The use of next generation sequencing for improving food safety: Translation into practice.
Jagadeesan B, Gerner-Smidt P, Allard MW, Leuillet S, Winkler A, Xiao Y, Chaffron S, Van Der Vossen J, Tang S, Katase M, McClure P, Kimura B, Ching Chai L, Chapman J, Grant K
Food Microbiol. Jun 2019
COMMENT: The implementation of NGS for food safety and the food industry offers several advantages over the traditional microbiological methods of detection. Whole genome sequencing (WGS) of bacterial food pathogens has been already introduced into public health surveillance for retrospective analyses of foodborne outbreaks and for prospective surveillance in four countries. Metagenomics and metabarcoding allows the identification of complete microbial populations associated to food products without the requirement of bacterial cultures. However, many challenges need to be addressed before the widespread use of NGS for the food industry. One of the limitations of using metagenomics in food safety is the absence of a well-curated and high-quality standard database of genomic sequence for pathogenic, probiotic, and functional microbes. This review summarizes the main applications and challenges of NGS in the food industry and provides a list of genomic reference databases for key food pathogens and a list of bioinformatic tools and pipelines available for WGS analysis from bacterial isolates.
Shotgun metagenomics can provide a valuable, rapid view of the presence of genetic markers specifying species, serotype, virulence and AMR genes etc. although, at present, these markers usually cannot be assigned to specific bacterial genomes due to the complexity of the metagenomic data.
Recently, an outbreak benchmark dataset has been publicly released consisting of sequence data, sample metadata and corresponding known phylogenetic trees for L. monocytogenes, S. enterica ser. Bareilly, Escherichia coli, and Campylobacter jejuni and one simulated dataset (https://github.com/WGS-standards-and-analysis/Datasets), for laboratories to use to assess their bioinformatic tools and pipelines.
Groups such as the Consortium for Sequencing the Food Supply Chain (CSFSC), founded by IBM and Mars Incorporated, are putting efforts into collecting genome information on pathogenic bacteria across the food supply chain, as well as characterising and quantifying the microbiome before and after processing to use genomic and metagenomic data to assure food safety, authenticity and traceability.
Critical improvements in the sequencing technologies and bioinformatics are needed before metabarcoding or shotgun metagenomics can be implemented cost-effectively for diagnostics and subtyping of foodborne pathogens in support of public health and food safety. However, the rapid progress of developments in NGS is likely to herald the demise of bacterial culture as one of the principle methods in food microbiology.
The current stage of validation and standardization with respect to strain detection as well as the assignation of virulence and resistance markers to specific species or strains is more advanced in WGS compared to metagenomics.
Metagenomic tools can improve understanding of the microbial ecology of food processing lines. Within a microbial community, interactions between pathogens and the associated microbiome may indicate the existence of a specific pathogen species or impact its colonization.
Food producers will be able to either validate or improve current microbial hazard management using the metagenomic approach to monitor the occurrence and abundance of microbes and genes in the microbial community of food processing lines.
Metagenomic tools can help anticipate microbial spoilage by studying changes in the diversity or proportion of spoilage associated microbes in the microbiota of food products.
There are challenges regarding utilization of the metagenome for the food industry including the detection of DNA originating from dead microbes as well as low sensitivity of detection compared with culture based methods as well as the relatively high costs and further developments in these areas are being pursued.