Precision Food Safety: a Paradigm Shift in Detection and Control of Foodborne Pathogens

Abstract

The implementation of whole-genome sequencing in food safety has revolutionized foodborne pathogen tracking and outbreak investigations. The vast amounts of genomic data that are being produced through ongoing surveillance efforts continue advancing our understanding of pathogen diversity and genome biology. Produced genomic data are also supporting the use of metagenomics and metatranscriptomics for detection and functional characterization of microbiological hazards in foods and food processing environments. In addition to that, many studies have shown that metabolic and pathogenic potential, antimicrobial resistance, and other phenotypes relevant to food safety can be predicted from whole-genome sequences, omitting the need for multiple laboratory tests. Nevertheless, further work in the area of functional inference is necessary to enable accurate interpretation of functional information inferred from genomic and metagenomic data, as well as real-time detection and tracking of high-risk pathogen subtypes and microbiomes.

Big Data Impacting Dynamic Food Safety Risk Management in the Food Chain

“…The rapid growth of "big data" in the food industry has revolutionized the field of microbial food safety and has led to the term, "precision food safety, " to describe all the various new data sources that can be used to improve food safety risk management (Kovac et al, 2017;Kovac, 2019). For example, genomics-based approaches based on whole genome sequencing (WGS) are greatly advancing our ability to retrospectively detect food safety outbreaks, and WGS is now being routinely used to characterize human, food, and environmental isolates of all key foodborne pathogens, bringing a high level of precision to interpretation of foodborne disease outbreaks (Ronholm et al, 2016;Brown et al, 2019).…”

“…In 2018, two outbreaks of E. coli O157:H7 were linked to the consumption of romaine lettuce in Canada and the United States (Centers for Disease Control, 2018Control, , 2019Public Health Agency of Canada, 2018, 2019. In the first outbreak, clusters of E. coli O157:H7 were linked by WGS sequences, and leafy greens from Yuma growing region identified as the likely source (Food and Drug Administration, 2018a).…”

“…The emergence of precision agriculture, often referred to "smart farming, " using digitalization in farming practices (Bhakta et al, 2019;Shafi et al, 2019) and "omics-based" precision food safety (Kovac et al, 2017;Kovac, 2019) leverages linked data for foodborne outbreak traceability, predictive analytics, artificial intelligence (AI) and machine-learning in the realm of food safety management. Digital transformation in food manufacturing and supply chain enables better utilization of data for more dynamic risk management, automated adjustment for deviations, real-time transparency of food safety and quality control parameters, product release, defect rate reduction, and trend analysis.…”

FoodMicrobionet v4: A large, integrated, open and transparent database for food bacterial communities

“…Shotgun metagenomics offers significantly higher resolution (down to the strain and perhaps to single nucleotide polymorphism variants (Hildebrand, 2021) and paves the way to accurate source tracking for contamination (De Filippis et al, 2020) and to a new paradigm in food safety (Kovac, 2019). However, amplicon targeted approaches still have the power to describe, in a sensitive and cost-effective way, the structure of food microbial communities down to the genus level and possibly below (Callahan et al, 2016a;Johnson et al, 2019).…”

FoodMicrobionet v4: a large, integrated, open and transparent database for food bacterial communities

“…While amplicon targeted approaches are still prevalent, with the decreasing cost of sequencing and the increase in power of sequencing platforms and of computational tools the number of studies using metagenomic or multi-omics approaches is rapidly increasing (Yap et al, 2021). Shotgun metagenomics offers a significantly higher resolution (down to the strain and perhaps to single nucleotide polymorphism variants (Hildebrand, 2021) and paves the way to accurate source tracking for contamination (De Filippis et al, 2020) and to a new paradigm in food safety (Kovac, 2019). However, amplicon targeted approaches still have the power to describe, in a sensitive and cost-effective way, the structure of food microbial communities down to the genus level or below (Callahan et al, 2016a).…”