Next-Generation Sequencing in the Food Industry: Friend or Foe?


The FSNS Innovation and Quality (FSNS IQ) Food Safety Center of Excellence provides consultation, client project services, R&D, and education in food safety. Traditional microbiological diagnostics and customized client studies are offered, as well as cutting-edge services that leverage Next-Generation Sequencing (NGS) techniques.

The power of NGS methods is promising and exciting, yet can be frightening to food producers fearful of the unknown. It is true, what you do not know about the microorganisms in your production environment can hurt you. Fortunately, those willing to embrace NGS-derived information have a tremendous opportunity to stay ahead of regulators, fortify their food safety programs, and protect consumer health. A new level of microbial “fingerprint” identification is possible thanks to NGS techniques, which have opened doors to fascinating possibilities in the realm of identification of allergens and pathogens from a single sample, predictive microbiome interpretation, detection of genetic modifications, and verification of raw material and finished product authenticity. As the Food and Drug Administration (FDA) and the United States Department of Agriculture (USDA) begin utilizing whole genome sequencing (WGS) techniques for clinical outbreak investigations and tracking of food product and facility pathogen isolates, many in the industry are weary of the terms “NGS” and “WGS”. When appropriate, FDA investigators compare pathogenic isolates from food and production environments to the Genome Trakr sequence database, which can be considered the next iteration of the PulseNet database that utilizes lower-resolution pulsed field gel electrophoresis (PFGE). If a pathogen sequence from a food product in commerce matches a public illness with corresponding epidemiology, then yes, high-resolution sequence information might be a bad thing for the food producer. However, NGS techniques can be leveraged as preventive tools to help stay ahead of adverse events, and may provide utility in other avenues. Here, NGS techniques are further described, providing support that these techniques should be considered your friend and not a foe. FSNS IQ is a resource for guidance on these techniques.

The rise of NGS and its use for WGS and other approaches occurred quickly due to technological advances that dropped both sequencing cost and turnaround time. What once took months and thousands of dollars to sequence a bacterial genome, now takes a few hundred dollars and 1-2 weeks, or less. WGS can be used to define the genomic sequence of a foodborne pathogen with high resolution. Unlike serotyping by PFGE, WGS allows for strain differentiation by the number of single nucleotide polymorphisms, or SNPs (an SNP is a single nucleotide base difference between two bacterial genomes that can be anywhere from 2 to 5 million nucleotide base pairs). As much as a high resolution genetic match can add to the weight of the evidence in an outbreak investigation, the resolution may also be exculpatory as the potential for inaccurate outbreak strain identification is decreased. Public databases containing pathogen sequences (such as Genome Trakr) demonstrate the presence of identical clonal pathogen isolates across the country, devoid of epidemiological linkage. The phenomena highlights the point that sequence data alone should not be exclusively inculpatory in outbreak investigation, and that outbreak epidemiology data is more imperative than ever for assignment of responsibility.

Genetic fingerprinting can also be used to differentiate between resident persistent and transient isolates, which for example, could be of value during Listeria monocytogenes Seek and Destroy efforts. A persistent characterization provides insight that the previous approaches were not effective at removing the target pathogen whereas the transient characterization provides knowledge that different isolates of the same pathogen are being introduced into the facility by supplies, equipment, or people. QA and sanitation managers with increasingly specific pathogen isolate information present in the production environment or product supply lines can take more precisely targeted, aggressive, and effective actions.

The sky is the limit with the creative use of genetic sequencing in food microbiology. As another example, WGS may be used to maintain or enhance food quality of fermented products such as beer, wine, cheese, or soy by verifying the genetic stability of starter cultures prone to mutation over time (e.g. yeasts, molds, lactic acid bacteria, etc.).

WGS is not the only useful application of NGS in the food production facility. FSNS IQ customers can now fully characterize the environmental microbiome via metagenomic fingerprinting, which may provide invaluable, cost effective insight to pathogen and spoilage risks associated with raw materials and finished products. Our clients may select samples collected from their standard environmental monitoring program for metagenomic sequencing. Over time, clients may build a map of frequently occurring genes (i.e. housekeeping genes) that will allow for the determination of all microbial families, genera, and species present. In defining a baseline of microbial presence and the metagenomic fingerprint, Quality Assurance and Sanitation teams can keep a pulse on the effects of any changes to cleaning and sanitation procedures or new raw material types or sources have on the environment’s genetic background. Some of our clients are exploring ways characteristic changes in the microbiome may be predictors of pathogens, spoilage organisms, and even allergens.

Other hot questions in food testing can be answered by NGS methods as well. GMO-testing, meat speciation, allergen testing, pathogen detection, and authenticity testing can all be completed via rapid sequence characterization. For example, the genetic markers specific to genetically modified soy or corn can be rapidly detected in order to verify claims of “non-GMO”, or authentic sourcing. Meat speciation can be a useful tool in verifying kosher compliance, and authenticity and allergen testing can be performed to determine if procured raw ingredients are correct, such as “gluten-free” grains, spices, or olive oil.

FSNS IQ is prepared to deploy a full arsenal of NGS-driven weaponry to enhance the fight to protect your brand and public health by providing wholesome foods, backed by genetic evidence. From environmental metagenomics, to GMO, authenticity, pathogen and allergen testing, to the sequencing of entire isolate genomes, NGS should be fully embraced by areas from farm to fork, and considered an ally in food safety.

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