And metagenomics will radically change the way shelf-life testing of foods is undertaken, added Betts.
The time of genomics – the use of DNA sequencing of organisms in microbial detection and the study of pathogens – has arrived, said Betts.
“WGS is probably the ultimate method of microbiological typing,” said Betts. “You can’t get any deeper than the DNA of an organism.”
The sequence of “base pairs” in the DNA is “totally specific” to any particular organism, he reported. “Not just to E.coli, for example, different types of E.coli have different DNA sequences.”
Analysed at different levels, this DNA gives different levels of information, he said. “We can now sequence the complete DNA of a microorganism in one day,” claimed Betts.
Sequence one enzyme of E.coli
This compares with up to three years that it took to sequence one enzyme in E.coli in the 1980s, he added.
The cost of WGS has now dropped “hugely” and it allows microbiologists to tell whether organisms are the same or different for strain comparison.
By using DNA sequencers together with very powerful computing tools, it is possible to put together the whole genome sequence for an organism.
It allows the comparison of pathogen strains with those held in a database called Genome Trakr, developed by the US Food and Drug Administration.
This database currently holds around 61,000 whole genome sequences, covering salmonella, listeria, E.coli and campylobacter for different countries – including the UK – and is increasing by about 1,000 sequences a month, said Betts.
“With WGS, we can track outbreaks that might be occurring consistently at very low levels over very long time periods and trace them,” he said.
‘Fingerprint the organism’
“We are now looking at WGS as being so specific, we can actually fingerprint the organism and trace it exactly back to where it came from – the food, the company, the factory, whatever, and you can do that all the time.”
Metagenomics is an “population dynamics and ecology tool” that gives an idea of the total flora of micro-organisms present in a food sample.
“Metagenomics is using DNA at a different level,” said Betts. “It doesn’t go into the depth of detail [of WGS] so we are not looking at strain-type here. It will probably take us to a genus level identification.”
It examines the “population genomics”, looking at populations or “ecology in foods” and how they change over time.
“It can be used in things like shelf-life testing and how populations change during the shelf-life of a product or how populations change during fermentation,” said Betts.