The Scottish Government
SPASE Background Funded Institutes Projects Impact Management Contact

The impact summary for 2013-2014 can be found here.

Impact (2014-2015)

1. Supporting Policy and Practice

Stakeholder Engagement

Stakeholder Workshop: potential of pathogen genome sequencing in tracking zoonotic bacteria (WSs 1.1.3, 1.1.4, 1.2.4, 1.2.5)

SPASE scientists working on ruminant bacterial infections contributed to stakeholder interactions as part of CoZEE. At the Nov 2014 Conference, they addressed the topic, “The role of high-throughput sequencing in surveillance, diagnostics and tracking zoonotic bacteria”. This took the form of short presentations and a workshop. As well as participants from MRPs and HEIs, contributors were from the Food Standards Agency (FSA), reference laboratories (Scottish E. coli O157/VTEC Reference Laboratory, Scottish Salmonella, Shigella and Clostridium difficile Reference Laboratory, Health Protection England) and local authorities. A workshop, led by FSA Scotland, was undertaken to consider whether genome sequencing could play a role in real-time outbreak support.*
* Report available

Survey of tick-borne pathogens in Scottish farms: farmer feedback (WS1.2.8)

In WS1.2.8, the Tick-tag project, sampling of livestock was undertaken at several North of Scotland farms suffering from problems with tick-borne disease. Over the last 12 months, approximately 200 ruminant samples were assayed for the presence of tick-borne pathogens such as Babesia, Theileria and Anaplasma species. The analysis demonstrated that a high proportion of the sheep sampled have Anaplasma phagocytophilum infection and a number of sheep also carried the zoonotic pathogen, Babesia venatorum. This information was fed directly back to the farmer stakeholders involved in the sampling cohort so that they could take appropriate action on-farm.

Communicating the importance of best practice in the husbandry of mothers (WS2.1.3)

Within the range of normal on-farm practice, husbandry conditions under which pregnant ruminants are kept can have programming effects that will affect the health, welfare and productivity of their offspring. SPASE WS2.1.3 scientists gave talks to farmers (‘Mothers matter: how management of farm animals during pregnancy affects progeny health, welfare and productivity’) at the SRUC Beef and Sheep KT day (Sept 2014) and to veterinarians (‘How stress during pregnancy affects the offspring’, 7th Boehringer Ingelheim Expert Forum on Farm Animal Well-being (June 2014). The research, and emphasis of these presentations, was the importance of careful handling of pregnant farmed livestock.

Benefits to other stakeholders

SRuC Beef Open Day attended by policy makers (WS1.2.9) 

A Beef Open Day was held at SRuC near Edinburgh in Nov 2014. This workshop targeted policymakers, as well livestock industry  members. The workshop included a presentation on the collaborative work carried out under SPASE between MRP partners, Roslin Institute, the feed industry and the biotech industry. The presentation highlighted the dietary and microbiological pointers that can be deduced that can decrease methane emissions.

Methodologies developed in SPASE now being used to quantify the dynamics of tuberculosis in badgers (WS3.2.2)

Bovine tuberculosis is a major economic burden to the UK cattle industry and a threat to Scottish livestock. Badgers are a potential wildlife reservoir for tuberculosis and are seen as a major component of the bovine tuberculosis problem. Methods developed in SPASE WS3.2.2 are now being deployed to quantify the dynamics of tuberculosis in badgers as part of a DEFRA-funded project to develop and test operational models of bovine tuberculosis in British cattle and badgers. The results of these studies will help inform UK policy decisions with regard to tuberculosis control.

Public health and cryptosporidiosis (WS3.2.3)

Cryptosporidiosis is one of the leading infectious causes of gastrointestinal disease in humans worldwide. In the UK, around half of human infections are caused by Cryptosporidium parvum, a potentially zoonotic species. C. parvum is highly prevalent in young livestock and resistant oocysts can then be transmitted to humans directly or, more commonly, via contaminated water. Through SPASE WS3.2.3, scientists have developed a molecular typing scheme that could be used to inform policymakers by tracking the source of human outbreaks, thereby informing the design of interventions that will reduce future risk to public health.

2. Supporting Innovation and the Economy

Industry-relevant outputs

Report on prenatal programming effects on cattle & sheep (WSs 2.1/3, 2.3.1)

A substantial report on the potential production effects of prenatal programming in ruminants was prepared by SPASE scientists and Nottingham University for EBLEX. The report was presented and discussed with EBLEX and their advisers in Jul 2014 at their Research Day. The report provides a reference point for understanding the process of epigenetics and programming, and a comprehensive literature review of these effects on outcome measures of relevance to UK production systems. The gaps in knowledge and potential areas for further work were identified as well as an executive summary highlighting main areas of concern for the industry.

Rapid typing of VTEC (WS3.3.3)

Work under SPASE WS3.3.3 has developed a pipeline for data handling and processing for VTEC infections. The testing and refinement of a predictive modelling system for rapid typing is now underway. The software is developed in an open source platform. Subject to predictive methods meeting specificity and sensitivity requirements, further discussions will be held with the Food Standards Agency and reference laboratories such as the Scottish E. coli O157/VTEC Reference Laboratory, to guide process towards implementation.

Industry Collaborations

Industry collaboration on salmon alphavirus (WS1.2.6)

In collaboration with the breeder Landcatch, scientists working in WS1.2.6 analysed samples from a salmon alphavirus (SAV) challenge trial and were able to assist in identifying a fish family that showed significantly reduced virus replication. The results of this collaboration have sparked off a discussion to improve the challenge model and a joint application is being drafted to optimize SAV challenge models for selection of more SAV-resistant fish.

Sensor technologies to monitor rumen microbiome (WS1.2.9)

WellCow is a private company that manufactures a pH-sensing device that can be implanted in the rumen and used to predict problems associated with ruminal acidosis. Embedded Technology Solutions Ltd. has developed a motion sensing device that is intended also to detect abnormalities in rumen function. SPASE scientists based at RINH have now undertaken collaborative experiments with both companies to investigate links between these monitoring outputs and the ruminal microbiome.

Uptake by Industry

Developments in rapid typing of VTEC (WS3.3.3)

A face-to-face meeting was held between SPASE WS3.3.3 researchers and Food Standards Agency Scotland representatives to demonstrate developments towards rapid, reliable typing for E. coli O157:H7 and related, high risk foodborne pathogens.  Scientists from MRI and BioSS conducting this work carried out a detailed talk-through event summarising the background, developments and prospects. FSA Scotland recognised the potential utility of this approach subject to further proposed alignment of this method to currently-used typing methodologies.

E. coli O157 super-shedding in cattle; mitigation of human risk  (WS 3.1.2)

Recent data suggests that certain E. coli O157phage-types (PTs) are more likely to be excreted by cattle at high levels, suggesting that bacterial factors are important determinants of super-shedding. These PTs are more likely to cause human infection. To understand implications of strain-specific heterogeneity in shedding, a number of challenge studies were performed under Food Standards Agency funding with E. coli O157 strains representative of a super-shedding (PT21/28) and non-super-shedding (PT32) type. The studies demonstrated that PT21/28 is excreted at higher levels. These strains exhibit different transmission dynamics. In SPASE WS3.1.2 this strain-dependent heterogeneity is being incorporated into mathematical models of herd-to-herd transmission, with implications for future control strategies.

3. Collaboration and Multidisciplinary Working

Multi-centre collaborative project on anthelmintic resistance (WS1.2.7)

The focus here was to contribute to the long-term aim of developing genetic markers for early diagnosis of ivermectin resistance. A number of candidate resistance genes were previously described in Haemonchus contortus and offered promise as genetic markers. However, SPASE-funded analysis suggests that these genes are not major contributors to resistance in UK isolates and thus will not provide robust resistance markers for British farmers. Based on this, the SPASE partners developed a multidisciplinary genome-wide approach (including partners from the Sanger Institute and Bristol University) to identify markers and have started a new BBSRC project to expand this work.

Worldwide collaborations established for Archeal community analysis (WS1.2.9)

An international ring test has been completed, with RINH as organiser, whereby leading laboratories in Canada, Australia, New Zealand, Ireland and Wales, as well as Roslin Institute, were supplied with eight samples of rumen microbial DNA from cattle, sheep and deer.  They used their in-house, favoured methodology to prepare a description of the community present in each sample. The results were stunning: microbiome analysis from each collaborator was different, particularly with the methanogenic archaea, a completely different community resulted. RINH and the collaborators are now analysing the amplification techniques and bioinformatics pipelines used in order to explain this concerning finding.

4. Supporting Scientific Excellence


Publication on how birth weight and gender influence adipocyte development (WS2.3.1)

Low birthweight is a risk factor for inappropriate carcass composition. We investigated lipid biomarkers and adipose tissue genes in low and normal birthweight lambs and related to adiposity at age 3-months. Plasma triglycerides, nonesterified fatty acids and glycerol were elevated in low birthweight males but body fat was independent of prenatal growth. Females had higher carcass fat content and larger adipocytes than males and gender influenced 8 of 10 genes involved in adipocyte proliferation and function. Thus higher lipids may predict later onset obesity, but in early postnatal life gender is the dominant influence on adipose tissue gene expression reflecting sexual dimorphism in body composition.
Reference: Wallace JM, Milne JS, Aitken RP, Adam CL (2014) Influence of birth weight and gender on lipid status and adipose tissue gene expression in lambs. Journal of Molecular Endocrinology. 2014, 53:131-144.

Publication on the importance of the gestation period for offspring survival (WS2.1.2)

A major review of the welfare and offspring survival implications of the prenatal period, and the husbandry of the mother, in sheep has been published. Maternal under-nutrition in the last third of pregnancy consistently affects lamb development, vigour and survival, whereas the impacts of earlier periods of under-nutrition are more variable. Social and husbandry stressors, whilst having a negative impact on the mother, may have neutral or beneficial affect on the early vigour or growth of the offspring. This work was also presented as part of a ‘Challenge’ session on lamb survival at EAAP, Copenhagen, Denmark, 25th-29th August, 2014.

  • Rutherford KMD, Arnott G, Rooke JA. Mother matters: how management of animals during pregnancy affects their progeny. Veterinary Ireland Journal. 2014. 4: 532-35. 5.                    

Publication on the diversity and community composition of methanogenic archaea in the rumen of Scottish upland sheep (WS1.2.9)

Methanogenic archaea are part of the anaerobic microbial community of the rumen. They are less abundant than bacteria but have received attention due to their ability to synthesise methane. Here, ruminal archaeomes of two sheep grazing in the Scottish uplands were analysed by different sequencing and analysis methods to compare archaeal communities. All methods revealed that the majority of methanogens belonged to the Methanobacteriales order, but important differences were identified among methods. The results showed that, although much information may be extracted from other methods, Illumina amplicon sequencing of the V6-V8 16S rRNA gene is the method of choice.

  • Snelling T J, Genc B, McKain, N, Watson M, Waters SM, Creevey CJ, Wallace RJ. Diversity and community composition of methanogenic archaea in the rumen of Scottish upland sheep assessed by different methods. PLoS One. 2014.  9, e106491. PubMed Central

Scientific tools

Quantitative PCR for Anaplasma phagocytophilum (WS1.2.8)

In collaboration with Moredun, a SPASE-funded PhD student based at Glasgow University was involved in the development of a quantitative (q)PCR assay for the detection of Anaplasma phagocytophilum infection in livestock. In the course of this work, a substantial amount of field samples were collected and PCR analysis has resulted in a collection of pathogen-positive material. A subset of this collection was used to optimise a qPCR developed at MRI and this PCR is now being made accessible to farmers via an ongoing collaboration with SRuC.

Searchable database of scientific publications of prenatal effects in farmed livestock (WS 2.1.2/3)

As part of Module 2, a comprehensive searchable database of animal welfare, stress and production outcomes for a wide range of prenatal impacts has been developed. This was completed in part in conjunction with a DEFRA-funded project and covers pigs, sheep, cattle, chickens and fish. The database has informed the work of Module 2, but has also been used for other grant applications, PhD and MSc studentship projects and is a valuable resource to guide future work, as well as for generating review publications and metadata on the effects of prenatal challenge on a range of scientific and industry-relevant outcomes.