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Evidence Project Final Report

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Evidence Project Final Report General Enquiries on the form should be made to: Defra, Procurements and Commercial Function (Evidence Procurement Team) E-mail: [email protected] Evidence Project Final Report Note In line with the Freedom of Information Project identification Act 2000, Defra aims to place the results of its completed research projects in the public domain wherever possible. 1. Defra Project code SEO313 The Evidence Project Final Report is designed to capture the information on 2. Project title the results and outputs of Defra-funded Improved molecular tools applicable to Brucella research in a format that is easily surveillance. publishable through the Defra website An Evidence Project Final Report must be completed for all projects. 3. Contractor Department of Bacteriology This form is in Word format and the organisation(s) Animal Health and Veterinary boxes may be expanded, as appropriate. Laboratories Agency Woodham Lane ACCESS TO INFORMATION New Haw The information collected on this form will Addlestone, KT15 3NB be stored electronically and may be sent to any part of Defra, or to individual researchers or organisations outside 54. Total Defra project costs £ 655,025 Defra for the purposes of reviewing the (Agreed fixed price) project. Defra may also disclose the information to any outside organisation 1st April, 2009 acting as an agent authorised by Defra to 5. Project: start date ................ process final research reports on its behalf. Defra intends to publish this form st end date ................. 31 March, 2012 on its website, unless there are strong reasons not to, which fully comply with exemptions under the Environmental Information Regulations or the Freedom of Information Act 2000. Defra may be required to release information, including personal data and commercial information, on request under the Environmental Information Regulations or the Freedom of Information Act 2000. However, Defra will not permit any unwarranted breach of confidentiality or act in contravention of its obligations under the Data Protection Act 1998. Defra or its appointed agents may use the name, address or other details on your form to contact you in connection with occasional customer research aimed at improving the processes through which Defra works with its contractors. EVID4 Evidence Project Final Report (Rev. 06/11) Page 1 of 28 6. It is Defra’s intention to publish this form. Please confirm your agreement to do so. ................................................................................... YES NO (a) When preparing Evidence Project Final Reports contractors should bear in mind that Defra intends that they be made public. They should be written in a clear and concise manner and represent a full account of the research project which someone not closely associated with the project can follow. Defra recognises that in a small minority of cases there may be information, such as intellectual property or commercially confidential data, used in or generated by the research project, which should not be disclosed. In these cases, such information should be detailed in a separate annex (not to be published) so that the Evidence Project Final Report can be placed in the public domain. Where it is impossible to complete the Final Report without including references to any sensitive or confidential data, the information should be included and section (b) completed. NB: only in exceptional circumstances will Defra expect contractors to give a "No" answer. In all cases, reasons for withholding information must be fully in line with exemptions under the Environmental Information Regulations or the Freedom of Information Act 2000. (b) If you have answered NO, please explain why the Final report should not be released into public domain Executive Summary 7. The executive summary must not exceed 2 sides in total of A4 and should be understandable to the intelligent non-scientist. It should cover the main objectives, methods and findings of the research, together with any other significant events and options for new work. EVID4 Evidence Project Final Report (Rev. 06/11) Page 2 of 28 Brucellosis remains a zoonotic disease of great global significance that causes reproductive problems (abortion and sterility) in many livestock species and a potentially chronic and debilitating disease readily transmitted to humans. Great Britain has official Brucellosis free status for sheep, pigs and cattle, with Official Bovine Brucellosis Free status being granted by the OIE in 1985 following a lengthy and expensive eradication campaign. This has been successfully maintained as a number of introductions have been identified speedily and stamped out successfully. However, with brucellosis still endemic in much of the world, including significant parts of the EU, it is crucial that vigilance is maintained to reduce the risk of reintroduction and that appropriate tools are in place to ensure the organisms is rapidly identified and controlled in the case of future incursions. Much of the research carried out within the Brucella group at AHVLA supports the maintenance of disease freedom by working to develop and implement the most modern detection, diagnostic and molecular typing tools. The project described here included a number of seemingly discrete areas of work but all supported the overall strategy of the development of improved tools for detection and characterisation of Brucella. As part of this work we have undertaken the following. (i) Investigated whether the inclusion of additional compounds to selective media might be effective in reducing the growth of confounding non-Brucella organisms. This work identified two compounds 4- hydroxycoumarin and manganese chloride that might be useful additional components in currently used selective media. (ii) Investigated whether rapid molecular approaches (PCR) might offer a useful additional tool for confirming a true Brucella infection from serum samples. While this approach appeared specific results suggested very disappointing sensitivity and the tool as stands would be of limited value as a confirmatory diagnostic. As a result of these findings we have suggested that further studies should focus on investigating approaches that might enrich DNA both physically and involve the use of alternative components from blood samples. (iii) Extended a previously developed typing scheme based on single nucleotide polymorphisms (SNPs) that identified Brucella isolates to the species level and differentiated vaccine isolates. As well as being extended to include all newly described species the scheme resolution has also been extended to divide isolates at the subspecies level. Because the classical epidemiological subdivision of biotype applied to Brucella, and based on phenotype alone, was shown not to be wholly congruent with relationships based on genotype the concept of ‘genomovar’ was introduced to divide Brucella groups into epidemiologically significant clusters. This approach offers an exemplar for future developments – the involvement of AHVLA as a partner in ongoing genome sequencing projects and the rapid technological developments in whole genome sequencing promise that genome sequencing and SNP typing based on comprehensive assessment of genomes will become a mainstay of Brucella epidemiology in the near future. As a result of these findings we have suggested that future work should focus on assuring that AHVLA remains at the forefront of Brucella whole genome sequencing and ensures it has suitable embedded skills to continue to utilise these data. (iv) Developed new molecular assays for both detection and typing, particularly a LAMP assay, representing an emerging molecular amplification approach that offers a potentially more robust, rapid and cost-effective alternative to traditional PCR based approaches. (v) Continued to develop and exploit multi-locus sequence typing (a tool based on the DNA sequence of multiple fragments of the bacterial genome) as a tool to understand the relationship between Brucella strains at a global level and to provide a framework for characterisation of newly emerging or atypical isolates and for understanding the evolution and emergence of such strains. As part of the work described here we have developed an entirely novel approach that enables us to characterise not only Brucella but its nearest genetic neighbours in a single approach. This is important as many novel and atypical isolates of both Brucella and the nearest genetic neighbours are currently being described that are closing the ‘genetic space’ that traditionally separates these groups. This tool provides a unique approach to empirically establishing the relationship of any new isolates to both Brucella and nearest neighbours and will help maintain an accurate understanding of the relationships within this important group of bacteria at a time when there is potential for significant confusion. Within this study we have also used MLST to more widely characterise the emerging Brucella from marine mammals and to add to the body of evidence that suggests that a genotype previously associated with zoonotic infection of EVID4 Evidence Project Final Report (Rev. 06/11) Page 3 of 28 humans may not be a significant threat in European waters. MLST has also been a crucial tool in the completed and ongoing descriptions of novel groups of Brucella associated with novel hosts. All these studies are crucial in furthering understanding of the group and allow us to maintain awareness and rapidly assess whether
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