Whole Genome Sequencing: A Powerful Tool for Food Safety and Public Health
What Is Whole Genome Sequencing?
Whole genome sequencing (WGS) is the process of determining the complete DNA sequence of an organism’s genome whether human, bacteria, or animal. It provides detailed insights into both the identity and characteristics of a sample, making it a vital tool across disciplines from medicine to food safety.
A Brief History of Genome Sequencing
Genome sequencing has come a long way since its origins in the 1970s with Sanger sequencing, a slow and costly method at the time. The 1990s ushered in the Human Genome Project, which introduced second-generation sequencing—faster, but still expensive, with costs in the millions for a single genome.
By 2003, the Human Genome Project was completed, paving the way for next-generation sequencing (NGS). Companies began to adopt this faster, more affordable technology. In 2007, sequencing a genome cost tens of thousands of dollars; by 2015, that dropped to around $1,000. Today, thanks to continued innovation in kit chemistry and instrumentation, sequencing is faster, more precise, and more accessible than ever.
Next-Generation Sequencing in Food Safety
NGS comes in two main forms:
- Long-read sequencing: Uses technologies like nanopores to read DNA sequences up to 100,000 base pairs. Ideal for identifying structural features of organisms.
- Short-read sequencing: Focuses on smaller fragments with high accuracy. Widely used for analyzing functional gene characteristics.
These technologies are transforming food safety. For example, during a Salmonella outbreak, WGS can identify the specific strain and trace its path through the food supply chain, environment, and clinical cases. This level of resolution enables preventative monitoring and faster response—capabilities that were unimaginable just decades ago.
Spotlight on Cronobacter sakazakii in Infant Formula
Cronobacter sakazakii is a resilient, opportunistic pathogen that thrives in dry environments. First isolated in the 1950s, it has become a growing concern in powdered infant formula, where even trace contamination can pose serious risks to vulnerable infants.
Contamination can occur not only through ingredients but also during formula preparation—via unclean surfaces, improper handling, or environmental exposure. Its prevalence and resistance make it a formidable challenge for manufacturers and caregivers alike.
FDA Action and Genomic Oversight
The U.S. Food and Drug Administration (FDA) is actively working to raise awareness about Cronobacter risks and promote microbiological sanitation practices. Their efforts include:
- Developing models to identify contamination points in manufacturing and distribution
- Promoting education and best practices among manufacturers
- Recommending whole genome sequencing to confirm presumptive positives and characterize to the strain level
The National Advisory Committee on Microbiological Criteria for Foods (NACMCF) is supporting the FDA with two key initiatives:
- Genomic risk profiling: Scientists are using WGS to better understand the risks associated with different Cronobacter strains.
- Public education: Helping consumers and caregivers understand the illness, its risks, and how to follow FDA guidance.
Why Whole Genome Sequencing Matters
Whole genome sequencing is no longer just a research tool. It’s a critical asset in food safety, outbreak response, and public health protection. From identifying pathogens to tracing contamination sources, WGS empowers labs, manufacturers, and regulators to act swiftly and precisely.
As technology continues to evolve, so does our ability to safeguard the food supply and protect the most vulnerable populations.
Conclusion
Understanding organisms like Salmonella and Cronobacter is critical, especially given their widespread presence and the serious risks they pose to vulnerable populations, including infants. As technology advances, whole genome sequencing continues to transform our ability to detect, characterize, and respond to microbial threats with greater precision. By staying aligned with FDA guidelines and leveraging cutting-edge genomic tools, manufacturers and laboratories can ensure safer products, stronger prevention strategies, and greater confidence in public health protection.
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