What does whole genome sequencing tell us?
Whole genome sequencing can lead us to a safer, healthier, and more resilient food supply chain, writes Dr Daniel Hurley
Advancements in technology have played a vital role in ensuring the wellbeing of consumers. One such groundbreaking innovation is the adoption of Whole Genome Sequencing (WGS) in microbial food safety. At its core, WGS is a cutting-edge analysis technique that gives unprecedented detail about the genetic makeup of microorganisms, including the ‘bad’ bacteria that can cause foodborne illnesses, as well as the ‘good’ bacteria living in our gut that help us to digest our food.
Traditionally, identifying and tracking microbial pathogens, the ‘bad’ bacteria responsible for foodborne outbreaks, required many different laboratory tests specific to the question being asked and, in some cases, specific to the type of bacteria being questioned! This posed significant challenges as a great deal of skill was needed to perform these different analysis methods and optimise them for each of the various pathogens. However, with the advent of WGS, food safety now has a powerful tool that enables us to delve deep into the low-level DNA differences between individual isolates of pathogens. With careful analysis, the genetic information generated by this tool benefits consumers, regulators, and food producers, enabling us to take significant strides towards ensuring a safer and more secure food supply chain.
Microbial pathogens lurking in our food supply chain can pose severe threats to public health, leading to foodborne illnesses and even outbreaks. Traditionally, identifying the culprits behind foodborne outbreaks relied on limited methods that could only offer a partial or obscured view of what is understood to be a much more complex microbial landscape. This often made it challenging, or impossible, to pinpoint the exact source of a contamination event, resulting in delayed responses and prolonged investigations.
Having the genome blueprint for an outbreak pathogen can distinguish one isolate from a lineup of potential suspects with remarkable accuracy and confidence.
Whole Genome Sequencing has transformed our understanding of microbial pathogens and their role in food safety. Unlike conventional methods, WGS allows us to examine the entire genome of these microorganisms with unparalleled precision. Having the genome blueprint for an outbreak pathogen can distinguish one isolate from a lineup of potential suspects with remarkable accuracy and confidence. This capability to differentiate pathogens at the isolate level has immense implications for food safety: during an outbreak, we can now rapidly characterise the type of bacteria responsible and use this information to inform traceback investigations so that food safety experts and regulators can identify its origin to act swiftly, contain the spread, and prevent further illnesses.
Separate from source tracking and traceability in an outbreak context, the very same data generated by WGS for the initial purpose of pathogen detection and surveillance activities can be separately analysed to answer an entirely different question. This is an important point to highlight as one of the main strengths of WGS.
The same technique will generate data that can be used to answer a survey of questions rather than performing different tests for individual questions. One such example is antimicrobial resistance, where WGS assists in monitoring the presence or absence of specific known antimicrobial resistance genes. If the genome blueprint of a bacterium includes an antimicrobial resistance gene, this means that the bacterium has the information it needs in its arsenal to be able to survive and continue to grow in the presence of an antibiotic that we would typically use in a clinical or medical setting to kill the bacterium and clear an infection when we are ill.
Identifying antimicrobial-resistant bacteria through WGS empowers the food industry to implement targeted control measures and mitigate the spread of antibiotic resistance in the food supply, safeguarding the efficacy of essential antibiotics in the long run.
Unfortunately for us as humans, in the microbial world, antimicrobial-resistance genes are not trade secrets and are frequently shared among neighbours in a microbial community. This sharing of genetic material between different microbes means that the risk associated with infection by a pathogen is constantly changing based on how these microbes have been living in their environment and what they have experienced or been exposed to should we encounter them down the line.
Knowing which antibiotic is more likely to be effective as part of a course of treatment is crucial in the battle against antimicrobial resistance, a global health concern. Identifying antimicrobial-resistant bacteria through WGS empowers the food industry to implement targeted control measures and mitigate the spread of antibiotic resistance in the food supply, safeguarding the efficacy of essential antibiotics in the long run.
While WGS has been revolutionising food safety systems, its implementation has been challenging. One of the primary challenges is the significant investment associated with introducing WGS technology, especially for smaller food industry players. The equipment and infrastructure required for high-throughput sequencing can be expensive and requires ongoing expenditure for maintenance and upgrades. However, many microbial testing solutions are available to engage with WGS and these types of data before the plunge is taken to set up in-house sequencing capability. As with many areas of technology, WGS is becoming more affordable. The cost of generating sequencing data has come down exponentially over the last two decades, and the instruments required have shrunk to roughly the size of a handheld stapler rather than a large domestic fridge.
The cost of generating sequencing data has come down exponentially over the last two decades, and the instruments required have shrunk to roughly the size of a handheld stapler rather than a large domestic fridge.
Managing the massive amount of data generated by WGS demands robust infrastructure. To put the scale of these data in context, if you took all the text from Wikipedia, the smallest WGS instruments today could generate ten to a hundred times more data daily. Engaging with modern solutions to ensure data accessibility, integrity, and security is essential to achieving ongoing value from historical and new sequencing data.
Interpreting these WGS data can be overwhelming, and it is only possible to effi ciently manually analyse with specialised bioinformatic techniques, which may only be readily available to some food safety stakeholders. Bioinformatics is a mix between biology and computer science, and bioinformaticians are experts in translating terabytes of sequencing data into meaningful biological features that inform risk assessments. Training staff to handle the complexities of data analysis and interpretation is essential for realising the benefits of whole genome sequencing.
While WGS has primarily been used to study the ‘bad’ bacteria and other pathogenic microorganisms, there are many opportunities in food safety to focus on the ‘good’ microorganisms as well. Beneficial bacteria can be used as biopreservatives to naturally extend the shelf life of food products. Researchers have used WGS to identify strains with antimicrobial properties that can inhibit the growth of other pathogenic and spoilage bacteria. Incorporating these beneficial bacteria as biopreservatives into food formulations can reduce the need for chemical preservatives which will better align with consumer demands for clean-label and more natural food products.
Beneficial bacteria can be used as biopreservatives to naturally extend the shelf life of food products. Researchers have used WGS to identify strains with antimicrobial properties that can inhibit the growth of other pathogenic and spoilage bacteria.
Probiotics and probiotic supplements are increasingly popular and contain live bacteria that give us health benefits when we take them or eat foods that contain them. Using WGS, the probiotic strains used in these supplements can be characterised to ensure their safety, the absence of antibiotic resistance genes or harmful traits, and identifying new beneficial bacteria with specific health-promoting properties. This information is crucial for consumers to make informed choices and for food producers to develop functional foods enriched with these beneficial bacteria to support digestive health and overall well-being.
Our body has as many bacteria and other microbes as our human cells. Whole genome sequencing can help us understand our complex gut ecosystem to promote a balanced and healthy microbial community, maintaining overall immunity and well-being. Foods such as kefir, kimchi, sauerkraut, and yoghurt contain beneficial bacteria produced during fermentation. Monitoring the microbial dynamics during fermentation ensures that the desired beneficial bacteria dominate the process. This level of control optimises product quality and safety and is greatly enabled by WGS.
Despite the challenges in making WGS more accessible and practical for food safety applications, there are undoubtedly benefits and opportunities that far outweigh the initial implementation hurdles. While WGS has been primarily applied to pathogenic microorganisms, embracing the exciting opportunities to focus on beneficial bacteria will pave the way for a more holistic and balanced approach to food safety, encompassing both the risks posed by pathogens and the benefits of health-promoting bacteria. By collaborating and investing in training staff, the food industry in Ireland can shift from a reactive to a proactive approach and take preventative measures in managing food safety, leading us towards a safer, healthier, and more resilient food supply chain.
About Dr Daniel Hurley
Dr Daniel Hurley is a Lecturer / Assistant Professor in food microbiology and Safety at the UCD School of Agriculture and Food Science. Daniel is the Programme Director of the part-time, online MSc in Food Safety.