The development of molecular biology over the last 30 years – and especially in the last decade – has led to some remarkable advances in the techniques available to microbiologists for investigating foodborne disease outbreaks. The use of PCR and other analytical methods to examine the DNA of microbial pathogens has provided an entirely new toolbox for detecting, identifying and characterising microorganisms at a level of detail previously inconceivable.
The latest, and potentially the most exciting, of these molecular techniques is whole genome sequencing (WGS), which as the name suggests, allows the genome of the organism to be analysed in its entirety. The result is a genetic blueprint rather than a genetic fingerprint. Just a few years ago that would have been a completely impractical exercise requiring a great deal of time and money to accomplish, but the development of next-generation sequencing platforms has made WGS within days a viable proposition. Now huge amounts of genetic data about a specific pathogen can be generated very quickly. Analysing that data is getting easier too, as the rapidly growing science of bioinformatics builds online databases of genetic information that can be interrogated by researchers keen to compare their findings with what is already known.
Just how useful this technology can be is illustrated by a recently published study carried out by a team of Austrian researchers who examined two strains of Listeria monocytogenes isolated during an outbreak of infection linked to contaminated curd cheese in 2009-2010. Both strains belonged to serotype 1/2a and were closely related. In fact it might not even have been possible to differentiate them at all not so long ago. But WGS enabled the Austrian team to show that they were different in some important ways. Each possessed different virulence factors, which explained why they were so infectious and why eight of the 34 people infected in the outbreak died. There were also differences in genes related to their resistance to environmental stress. The differences were enough for the researchers to conclude that the two strains entered the food chain independently, despite their close similarities. Without WGS, it would be virtually impossible to draw such a conclusion.
This sort of research can tell us an awful lot about the sources of foodborne pathogens, how they get into our food and how they survive processing and end up in the finished product. The more we know about pathogens, the better we will be able to devise effective strategies to keep them out of the food supply. I think we have only just begun to scratch the surface as far as the potential applications of WGS are concerned. Faster and cheaper sequencing, exponentially expanding genetic databases and better analytical software will open up a completely new understanding of microbial pathogens that can only benefit the safety of our food in the future.