Nanopore sequencing for rapid, intelligent food safety testing

Foodborne contaminants cause 9.4M illnesses in the United States each year; the average recall costs food manufacturers $15M per incident. Salmonella alone causes one million of these illnesses.

When pathogens enter a factory or food supply chain, they can spread rapidly, causing harm to consumers and disruption to the industry. Gaining rapid insights into whether pathogens are present, and what they are is vital in this situation, enabling industries to intervene early with precise actions for better outcomes.

Nanopore sequencing, automated at scale

Today, Clear Labs announced that their ‘Clear Safety’ food safety solution integrates nanopore sequencing by using the GridION X5 for quick-turnaround pathogen testing.

Clear Labs has developed a fully-automated robotics-based sample-to-answer solution to serotype and characterise pathogens in under 24 hours, at high volume. We’re excited about this high-impact application of nanopore sequencing.

Oxford Nanopore sequencing: towards more routine testing

This is the first time (to our knowledge) that Oxford Nanopore’s DNA sequencing technology is being used for a fully-automated test, including robotic library prep. Moreover, the food safety test is AOAC accredited*.

Easier, or more automated use of nanopore technology for high-volume, rapid testing could benefit many industries, whether in a research or more regulated environment. Here are some of the ways we are preparing to broaden these routine uses of nanopore sequencing:

Automation or ease of use

• In-house, we have been developing workflows for partnering nanopore sequencing with robotic methods of high-throughput library preparation. We will be talking more about this soon.
• VolTRAX V2, our automated, programmable, USB-powered preparation device, is now in early access [links]
• MinION Mk1C is a device that incorporates MinION or Flongle flow cells with powerful computing and screen, for rapid sequencing in any environment without the need for a laptop.

High throughput, frequent use

• On-demand sequencing:  The design of PromethION and GridION is modular, so that users can run a single flow cell immediately – without the requirement for sample batching – to obtain rapid results.
• If the test requires only a small volume of sequencing data, then the new Flongle is designed for low-cost, rapid tests. At $90 per flow cell we are excited about seeing what applications Flongle will first be used for; pathogen ID?  Targeted sequencing?  Testing a sample before larger scale sequencing? Education?
• We are continuously scaling up our manufacturing to reflect increased demand for our products, and will be opening a new high-tech production facility this year

Real-time data

• Nanopore sequencing uniquely streams sequence data in real time, meaning that data can be analysed immediately after starting the experiment. Insights can therefore be generated rapidly; critical in many decisions, for example food safety testing.

Quality standards and systems

• Oxford Nanopore has recently achieved certification to ISO 9001:2015, an important step as a rapidly-growing company. This helps us to continue to build on and improve the tools and methods necessary to maintain high levels of quality within our business processes.
• It provides customers, particularly those that have specific requirements in securing their supply chain, with the ongoing assurance that Oxford Nanopore is committed to providing high-quality products that conform to their needs and expectations.
• ISO 9001:2015 also provides a Quality Management platform that Oxford Nanopore plans to build on, for entry into future markets

Read more at AgFunder News

*Association of Official Agricultural Chemists (AOAC), now AOAC International, publisher of standardised methods, most notably in chemical or microbiological analysis.  AOAC standards are often required by government agencies or other organisations.