Nanopore whole-genome sequencing of foodborne pathogens

Overview

Food safety is a top priority, and addressing microbial foodborne pathogens is crucial for protecting public health and the food supply chain. Food safety and public health laboratories play a key role in isolating, sequencing, and characterising foodborne microbial contaminants to trace the sources of outbreaks and implement effective control measures. This valuable information supports food manufacturers and the public health community in preventing, identifying, and controlling contamination/outbreaks.

The increasing accessibility and adoption of next-generation sequencing in public health settings is making whole-genome sequencing an indispensable tool for detecting, identifying, and classifying foodborne pathogens. Recent advancements in the machine learning algorithms used for basecalling nanopore data have enhanced the accuracy of generating closed microbial genome assemblies using only nanopore reads. This application note highlights the potential of nanopore sequencing as a robust and standalone platform for whole-genome sequencing of foodborne pathogens, offering a promising approach for improving food safety.

Workflow: bacterial isolate sequencing

To learn more, you can also download a rapid end-to-end workflow for whole-genome sequencing of bacterial isolates, using MinION Flow Cells on MinION or GridION sequencing devices and the EPI2ME analysis platform.