains from outbreaks. These findings suggest that ONT sequencing has the potential to be a promising tool for rapid whole-genome sequencing of bacterial pathogens in public health laboratories for epidemiological investigations.