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Animal disease epidemiology

Work Package 2.2 - Livestock production, health, welfare and disease control

Research Deliverable 
2.2.6 Animal disease epidemiology
Leading Ideas 
Climate and the Environment
Plant and Animal Health


Embedded within the overall theme of livestock production, health, welfare and disease control, is the science of epidemiology: the study of the occurrence of diseases within populations and ultimately seeks to provide better ways to preventing or control target diseases.The skills and resources to gather and analyse large data sets from a variety of sources provides us with the means to understand the epidemiology of given diseases. In this programme of research we use these skills to help with identification of threats, rapid disease detection, adoption of strategies to minimise the risk of infection, application of measures to prevent spread and these are adopted to a contribute to sustainable livestock systems and to explore potential threats to public health.

The ever-increasing global focus on our use of antimicrobials (AMU) in livestock systems and associated antimicrobial resistance (AMR) with the implications for human health, also fall within the remit of Research Deliverable 2.2.6. (RD 2.2.6). In addition to exploring behaviours in relation to AMU reasons for reluctance or failure by livestock producers to adopt alternative and recommended strategies for disease control are wide ranging.The work within RD 2.2.6 therefore recognises the need to better understand these socio/economic factors and seeks to identify pathways to break these barriers down.

Aim of Research

To advance our knowledge of how to improve disease control strategies through epidemiological and socio-economic approaches.  This includes research into the spread of important, targeted, endemic pathogens and antimicrobial resistance (AMR) via livestock and the environment including transmission of such pathogens to humans. 

In order to achieve this, we will more specifically:

  • analyse existing, large data sets to improve knowledge of the threat of disease incursion and to aid the rapid detection of endemic livestock diseases.
  • investigate new strategies for disease control and investigate two zoonotic pathogens (Verotoxigenic Escherichia coli (VTEC) and Cryptosporidium parvum) with the aim of minimising human exposure.  

In addition, we will improve understanding of antimicrobial resistance and finally put recently developed, novel diagnostic tools to use in the spheres of identifying abundance of pathogen populations and provide methods to help treat internal parasites (worms) in lambs.



The progress for the research undertaken on the Research Deliverable is wide ranging, involving disease threats to cattle, sheep and pigs as well as to humans, so to ease comprehension the strands are presented together as follows:

Zoonotic diseases (infectious diseases that can be transmitted between animals and humans and vice versa) includes research into verocytotoxigenic E. coli (VTEC) and cryptosporidium.  We have explored the genetic basis as to why some VTEC isolates are more successful at surviving and persisting in the environment.  Genetically divergent E. coli isolates were identified, so providing evidence of an extensive E.coli gene pool.  Research into the parasite Cryptosporidium parvum suggested that adult cattle might not be a major source of transmission of to their calves as was previously believed.

Antimicrobial resistance (AMR) in livestock is seen as a potential hazard to human health. On a positive note, AMR levels in bacteria from clinical cases of mastitis in sheep were found to be low.  The geographic picture of AMR created from analysis of soil samples collected from across Scotland (Yrs 1 and 2) was overlaid with soil metadata and land management providing a reflection of the impact of agricultural practices on resistance.  Research into methods that quantify the variation of AMR at different levels, for example animal compared to farm, were shown to help identify likely causes of AMR.  In addition, a comparison of different methods used to test for AMR were extended to samples from different species and confirmed that there are differences in prevalence between host species.

Exploring ways to control diseases currently found/present in Scottish livestock, endemic diseases, focussed on viral and parasitic diseases of both cattle and sheep.  The researchers help support the government’s strategy to eradicate bovine viral diarrhoea virus (BVD) from our cattle herd.  Spatial cluster models developed to inform detection of the source of BVD virus in positive herds towards the end of the eradication scheme have been accepted for publication.  The Scottish BVD eradication scheme has been used as an exemplar to help develop a Europe-wide framework to assist in providing confidence for disease-free cattle trading between certain countries and funding is matched to work in this RD.  Linked to this work a more general survey targeting vets and farmers to identify barriers to disease control was conducted.

Research into endemic parasitic diseases of sheep included analyses of data from the sheep scab transmission study trials previously reported with a model on the transmission dynamics constructed to allow novel interventions to be tested.  Samples from lambs infected with gastrointestinal nematode worms were separated for a “high” or “low” wormer need (to deal with a specific worm challenges) and the results were analysed and compared. Liver fluke are an increasing problem so the application of methods developed in this RD, associated with the stages to target in the liver fluke life cycle have been presented and discussed with Stakeholders.  Environmental DNA assays were evaluated and shown to hold great promise for environmental applications.

Data derived at population level has also been analysed including farm mortality data associated with disease outbreaks– specifically African Swine Fever (ASF) in pigs – and has been shown to give reliable estimates for potential outbreak characteristics.  Sheep movement data has identified key options for future surveillance strategies.


Analysis of research data suggested that sampling for E.coli O157 pre-slaughter is not a reliable indicator of the identification of high contamination of cattle or sheep carcases for human consumption.  Progress was made on distinguishing if environmental verocytotoxigenic E. coli (VTEC) is of a bovine or human source.  The Salmonella model developed in Year 1 was used to identify the most effective intervention to reduce bacterial shedding.  Different methods used to test for antimicrobial AMR in both fresh and stored (cattle) faecal samples produced different results, suggesting freezing and long term storage of samples was of limited value.  Using a range of soil samples collected from across Scotland, a model was developed to explore AMR in the environment.  A ‘Resistant Gene’ atlas for Scotland was created identifying hot spots.  Widespread resistance to Vancomycin detected.

Research into endemic disease provided information to Scottish Government in relation to the distribution of the retention time of BVD positive cattle to assist with the administration of the latter stages of the Scottish BVD eradication scheme.  The team increased the number of environmental sampling techniques to quantify the risk of liver fluke to grazing livestock.  Developed prototype environmental DNA assays for liver fluke and the associated mud snail. Developed methods for extracting and amplifying fluke DNA.  Developed methods to assess the viability of liver fluke cysts in forage.  Other work differentiated Cryptosporidium parvum species from a range of farmed animal sources.  Targeted Selective Treatment (TST) studies demonstrated that anthelmintic support for lambs within a flock to reach similar liveweight gains varied significantly.  By transmission study trials, we increased our understanding of the transmission of Psoroptes ovis – the mite responsible for sheep scab. Methodology developed in Year 1 to model TB control was trialled and it is now possible for analysis to account for individual animals and their life history events.


A very diverse RD deals predominantly with using epidemiological methods to evolve new ways of measuring disease in livestock populations and epidemiological approaches to establishing improved control.  Research was initiated into zoonotic diseases and to establish barriers to farmer and veterinary behaviours that impede better adoption of control strategies.  Initial effort was focussed on developing epidemiological tools to control zoonotic diseases, to determine if the presence of E.coli O157 in an animal prior to slaughter can be an indicator of a later risk to human health and to investigate the hypothesis that the environmental persistence of E.coli is dependent upon a specific set of gene.  In addition, developing verified Cryptosporidium parvum DNA based control material for use in diagnostic tests and adapting a within-herd Salmonella transmission model for use under Scottish pig production systems.  Steps were taken to identify the prevalence of antimicrobial resistance in samples from Scottish cattle populations.

In relation to endemic livestock disease, information was provided to Scottish Government to assist with the development of the Scottish bovine viral diarrhoea (BVD) eradication scheme.  Different methods to determine liver fluke risk were evaluated including a method of testing environmental samples for liver fluke infection on pastures.  Big data approaches were used to describe Scottish sheep movement relating to the slaughter population and acknowledging that diagnostic test results for TB do not take historical or movement data into account, outbreak data was used to develop a model that gives better estimates for disease transmission.

Future Activities

Analysis of the BVD eradication scheme data available to date to determine critical control points of the ‘end-game’ in agreement with Scottish Government.  Present and discuss findings of the associations between the movement network and BVD clusters to stakeholders.  Future work on data to include linkage of sheep movement data to related EPIC research; apply new methods to suitable data sets and using the model, assess different control measures for on-farm disease spread.

Finalise the model for Salmonella and assist in the development of the Scottish pig PRRS control programme.  Updated data on the genomics and metadata of environmental Escherichia species will be available to provide a state-of-the art final database to inform on E. coli / Escherichia spp. taxonomy, and inform on the potential for emergence of new pathotypes.  We will produce guidelines of how to manage Cryptosporidium parvum infection in calves in order to reduce disease and environmental contamination and further evaluate Cryptosporidium parvum transmission routes on a farm.  Metagenomic analysis of DNA will seek antimicrobial resistance (AMR) gene ARG–like sequences. Research will continue to estimate variation in antimicrobial resistance (AMR) between isolate, sample and animal levels.  Parasite research will focus on improving the diagnosis of levels of infectious liver fluke stages in the environment, develop guidance on good practice for fluke control in agri-environment schemes; progressing the sheep scab vaccine trial and assess the effect of vaccination on transmission of sheep scab.  In consultation with farmers and vets, submit findings and recommendations related to motivations associated with disease control. The STOC-FREE (Surveillance analysis Tool for Outcome based Comparison of the confidence of FREEdom from infection) project will identify the list and characteristics of non-regulated cattle diseases for which control, eradication and/or surveillance are currently being conducted in the EU. This work will help complete the roadmap on prioritised development of STOC free tools so they can be generalised to other endemic diseases.

Selected Outputs

  • Report: “The Pig Industry Medicines Hub”.
  • Relating growth potential and biofilm formation of Shigatoxigenic Escherichia coli to in planta colonisation and the metabolome of ready-to-eat crops doi:  
  • Influence of Plant Species, Tissue Type, and Temperature on the Capacity of Shiga-Toxigenic Escherichia coli To Colonize, Grow, and Be Internalized by Plants doi:  
  • An empirical comparison of isolate-based and sample-based definitions of antimicrobial resistance and their effect on estimates of prevalence.
  • Difficulties arising from the variety of testing schemes used for bovine viral diarrhoea virus (BVDV).
  • Insights for the assessment of the economic impact of endemic diseases: specific adaption of economic frameworks using the case of bovine viral diarrhoea.
  • Research Brief to Scot Gov on 23/08/17 – “Retention of BVDV persistently infected bovines on farms: consequences for BVD eradication scheme.
  • Research Brief "Where do PI bovines die? Analysis of the BVD eradication scheme data" sent to Scot Gov on 1/12/17.
  • Draft Policy Brief, “Determining herd level disease status by spot test screening young stock for antibodies - optimising the number of animals to test and cut points for BVDV" sent to Scot Gov on 15/8/2107.
  • Strategies for screening young stock for antibodies - optimising numbers to test, cut-points, & predictive values for bovine viral diarrhoea virus.
  • Patchy promiscuity: machine learning applied to predict the host specificity of Salmonella enterica and Escherichia coli.