The World Health Organization (WHO) has estimated that in 2010 alone, 600 million cases of foodborne illnesses occurred globally resulting in 420,000 deaths.1 Other annual estimates place these numbers even higher.2 The majority of such cases are due to the contamination of food with microorganisms and/or their toxic waste products.
There are many possible routes of microbial contamination, which include contact with animal waste during slaughter, poor hygiene or infection of food handlers, unsanitary food processing equipment and areas, and washing of produce with water contaminated with animal or human feces.3,4
Along with the ever-growing global trade in food, there is an increasing demand for healthy eating and minimal processing.5 As Dr. Wendy Bedale of the University of Wisconsin-Madison’s Food Research Institute says, “While people are trying to eat more fruits and vegetables, many types of raw produce are being increasingly associated with significant foodborne disease outbreaks. Consumer food trends for “natural” products such as “raw” (unpasteurized) dairy products occur without an understanding of food safety.”
Major pathogens implicated in foodborne illnesses
While viruses such as norovirus and Hepatitis A are responsible for the majority of cases of foodborne illnesses in the developed world, most hospitalizations and deaths are due to bacterial agents.2 Over 90% of food-poisoning illnesses of bacterial origin are caused by species of Staphylococcus, Salmonella, Clostridium, Campylobacter, Listeria, Vibrio, and Bacillus, and strains of Escherichia coli (E. coli). Foods that commonly contain microbial hazards include raw or partially cooked foods of animal origin (eggs, meat, milk, shellfish), and fresh fruits and vegetables. Even drinks such as beer can be affected.
Common symptoms of foodborne illness include nausea, vomiting, stomach cramps, and diarrhea.6 The young, elderly, pregnant, and immunocompromised are particularly vulnerable. Foodborne illnesses carry a high economic burden, with the US economy alone being affected with losses of up to $93.2 billion per year.3 A particular cause for concern is that the overuse and misuse of antimicrobials have led to the emergence of resistant bacteria that do not respond to current treatments, which further exacerbates the impact of certain food pathogens.
Norovirus currently causes the highest number of cases of foodborne outbreaks within the USA, EU and many other countries around the world.3 Foodborne norovirus outbreaks typically stem from contaminated vegetables, fruits, cereals, sprouts, herbs, and spices. Non-heat-treated raspberries, for example, have been a common source of past norovirus outbreaks in Europe. For viruses like these, for which survival rather than growth is key, many of the current food decontamination strategies may not be effective, however.
Rapid and accurate detection of foodborne pathogens is, therefore, essential to prevent foodborne illnesses and to mitigate the associated economic losses.
The impact of next-generation sequencing on food safety
Among the many emerging technologies for use in food microbiology, next generation sequencing (NGS) arguably has the most potential to revolutionize how we prevent and respond to microbial food contamination.7,8 NGS can be used to sequence the whole genomes of target pathogenic microorganisms present in a sample, used as part of a shotgun approach to identify all the microbes in a sample (“metagenomics”), or used to determine which genes are actively being converted into their protein products (“transcriptomics”).
Food safety applications of whole genome sequencing (WGS)
Various traditional subtyping methods (such as PCR, PFGE, antigen-based assays, and MLVA) have proven invaluable for identifying sources of microbial food contamination and tracking the transmission of pathogens from farm to fork.7,8 However, such methods typically require isolation and culture of strains, and it can consequently take up to a week to yield results. Furthermore, these methods can only analyze small portions of the microbial genome unlike WGS, which analyzes the entire genome. WGS has been shown to discriminate between highly clonal pathogens and specific subtypes, e.g., Salmonella serovars, where traditional subtyping methods have failed. Thus, WGS is more accurate for comparing isolates and has the added advantage of being faster than traditional, culture-dependent techniques.
Besides identifying causative pathogens, WGS can be used to predict traits such as virulence and antimicrobial resistance.7 This technology also facilitates the rapid development of assays to detect microbes and strains for which no detection methods are currently available, as illustrated by the European E. coli O104:H4 outbreak in 2011.8 Whole genome sequences for multiple isolates were generated within weeks of the outbreak being reported. These sequences were deposited publicly, enabling the rapid development of PCR assays that could specifically detect the outbreak strain.
Although initially used retrospectively to analyze outbreak-causing pathogens, WGS of microbial pathogens in now increasingly applied to the prospective surveillance of foodborne microbes in the USA, UK, and other parts of Europe.7 For example, in 2013 the Centers for Disease Control and Prevention (CDC) in the USA introduced WGS for listeriosis surveillance, which has led to more and smaller outbreaks being detected earlier, allowing more effective management.
Food applications of metagenomics and transcriptomics
Besides identifying all of the microbes in a sample, metagenomics and transcriptomics can be used to determine isolate traits without the need for culture.7,8 For example, these technologies can be used to examine the factors affecting microbial spoilage, how the microbial ecology changes along the food processing line, and how microbes respond to different antimicrobial strategies. Such data has significant potential for the rational development of new microbial control compounds and strategies.
There are, however, several challenges regarding the use of NGS for food safety.7 These include the detection of DNA originating from both live and dead microbes, and the, sometimes lower, sensitivity of detection compared with culture-based methods. NGS technologies also remain relatively expensive, which prevents access by less-developed countries and may hinder implementation for routine use.
Besides NGS, many other technologies such as electrochemical-, optical-, and nanomaterial-based biosensors have been developed to detect microbial pathogens, although these are typically focused on the detection of single, specific pathogens.9 Each developed method has its own advantages and disadvantages.
The promise of nanotechnology
Nanotechnology is another field of research that will likely have a major impact on food safety.10,11,12 Nanomaterials are now being used to manufacture smart food packaging to monitor food quality, as nanosensors to detect pathogens, and as edible nanopesticide coatings or additives to improve food preservation. Silver nanoparticles are already commercially used for their high antimicrobial activity, while gold nanoparticles have been widely studied for incorporation in biosensors. However, safety concerns remain regarding the accumulation of nanomaterials in the human body and the environment.
Smart sensors and food packaging
Food packaging is used to facilitate product handling, preserve nutritional value, reduce spoilage, and extend product shelf life. Smart packaging technologies could potentially provide additional functions such as communicating measurements of freshness, temperature, and microbial growth in real time.11 Indeed, smart sensors are a next-generation technology that will likely become extensively incorporated in the food packaging of the future. Microbial contamination can be detected by, among others, changes in gas composition within sealed packaging, changes in pH, and the release of volatile compounds. For example, an antitoxin-based RFID sensor was developed for the detection of E. coli and Salmonella in packaged foods. This sensor uses antitoxins immobilized on RFID tags that are incorporated within food packaging. Each sensor can be connected to a wireless network to provide real-time monitoring.
Advances in food preservation technologies
The focus on minimal processing has led to growing implementation of non-thermal preservation technologies such as high hydrostatic pressure (HHP), ultraviolet (UV) radiation, and cold plasma (CP) treatments.13 These offer the advantages of successful microbial reduction with minimal degradation of nutritional value. However, as with all food preservation technologies, the possibility of microbial survivors remains. Furthermore, viruses are more likely to survive such treatments, and at present, we do not have reliable tools to confirm virus inactivation.3 This can lead to overestimation of food safety, which can pose a significant hazard.
Another emerging trend in food preservation is the use of natural antimicrobial compounds, including ethanol, spices, and essential oil extracts of plants such as oregano, rosemary, and garlic.14,15 These have all demonstrated antimicrobial activity following incorporation into edible films.
For food safety to fully benefit from NGS technologies, we require well-curated NGS databases of food-associated microbes.7 As part of the global movement towards implementing NGS in food safety, in 1996 the PulseNet database was set up by the CDC to enable global strain comparisons. Other initiatives include the Sequencing the Food Supply Chain Consortium founded by IBM and MARS Incorporated, and the FOSCOLLAB food safety platform founded by the WHO. As Dr. Abigail Stevenson from the MARS Global Food Safety Center commented, “Technology development is generating more data than ever before, yet the infrastructure for storing and sharing this data is not yet established, preventing effective long-term monitoring of trends or better shared understanding of related incidents. We believe that regulators and food manufacturers have an important role to play in working together to fully embrace new technologies and drive transparency through data sharing. Such an approach could help maximize the value that new technology can bring in protecting the safety of the entire food chain.” Parallel to such developments, there is also an urgent need to close the technological gap between the developed and developing world to facilitate safe global food trade.7
Microbial food contamination poses a serious risk to human health that is associated with significant economic losses. The increasing globalization of the food trade and trends in consumer preferences will continue to place demands on the development of new and improved methods for ensuring food safety, as well as the drafting of matching regulation. “In the future, I foresee more widespread adoption of preventive (vs. reactive) approaches to food safety, and more product traceability requirements,” says Dr. Bedale, while Dr. Stevenson noted, “Globalization of the food supply chain means that an issue in one part of the world often impacts the global supply chain. Robust food safety management practices that ensure food is safe at all stages of production are more important than ever before.”
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