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Food Safety: The Rise of Next-Generation Sequencing & Whole-Genome Sequencing

Harini Venkataraman, Ph.D., Analyst
November 24, 2020

Next-generation sequencing (NGS) is a broad term that encompasses several novel DNA sequencing methods, having a profound impact on multiple application areas in the agrifood and health sector. Specifically, there is growing interest in implementing NGS-based methods for food safety applications for use cases like food pathogen detection, food authenticity testing, and tracing the origin of disease outbreaks.

Key players IN the Next-generation sequencing food safety landscape

Given the high impact of NGS in food safety, a good number of established and emerging players are entering this landscape. Hardware innovations in NGS are confined to incremental improvements in speed and scale and dominated by a few big players, as depicted below. Illumina emerges as the most dominant player in the space with its tech applied to food safety, with the company rolling out a new high-throughput sequencer every two to three years. Most food safety labs that provide NGS-based services are likely to use an Illumina machine.

Next-Generation Sequencing NGS Food Safety Palyers

Nevertheless, startups like Clear Labs take a targeted NGS approach to achieve higher accuracy. Clear Labs' targeted NGS helps to identify multiple genetic markers within a broader pool of genetic material. The company claims that its Clear Safety offering can screen for an array of pathogens in a single test. Additionally, long-read sequencing methods developed by companies like Oxford Nanopore Technology and Nanopore Diagnostics form a part of the third-generation sequencing methods and look to compete with Illumina. For instance, Oxford Nanopore Technology (ONT) recently collaborated with the Mars Global Food Safety Center to analyze whether whole-genome sequencing (WGS) data generated by the ONT sequencing platform could accurately predict Salmonella serotypes in comparison to Illumina WGS. Based on the results, the researchers concluded that all 38 Salmonella strains could be accurately predicted to the serotype level using WGS data generated from an Oxford Nanopore sequencer, with a turnaround of 24 hours.

Growing focus on whole-genome sequencing & its global adoption for food safety applications

Among the NGS technologies, WGS, which determines the presence of a single cultured and sequenced isolate, is noteworthy in the context of food safety. As of 2020, countries like the U.S. and a few other European countries show higher adoption rates of WGS for food safety. WGS will likely expand further in the coming years due to stringent food safety regulations. 

Developing robust testing methods for foodborne pathogen detection is of high importance in the food sector, in light of the recent pathogen outbreaks, including the 2018 Escherichia coli outbreak in romaine lettuce in the U.S. and Canada, where WGS played a crucial role in outbreak source identification. Additionally, the Food Safety Modernization Act (FSMA) that came into force in 2011 has been the main catalyst for the growth of WGS technology in the U.S. The FDA's GenomeTrakr is a prime example of a distributed network of laboratories utilizing WGS for pathogen detection and monitoring toward food safety. The number of uploads of raw sequences of Salmonella, E. coli, Campylobacter, Listeria, and other foodborne pathogens made publicly available for data sharing is close to about 250,000.

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The importance of streamlining the collection and interpretation of WGS data is also growing in the EU. In December 2019, The European Food Safety Authority (EFSA) published a scientific opinion on the applicability of next-generation sequencing (NGS) in foodborne outbreak investigations. The report calls for regional and global capacity building based on harmonized, quality-controlled operational systems within European laboratories as an essential requirement for the investigation of cross‐border outbreaks. The favorable regulatory landscape and policies of the EU will push the wider adoption of NGS, including WGS, in the EU.

However, the adoption of WGS in developing countries is hindered by the lack of supporting infrastructure and investment into these technologies. WGS data handling, storage, and interpretation by skilled experts are other factors that are challenging.

Future of NGS/WGS in food safety

In the post-COVID era, there will be heightened interest in food safety applications, given the pressing need to mitigate the risk associated with foodborne pathogens. This will provide a significant opportunity to improve food pathogen detection and traceability technologies and pave the way for wider adoption of NGS/WGS in food safety. Bioinformatics will remain central to the interpretation and application of biological data generated from NGS methods, offering a powerful combined approach. 

Those interested should look to capitalize on the gradual but inevitable rise of NGS methods in food safety. However, it is important to consider factors like speed, ease of use, accuracy, and cost for food pathogen detection technologies when looking to engage in this space.

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