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European foulbrood (EFB) is a honey bee brood disease caused by the bacterium Melissococcus plutonius. Large-scale EFB outbreaks have been reported in several countries in recent decades, which entail costly sanitation measures of affected apiaries to restrict the spread of this contagious pathogen. To mitigate its impact, a better understanding of the population dynamics of the etiological agent is required. We here used multi-locus sequence typing (MLST) to infer the genetic diversity and geographical distribution of 160M. plutonius isolates collected from EFB symptomatic honey bee colonies seven years apart. Isolates belonged to three clonal complexes (CCs) known worldwide and to 12 sequence types (STs), of which five were novel. Phylogenetic and clustering analyses showed that some of these novel sequence types have likely evolved locally during a period of outbreak, but most disappeared again. We further screened the isolates for melissotoxin A (mtxA), a putative virulence gene. The prevalence of STs in which mtxA was frequent increased over time, suggesting that this gene promotes spread. Despite the increased frequency of this gene in the population, the total number of cases decreased, which could be due to stricter control measures implemented before the second sampling period. Our results provide a better understanding of M. plutonius population dynamics and help identify knowledge gaps that limit efficient control of this emerging disease. This research was funded by the Swiss Federal Food Safety and Veterinary Office grant number 1.12.15, the University of Lausanne and Agroscope. EGH was funded by a BBSRC CASE studentship in partnership with Bee Disease Insurance and the National Bee Unit. GEB was funded jointly by a grant from BBSRC, Defra, NERC, the Scottish Government and the Wellcome Trust, under the Insect Pollinator Initiative (BB/I000801/1).

This study was designed to get a broad estimate of the presence and the types of antimicrobial resistance genes across 52 simple ready-to-eat foods. It was also carried out to understand the benefits and drawbacks of using metagenomic sequencing, a fairly new technology, to study AMR genes. An antimicrobial is any substance that kills or inhibits the growth of microorganisms. It includes antibiotics which are used to treat bacterial infections in both humans and animals. Given the relevant selective pressures, the bacteria itself can change and find ways to survive the effects of an antimicrobials. This results in the bacteria becoming resistant to the ‘killing’ effects of antimicrobials and is known as ‘antimicrobial resistance’. The more we use antimicrobials and antibiotics and the way that we use them can increase the chance that bacteria will become resistant to antimicrobials. This is important as it can lead to infections that become more difficult to treat with drugs and poses a risk to the public health. T Addressing AMR is a national strategic priority for the UK Government which has led to the development of a new 20-year Vision for AMR and the 5-year National Action Plan (NAP), which runs until 2024. The NAP lays out how the UK will address the AMR challenge and takes a ‘One-Health’ approach which spans people, animals, agriculture, food and the environment. The NAP includes a specific section on the importance of better food safety to limit the contamination of foods and spread of AMR. This section emphasises the need to strengthen the evidence base for AMR and food safety through research, surveillance and promoting good practice across the food chain. The FSA is playing its part by continuing to fill evidence gaps on the role that food plays in AMR through the commissioning of research and surveillance. We are also promoting and improving UK food hygiene (‘4Cs’ messages) across the food chain that will help reduce exposure to AMR bacteria.

The authenticity of foodstuffs is an important issue for consumers, regulators, producers and processors, as fraudulent practices can negatively affect consumer confidence and safety, as well as the operating models of legitimate businesses. This review provides an overview of the current landscape of Next Generation Sequencing (NGS) applications for food authenticity, and looks to identify the potential future developments for this technology. Specific areas highlighted include the range of NGS platforms and sequence databases available, validation of NGS, and limitations and appropriate uses of these technologies. Many NGS platforms are available, with different properties (such as sequence read length and output) suited to different analyses. Despite this wealth of options, more platforms are being brought out frequently, and advances such as reduced error rate will enable their expanded use for food authenticity. This rapid expansion in the use of DNA sequencing has led to an equally rapid enlargement in sequence databases, and the construction of contemporaneous, authenticated databases may be a useful innovation for the application of NGS to authenticity. Such applications will require robust quality control criteria and proficiency testing schemes, both of which are being developed. Despite several caveats, for example around effective extraction and amplification of DNA, NGS is a strong candidate to become a valuable aid or even the technology of choice to achieve regulatory compliance and reputation protection in a number of food fraud situations, particularly for highly complex food matrices.

Mastitis is a disease of the mammary gland which affects most mammals and is one of the costliest ongoing challenges in modern dairy farming. The most significant challenges in mastitis management are the speed and accuracy of diagnosis and the use of antibiotics. Current mastitis diagnosis in veterinary practices in the United Kingdom utilises culture-based techniques. However, this approach has some limitations including; processing time, species selection biases and culture failure. This ongoing PhD project seeks to assess the utility of high-throughput sequencing technology in addressing the current challenges in mastitis diagnosis. Samples were obtained from cattle from farms in North Yorkshire, United Kingdom. Cattle were selected from monthly somatic cell count records as mastitis positive cases with a cell count between 250 000 and 550 000 cells ml−1 or control animals with a count below 200 000 cells. Mastitis positive cases were further split into bacteriology positive and negative groups. During sampling a cow-side somatic cell test (California Milk Test) was performed to confirm the monthly database readings. All farms sampled were conventional dairy farms with comparable management systems. Samples were collected by trained veterinarians following a pre-defined protocol designed to limit sample contamination. Microbial community diversity, richness and composition will be compared between sample groups to survey for variations which may explain why culture fails in culture negative subclinical cases. 131 sample animals have been assigned to study groups with samples collected, DNA extracted and prepared for sequencing on the Illumina MiSeq platform with results expected in January 2019.

DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) enforcement officers to combat wildlife crime by preventing illegal trade of endangered plant and animal species. The objective of this research was to develop a multi-locus DNA metabarcoding method for forensic wildlife species identification and to evaluate the applicability and reproducibility of this approach across different laboratories. A DNA metabarcoding method was developed that makes use of 12 DNA barcode markers that have demonstrated universal applicability across a wide range of plant and animal taxa and that facilitate the identification of species in samples containing degraded DNA. The DNA metabarcoding method was developed based on Illumina MiSeq amplicon sequencing of well-defined experimental mixtures, for which a bioinformatics pipeline with user-friendly web-interface was developed. The performance of the DNA metabarcoding method was assessed in an international validation trial by 16 laboratories, in which the method was found to be highly reproducible and sensitive enough to identify species present in a mixture at 1% dry weight content. The advanced multi-locus DNA metabarcoding method assessed in this study provides reliable and detailed data on the composition of complex food products, including information on the presence of CITES-listed species. The method can provide improved resolution for species identification, while verifying species with multiple DNA barcodes contributes to an enhanced quality assurance.

The food production system throughout the European Union, which includes farm production, harvesting, transport, processing, storage, marketing and consumption, is vast, complex and open. The high volume of trade in fresh vegetables and fruits contributes to the vulnerability to contamination, whether by accident or intent. Outbreak investigation is critical to understanding the sources of contamination and the steps required to minimize it. The fact that much of the trade in these commodities is international makes it critical that mediation efforts and cooperative research cross national barriers, just as the pathogens do. Enhancing the biosecurity of food production requires assessment of the following: how is the food production system currently organized, in what ways might it be vulnerable to contamination, either accidental or deliberate, what are the primary factors that would allow discrimination between deliberate vs. accidental outbreaks, how can the epidemiological and surveillance systems in Europe be strengthened to shorten outbreak response and mediation times, how can implicated fresh produce be traced to its source, and what forensically valid subtyping method(s) is/are available for detection and discrimination of associated foodborne pathogens.

Melissococcus plutonius is the bacterial pathogen that causes European Foulbrood of honeybees, a globally important honeybee brood disease. We have used next-generation sequencing to identify highly polymorphic regions in an otherwise genetically homogenous organism, and used these loci to create a modified MLST scheme. This synthesis of a proven typing scheme format with next-generation sequencing combines reliability and low costs with insights only available from high-throughput sequencing technologies. Using this scheme we show that the global distribution of M.plutonius variants is not uniform. We use the scheme in epidemiological studies to trace movements of infective material around England, insights that would have been impossible to confirm without the typing scheme. We also demonstrate the persistence of local variants over time.

The Immersive Naval Officer Training System (INOTS) is a blended learning environment that merges traditional classroom instruction with a mixed reality training setting. INOTS supports the instruction, practice and assessment of interpersonal communication skills. The goal of INOTS is to provide a consistent training experience to supplement interpersonal skills instruction for Naval officer candidates without sacrificing trainee throughput and instructor control. We developed an instructional design from cognitive task analysis interviews with experts to serve as a framework for system development. We also leveraged commercial student response technology and research technologies including natural language recognition, virtual humans, realistic graphics, intelligent tutoring and automated instructor support tools. In this paper, we describe our methodologies for developing a blended learning environment, and our challenges adding mixed reality and virtual human technologies to a traditional classroom to support interpersonal skills training.1 2

The Warriors’ Journey is an interactive narrative experience that is part of the online, virtual world healing space of the Coming Home Project (www.cominghomecenter.org) at the University of Southern California’s Institute for Creative Technologies. This project is exploring new ways to reach veterans who are returning from recent conflicts and who often have mental health issues or difficulty fitting back into their home communities. We are looking at the affordances of online 3D virtual worlds to address some of the issues that may prevent or deter veterans from getting the help they need. We are exploring the use of specific therapies within the virtual world space, as well as social and enrichment activities designed around the needs of this group. The Warriors’ Journey is one such activity that engages participants in stories to emphasize and reinforce common ideals of honorable warriors throughout history. After experiencing these stories, participants are then encouraged to construct their own warior’s story within the Coming Home space. It is hoped that such activities may help contribute to a more positive sense of self-esteem, a restructured life narrative, and a feeling of control over the stresses incurred during their service to their country.