Whole-genome sequencing (WGS) is one of the new buzzwords in food safety. This article is a brief review of what WGS is and how it has revolutionized food safety in recent years. It has now become an integral part of public health surveillance and is increasingly used by the food industry in the United States and abroad to study foodborne bacterial pathogens, indicator and spoilage organisms, and the spread of antimicrobial resistance, virulence, and more. WGS in food safety has particularly focused on bacteria (the subject of this article), but it is equally efficient to use with viruses and parasites.
WGS determines the full genetic makeup of a cell—the “genome,” which consists of the chromosome and extrachromosomal elements, such as plasmids. Both are circular structures, but chromosomes are much bigger [1–6 million DNA base pairs (bp)] than plasmids (~500–a few hundred thousand bp). For many years, it was only possible to sequence short stretches of DNA up to a few thousand bp, but around 2000, it became possible to determine the whole genomic sequence by sequencing it many times in small, overlapping random pieces (~25–several thousand bp) in one reaction (massive parallel sequencing). These millions of overlapping sequences can then be aligned to each other like puzzle pieces, thereby, in theory, establishing the full contiguous sequence of the genome. This assembly is done electronically using special bioinformatics software. Other bioinformatics software can then be used to compare assembled sequences from different bacteria. The bioinformatics software is available online for free in the public domain as well as in commercial packages. Commercial software is typically more user-friendly than open-source software but costly. The cost of software may be recovered if the analysis can be done by existing personnel without hiring bioinformaticians. The actual sequencing reaction is called next-generation sequencing (NGS), and the whole sequencing, assembly, and analysis process is WGS.