FSA: WGS revolutionising outbreak investigation

By Joseph James Whitworth contact

- Last updated on GMT

Picture: FSA. WGS speed vs traditional steps
Picture: FSA. WGS speed vs traditional steps

Related tags: Bacteria

Increasing speed and decreasing costs of genome sequencing technology is having a ‘transformative effect’ on foodborne disease outbreak investigation, according to the UK Food Standards Agency’s chief scientific adviser.

The level of detail it now has will allow quick identification and control of the outbreak source, which is an increasingly difficult challenge in the globalised food system, he said.

Turnaround time for analysis of Salmonella isolates has been reduced from up to 20 days to around a week.

WGS changing outbreak investigation

Guy Poppy made the comments in the third issue of a Science Report​ which looks at whole genome sequencing (WGS), the science of mapping the genetic make-up of micro-organisms, and how the technology can help with the FSA’s work.

The previous two issues covered microbiological and chemical risks.

Professor Poppy said: “Whole genome sequencing is a great example of how the FSA can use state of the art technology to ensure that we deliver food we can trust for UK citizens. It’s fast, precise and, if implemented widely, cheap.

“The technology is already being utilised by the FSA and PHE to aid outbreak investigations; but it has a multitude of other potential applications in relation to food.

“While traditional microbiological, epidemiological and food chain investigation methods still have an important role to play, there is no doubt that WGS is revolutionising outbreak investigations, and is likely to have similar impact in other areas of interest to the FSA.”

Two ongoing projects are looking at possible ways to integrate sequence data with other associated information, such as geographical origin, to improve food safety.

Whole genome sequencing involves ‘reading’ the order of all the nucleotides, one by one

There are a few million nucleotides in the genome of bacteria and a few thousand for viruses – and can be sequenced for less than £100, and in just a few hours, said the report.

Poppy said, at present, different techniques are used to identify and characterise bacteria, and to distinguish between different strains of a species. The method varies depending on the species in question and on what information is required.

They include serotyping, phage typing, pulsed field gel electrophoresis (PFGE) and Multi Locus Variable Number Tandem Repeat Analysis (MLVA).

Poppy said these techniques do not have the resolving power that WGS has and maintaining the resources (including staff expertise) for them is a challenge for cost efficiency and resilience in public health laboratories.

Pending trials, Public Health England (PHE) will replace traditional microbiological methods for distinguishing strains with WGS, for routine analysis of Salmonella, Shiga toxin-producing E. coli, Campylobacter and Listeria.

The European Food Safety Authority (EFSA) held a meeting in 2014 and recommended WGS be initiated ‘as soon as possible’ to exploit its potential.

In the US, WGS has been used for Listeria monocytogenes since 2013 and the US Food and Drug Administration (FDA) has the GenomeTrakr network of laboratories, including three from the UK.

It has more than 51,000 isolates sequenced and more than 1,000 are being added each month.

Data integrity and authenticity potential

FSA is a member of the Global Microbial Identifier (GMI) group which started in 2012 with 25 participants but now has more than 200 experts representing 40 countries.

The GMI aim is to have one global system of databases for sharing the genomic sequence data from disease-causing microorganisms.

The detail provided by WGS gives a better ability to detect clusters and identify outbreaks otherwise thought of as independent, unlinked sporadic cases – and this helps to trace the source and prevent further cases, said Poppy.

He added for data from different sources to be compared meaningfully, there will need to be globally standardised, quality-controlled procedures and ways of recording it.

“Another big challenge in implementing the use of WGS more widely is how to handle the huge amount of data generated – how to store it, and how to interpret it. Correct interpretation of the data requires the skilled expertise of bioinformaticians, and thus it will be crucial to ensure that there are enough people trained in this discipline.”

Poppy said next generation sequencing could also be used for authenticity testing as they reveal all species in a particular sample, however, they tend to be less sensitive than traditional DNA-based methods such as real-time PCR.

Related topics: Food Safety & Quality

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