Genetic and environmental effects on virulence of European foulbrood, a bacterial pathogen of honey bees

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Honey bees (Genus Apis) are economically important pollinators of crops as well as producers of honey. They are under significant threats from emerging diseases and changes in management practices that adversely affect their feeding environment. In the UK, one of the most damaging diseases, treatable only by hive destruction, is American Foulbrood (AFB). A previous York-Fera BBSRC CASE studentship project developed a Multi-Locus Sequence Typing (MLST) scheme for Paenibacillus larvae, the causative agent of American Foulbrood. Outbreaks have, since 2014, been routinely typed, and we seek to build on this work to determine the extent to which this information can be used to predict occurrence and spread of AFB.Left untreated, AFB will kill a colony of bees. Spores are fed to larvae, where they germinate in the gut, and, after the hive cell is "capped", the bacteria proliferate, eventually killing the larva and forming millions of resistant spores that are later dispersed. There are many genotypes present in the UK, and they show high levels of strain variation, defined both by the MLST and comparative genomics. Recent research shows that community diversity and competition processes in the gut microbiome encountered by pathogens is important in determining the progress and outcome of infections. The gut microbiome in turn, is determined by external environmental factors, such as food resources. We therefore hypothesise that the outcome of AFB infection in a hive is a complex interaction between disease strain genotype and the larval gut environment it encounters.The overarching aim of this project is to link genotypes within and among Clonal Complexes (CC) that have been defined by the MLST, with disease symptoms and the environment in which they occur, and to translate this into an inspection and monitoring scheme that will further contribute to keeping this destructive disease under control.The studentship will address four research areas:1) Population Genetics: Building on previous analysis (Morrissey et al. 2015; see below), and using data collected subsequently using the MLST, what is the spatial and temporal pattern of AFB outbreaks? Can Clonal complexes (CCs) be used reliably to discriminate new outbreaks from re-infections?2) Comparative Genomics: isolates collected from CCs with known distribution and disease severity, genome sequence will be determined and extensive analysis of genes related to virulence analysed.3) Environmental Genomics: what environmental factors influence the patterns of disease prevalence and severity? The student will investigate bee host gut microbiomes, and their relationship to infection by particular types of AFB.4) Practical applications: There are a number of ways in which the studies may influence screening and management of AFB. If MLST type predicts disease severity, then outbreaks can be prioritized for destruction, and follow up inspection regimes recommended. More complex environmental factors such as food resources and gut microbiomes may predict which strains successfully infect the hive, or the severity of the disease once infection becomes established. The most promising route to practical mitigation of disease will be identified and developed by the student.The project will combine genomics techniques and analysis at the University of York, with the opportunity to carry out experiments at Fera, in collaboration with the Bee Unit, and their state of the art facilities for culturing and manipulating AFB.