Uses of Whole-Genome Sequencing
Whole-genome sequencing (WGS), has revolutionized biosciences since its development in 1976. This technology allows for the complete study of bacterial pathogens' genomes and the annotation of genes based on functions. By providing a genomic blueprint for all the phenotypes of the pathogen, WGS offers almost all the information you need for any laboratory purposes -- homology with other pathogens, possible association with diseases, association with the previous outbreaks, drug resistance, variants, and much more.
Like other scientific technologies, WGS has its fair share of advantages. For instance, it lets you scrutinize the entire genome of an organism, allowing you to effectively distinguish every single variant of a bacteria or virus. As such, it provides opportunity to know which diseases are associated with each variant or strain.
It also allows researchers to determine which and how many genes are involved in disease development. In human studies, this can identify predisposition to certain genetic diseases, allowing for more effective family planning. Further, the cost to sequence an entire genome has plummeted since its conception, allowing more researchers and laboratories to utilize this the technology for further applications.
Nevertheless, there are still some limitations with the use of WGS in research. The sheer mass of information makes it difficult to manage the data and to determine what's relevant and what's not. As such, there are still several genes with unknown functions and variants that can't be classified as pathogenic or benign. This large amount of data makes analysis and storage more difficult for researchers. What's worse, they don't always know if it's worth storing the data or not, especially with the added cost, issues on privacy, and ethical dilemmas with insurance companies.
What were its initial uses for the scientific community?
Initially, WGS was used to sequence shorter and simpler genomes of MS2 and phi-X174 bacteriophages. Since then, it was increasingly used for several applications in public health, basic research, and the food and supplement industries. In the United States, WGS is routinely used to detect and investigate a foodborne illness outbreak and other research concerning food safety.
How does WGS support the greater food industry?
Tracking foodborne illness
WGS is a valuable tool used to track a foodborne illness, along with inspection and verification of food safety standards. Food safety laboratories integrate the use of whole-genome sequencing to characterize pathogenic isolates as part of the routine inspection and verification processes to mitigate risks in food safety. The data obtained from WGS can help researchers to identify the bacterial strain responsible for foodborne illness outbreaks.
To have a centralized database of reliable, efficient, and location-specific data on WGS sequences, several laboratories, and health partners sequence the genome of food pathogens and upload the sequence data to the National Center for Biotechnology Investigation (NCBI) in real-time. This process provides their federal partners with the necessary information about pathogens, cross-contamination, source attribution, distribution, and other helpful data.
To aid in public health decisions, the United States Department of Agriculture's Food Safety and Inspection Service (FSIS) started sequencing Salmonella and Campylobacter in 2016 as part of the National Antimicrobial Resistance Monitoring System (NARMS). The FSIS together with other public health partners use the information from WGS and pulse-field gel electrophoresis (PFGE) in their regulatory decisions.
Identifying Transient or Residential Microorganisms
WGS is a great tool in Food Safety Plans and Environmental Monitoring Programs. When you receive a positive pathogenic result, you will want to investigate the root cause of contamination. WGS can be used to identify the species of pathogenic bacteria in order to help you determine if contamination is from transient microorganisms coming from outside your facility or is originating from residential ones inside your facility. From there, you will able to make informed and efficient decisions for your Corrective Actions.
Identifying Microorganisms in Fermented Food
If you're in the food industry and are aiming to improve your products such as kombucha, kefir, hot sauce, and other fermented foods, you can also employ WGS to identify the bacteria in your microbial cocktail. As they express metabolites based on the strain and their interaction with other bacteria in the cocktail, the taste, smell, and quality of your food products may vary with a change in the microorganisms present in your cocktail.
By knowing the exact species of bacteria in your library, you can mix and match them and create the perfect culture that will improve your product.
Eurofins is Your Partner in Whole Genome Sequencing and Food Safety
Eurofins has a keen focus on analytical methods, including WGS, to develop client-specific scientific testing solutions that exceed quality standards. We provide more than 200,000 analytical methods to characterize the purity and quality of food products and ingredients, detect allergens and contaminants, and provide relevant data on the quality of your food products. Our global network of food scientists and laboratories will help you minimize the risk of non-compliance in your raw ingredients and final products.
Partner with us and meet the market's emergent food quality and safety solutions. We pride ourselves on our industry-leading turnaround time and responsive customer service. To learn how WGS can help you provide safe and quality food for your consumers, contact us today!
