The power, potential, benefits, and challenges of implementing high-throughput sequencing in food safety systems

Abstract

The development and application of modern sequencing technologies have led to many new improvements in food safety and public health. With unprecedented resolution and big data, high-throughput sequencing (HTS) has enabled food safety specialists to sequence marker genes, whole genomes, and transcriptomes of microorganisms almost in real-time. These data reveal not only the identity of a pathogen or an organism of interest in the food supply but its virulence potential and functional characteristics. HTS of amplicons, allow better characterization of the microbial communities associated with food and the environment. New and powerful bioinformatics tools, algorithms, and machine learning allow for development of new models to predict and tackle important events such as foodborne disease outbreaks. Despite its potential, the integration of HTS into current food safety systems is far from complete. Government agencies have embraced this new technology, and use it for disease diagnostics, food safety inspections, and outbreak investigations. However, adoption and application of HTS by the food industry have been comparatively slow, sporadic, and fragmented. Incorporation of HTS by food manufacturers in their food safety programs could reinforce the design and verification of effectiveness of control measures by providing greater insight into the characteristics, origin, relatedness, and evolution of microorganisms in our foods and environment. Here, we discuss this new technology, its power, and potential. A brief history of implementation by public health agencies is presented, as are the benefits and challenges for the food industry, and its future in the context of food safety.

Quantitative prediction of disinfectant tolerance inListeria monocytogenesusing whole genome sequencing and machine learning

“…In practice, the implementation of genome sequencing applications in the food industry is relatively slow. Imanian et al have described some essential factors that influence the food industry’s interest in high-throughput sequencing, such as improvement or verification of control measure design, reduced food safety management costs, and the increased shift of governmental agencies towards WGS-based applications [12]. Our study proposes another possible application of WGS that could improve L. monocytogenes control measure design and reduce food safety management costs.…”

“…The recent rise of interest in sequencing-based applications in the food industry and the switch of many national pathogen surveillance programs to WGS approaches gives rise to copious genome sequencing data [12]. Disentangling the complex relationships between genotypic information and phenotypic traits in hundreds to thousands of bacterial samples is a complex task.…”

Nanopore sequencing technology and its applications

“…It can also confirm the specific typing of patient‐infected strains and detect drug resistance‐associated gene mutations 266 . Additionally, nanopore sequencing has been applied to the detection of foodborne pathogens through the detection of specific genes or whole‐genome sequencing to identify pathogen types and predict their potential virulence characteristics 267 …”

Dry surface biofilms in the food processing industry: An overview on surface characteristics, adhesion and biofilm formation, detection of biofilms, and dry sanitization methods

“…WGS is an accurate identification technique used to determining potential outbreak clusters (Baert et al., 2021; Yu et al., 2020). Through this technique, it is possible to obtain information on subtyping, serotype, virulence gene profile, and antibiotic resistance determinants (Imanian et al., 2022). The whole genome sequence obtained by WGS may be used for comparison to a PulseNet maintained database, which contains microorganism data, such as that for E. coli , Salmonella , and Listeria (Yu et al., 2020).…”