There is nothing short of a revolution underway in methods used to identify the vast number of microbial life forms in our foods and to learn about their genetic diversity. Many of the names assigned to these methods end in “omics” and include genomics, metagenomics, transcriptomics, proteomics and metabelomics. As the body of knowledge grows in terms of what makes up the microbial ecology in our food supply and how it responds to environmental changes, our ability to improve food safety increases exponentially.
A discipline within the field of genetics, genomics is the study of the composition of DNA and often includes many other disciplines. Genomics has provided numerous benefits to the food industry. From a food safety perspective, traditional plating methods only detect about one per cent of the microbial ecology on foods, limiting their usefulness in food outbreaks. A decades-old technology called pulse field gel electrophoresis (PFGE) can separate the DNA from the bacteria cultured by traditional methods into a unique pattern that can be used to identify the bacteria in question. PFGE is still the core technology used around the world to identify food and human pathogens. There is now a vast library of PFGE information to aid pathologists in their search to identify a pathogen.
Despite advances and refinements in PFGE over the years, this technology is not able to discriminate between closely-related subtypes of some pathogens like Salmonella. In this case a method called whole genome sequencing (WGS) can be used. WGS was used in confirming the source of the L. monocytogenes outbreak in Canada in 2008. This technology is quickly replacing PFGE as the preferred analytical method when establishing genetic identity is critical. Growing demand for and recent refinements in WGS technology have reduced the cost of sequencing a single genome to as little as US$50 per sample from an isolated culture.
Unlike PFGE, WGS is not dependant on cultured isolates. This attribute of WGS has led to development of the field of metagenomics, which attempts to identify bacteria from mixed cultures recovered from a sample and sequenced together without enrichment. Metagenomics has made it possible for us to analyze the entire ecology of our foods and the environments in which they are prepared in a level of detail that we could only dream about a decade ago.
Although WGS and metagenomics are game-changing advances in our quest for improving food safety, this technology is not without its issues – something anyone contemplating using these methods needs to keep in mind. These include:
- Data capture and analysis – Sequencing a mixed culture produces a staggering amount of data, which then has to be analyzed for distinct sequences to identify what species make up the microbial population. This would not be possible without the aid of advanced computer technology, sophisticated software and reference genetic databases of sequences from known species.
- Viability of the species – Unlike traditional culture methods which depend on viable bacteria to grow, WGS makes no distinction as to whether the DNA is from a live or dead species. This can be an issue when analyzing non-cultured samples from a product which has undergone steps to kill pathogens.
- Non-microbial DNA – Human stool samples will have significant amounts of human DNA which needs to be taken into consideration during analysis.
- Genetic stability – Bacteria constantly evolve to adapt to and thrive in changing environments but they can also remain unchanged over time if their environments do not change. The “so what” of all this is that their DNA sequences change by coding for the adaptation necessary to survive. This adds some degree of uncertainty to genetic analysis, and as a result one does not always get a 100-per-cent match with a known reference. On the other hand, it is possible for the same species to turn up in two different facilities if both facilities use or have used the same ingredients and if conditions in each facility are similar.
WGS, metagenomics and the other “omics” are now providing our industry with a means of improving food safety and better understanding the ecological changes that take place on food products. I’ll be writing about transcriptomics, proteomics and metabelomics in future articles.
Dr. R.J. (Ron) Wasik PhD, MBA, CFS, is president of RJW Consulting Canada Ltd. Contact him at [email protected]