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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.

Background Bacterial blotch is a group of economically important diseases affecting the cultivation of common button mushroom, Agaricus bisporus. Despite being studied for more than a century, the identity and nomenclature of blotch-causing Pseudomonas species is still unclear. This study aims to molecularly characterize the phylogenetic and phenotypic diversity of blotch pathogens in Western Europe. Methods In this study, blotched mushrooms were sampled from farms across the Netherlands, United Kingdom and Belgium. Bacteria were isolated from symptomatic cap tissue and tested in pathogenicity assays on fresh caps and in pots. Whole genome sequences of pathogenic and non-pathogenic isolates were used to establish phylogeny via multi-locus sequence alignment (MLSA), average nucleotide identity (ANI) and in-silico DNA:DNA hybridization (DDH) analyses. Results The known pathogens “Pseudomonas gingeri”, P. tolaasii, “P. reactans” and P. costantinii were recovered from blotched mushroom caps. Seven novel pathogens were also identified, namely, P. yamanorum, P. edaphica, P. salomonii and strains that clustered with Pseudomonas sp. NC02 in one genomic species, and three non-pseudomonads, i.e. Serratia liquefaciens, S. proteamaculans and a Pantoea sp. Insights on the pathogenicity and symptom severity of these blotch pathogens were also generated. Conclusion A detailed overview of genetic and regional diversity and the virulence of blotch pathogens in Western Europe, was obtained via the phylogenetic and phenotypic analyses. This information has implications in the study of symptomatic disease expression, development of diagnostic tools and design of localized strategies for disease management.

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.