Food Safety: NGS-based Methods of Surveillance
What is food safety?
Food safety is the set of practices to prevent harmful food contamination and foodborne illnesses.1
As a significant part of the global supply chain, food has extensive integration within a complex network of producers, distributors, and other entities before reaching consumers. Managing food safety is an essential part of the overall process to ensure public health.
Among the risks associated with food safety, foodborne illness related to microbial contamination from bacteria, viruses, and parasites represents a substantial threat to human health. Approximately 1 in 10 people worldwide become ill with contaminated food. In addition, food safety has a significant economic impact, resulting in $110 billion lost each year to productivity and healthcare costs from unsafe foods in low- and middle-income countries.2,3
How is NGS used in food safety surveillance?
Advanced sequencing technologies, such as next-generation sequencing (NGS), offer substantial improvements in food safety by providing sensitive detection coupled with high-throughput capabilities. Laboratory networks such as the GenomeTrakr Network use whole-genome sequencing to identify foodborne pathogens, including Salmonella, Listeria, E. coli, Campylobacter, Vibrio, Cronobacter, and more.4
Participating labs collect and share genomic and geographic data that can be accessed for comparison and analysis to assist in expediting public health responses.4 PulseNet is another such network that coordinates labs from all over the world using whole-genome sequencing to genomically identify foodborne illness outbreaks with known pathogens.5 These programs not only locate the source of foodborne illness but also alert the public and identify gaps in food safety systems.
Read below to explore how the power of NGS is used to advance food safety in areas of early detection, outbreak response, and clinical research.
Early detection
Detecting outbreaks early can limit the spread of foodborne contaminants from microorganisms. See how some researchers are using NGS to enable early detection of pathogens.
Advantages of high-throughput sequencing in food safety systems
This review article highlights the major advantages of high-throughput sequencing to detect harmful microorganisms, including solutions from Illumina.
Identifying foodborne pathogens in agricultural wastewater
Investigators provide valuable insight into NGS panels to detect multiple foodborne pathogens. Read more on how Illumina systems and products could play important roles in preventing foodborne disease outbreaks.
Outbreak responses
Surveillance networks allow public health officials to respond to outbreaks and guide important decisions. Read how NGS is playing an important role in shaping outbreak responses.
GenomeTrakr testing for foodborne pathogens
Read how whole-genome sequencing (WGS) is being used to support decisions in food safety and public health agencies by providing reliable data to monitor common foodborne pathogens.
Tracking antimicrobial resistance in the food chain with NGS
Learn more about how investigators used NGS to detect and track antimicrobial resistance in the food chain.
Clinical research
Clinical research is essential in identifying and characterizing foodborne illnesses, serving important roles such as data analysis for rapid interpretation to inform guided action for public health. Read examples of these advances in place that could impact future efforts.
WGS for food and feed safety with PulseNet and GenomeTrakr
Read about national efforts from the NIH, CDC, FDA, USDA, and other governmental agencies to use WGS data analysis (PulseNet and GeomeTrakr) to characterize virulence and antimicrobial resistance profiles for food safety.
Antimicrobial resistance in pig farms
See how researchers used NGS to detect genomic associations with antimicrobial resistance in pigs.
Featured Product
Illumina DNA Prep
A fast, integrated workflow for a wide range of applications, from whole-genome sequencing to amplicons, plasmids, and microbial species. With workflow times of around 3.5 hours and flexibility to accommodate variations in sample types and DNA input amounts, Illumina DNA Prep is optimized to deliver exceptional performance with robust reliability.
Featured workflow for food safety surveillance
Prepare Library
Illumina DNA Prep
A fast, integrated workflow for a wide range of applications, from whole-genome sequencing to amplicons, plasmids, and microbial species.
Sequence
iSeq 100
Leverage speed and affordability of complementary metal-oxide-semiconductor (CMOS) technology and the accuracy of sequencing by synthesis (SBS) chemistry for powerful next-generation sequencing (NGS) technology.
MiSeq
The MiSeq System expands your research with a wide range of sequencing applications. Capable of automated paired-end reads and up to 15 Gb per run, this system delivers over 600 bases of sequence data per read.
MiniSeq
The MiniSeq System delivers cost-efficient rapid sequencing, even for low numbers of samples. The small footprint allows it to fit seamlessly into laboratories, with no need for specialized, ancillary equipment.
Analyze Data
SRST2
The SRST2 app reports the presence of STs (sequence types) from a MLST database and/or reference genes from a sequence database of virulence genes, resistance genes, and plasmid replicons.
Related Content
Analyzing food safety capabilities with the NextSeq 2000
Learn more about how the NextSeq 2000 P1 and P2 600 cycle flow cells produce 2x longer reads with no reduction in sequencing quality for better discrimination with lower read depth for metagenomic datasets. This improved resolution enables higher throughput sequencing applications for food safety.
Efficient bacterial typing with the MiSeq system
This application note details the MiSeq capabilities to deliver rapid results using a streamlined workflow using L. monocytogenes samples for foodborne safety.
Finding sources of foodborne illness outbreaks
Download this infographic to learn more about how whole-genome sequencing is used in finding foodborne pathogens.
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- What does food safety mean? ask.usda.gov/s/article/What-does-food-safety-mean. Accessed November 27, 2023.
- CDC and Food Safety. cdc.gov/foodsafety/cdc-and-food-safety. Accessed November 27, 2023.
- Food safety. who.int/news-room/fact-sheets/detail/food-safety. Accessed November 27, 2023.
- GenomeTrakr Fast Facts. fda.gov/food/whole-genome-sequencing-wgs-program/genometrakr-fast-facts. Accessed November 27, 2023.
- Surveillance and Data Systems. cdc.gov/ncezid/dfwed/keyprograms/surveillance.html. Accessed January 17, 2024