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Whole Genome Sequencing

Microbial Whole Genome Sequencing and the food industry

Whole Genome Sequencing (WGS) is a technique that enables the complete DNA base sequence of a microorganism to be determined. As the DNA sequence is virtually specific to an individual cell within a population, it is a technique that can be used to identify an individual very precisely and differentiate it from other very similar, but different organisms.


This white paper discusses the potential applications of whole genome sequencing to the food industry.


Introduction


WGS has the potential to render other forms of microbiological identification obsolete. It is more accurate than a serotype, more discriminatory than a pulsed-field gel electrophoresis assay and it can prove relationships between strains with higher resolution than ever before. This is the method which has been adopted by regulatory agencies such as Public Health England and the Food and Drug Administration (FDA) in the USA to identify food poisoning outbreaks and link isolates from outbreaks with those from foods or environmental sources.. Food companies are starting to become more aware of this area and wish to have a constructive dialogue with government agencies; however, there can be a lack of knowledge regarding the technology and the potential uses of it in an industrial setting.


Method


The technique has become more prevalent in the last five years due to rapid advances in sequencing technology that have led to dramatic falls in cost of sequencing. It is now possible to sequence microbial genomes on a routine basis for a few hundred pounds each. Regardless of the technique used, the generation of huge amounts of sequence data has become entirely unremarkable. When a genome is sequenced, the initial output is hundreds of thousands of short sequences. Each of these sequences is a few hundred bases long and represents a tiny fragment of the total genome. The next challenge is to assemble these reads by comparing them to each other and ordering them according to their overlapping ends. This process is analogous to reconstructing an ancient document from fragments of parchment.