Foodborne pathogen surveillance with Oxford Nanopore sequencing

Explore how Oxford Nanopore Technologies is driving innovation in food safety and public health through rapid, high-resolution genomic surveillance of foodborne pathogens. In this webinar, experts from Eurofins and CDC PulseNet share how Oxford Nanopore sequencing is being applied in both commercial and public health laboratories to enhance outbreak response and improve routine monitoring — without the need to centralise testing or ship live pathogens.

Eurofins will introduce a harmonised, high-throughput workflow built on Oxford Nanopore technology, designed for accurate identification of Salmonella, Listeria, and Cronobacter species. Validated across laboratories in the US and France, the workflow enables consistent, strain-level pathogen profiling — supporting both proactive surveillance and reactive investigations.

CDC PulseNet will present findings from their extensive evaluation of nanopore-based sequencing for national and international foodborne pathogen monitoring. This includes comparisons with short-read platforms for genotyping precision, as well as progress towards standardised, scalable implementation of long-read sequencing across a distributed lab network. These efforts align with PulseNet’s aim to strengthen global capacity for genomic epidemiology.

Together, these talks highlight the role of Oxford Nanopore sequencing in enabling rapid, genomic surveillance — from routine monitoring to outbreak response.

Learning outcomes

• Understand how Eurofins has implemented harmonised, high-throughput workflows using Oxford Nanopore’s sequencing technology to identify key foodborne pathogens at strain level.

• Explore the design and validation of nanopore-based workflows for pathogen serotyping and SNV-level resolution.

• Learn how CDC PulseNet has evaluated Oxford Nanopore sequencing for data accuracy, reproducibility, and scalability, including comparisons with short-read technologies.