Animal disease epidemiology

This Research Deliverable combines the expertise of four partner Institutes working with a wide range of partners including the EPIC Centre of Expertise and International collaborators from the EFSA funded STOC-FREE consortium. The overall focus is on measuring and controlling animal diseases and epidemiological type investigations into major zoonotic pathogen risks plus antimicrobial resistance. The work orchestrates an unusually wide range of science disciplines, both qualitative and quantitative as it must to provide practical impact. Despite the Covid19 pandemic the work has generally progressed well. Field studies not completed by early 2020 have indeed been impeded but extension into year 2021-22 has provided the opportunity to complete these projects. Much of this research is in the process of being reported now to our stakeholders to help livestock keepers maintain Scotland’s deserved reputation for production of high quality, safe and environmentally sound products.

Highlights

• The method for measurement of AMR hugely affects results: a novel lab/statistical method that enumerates bacterial density and the proportion that are resistant was developed. The method was subsequently tested using faeces using structured studies involving two distinct groups of dairy calves. Very low within group but very high between group variation was demonstrated. Such differences may be due to group-level factors relating to previous antimicrobial exposure or within-group transfer of AMR. Interventions will now be explored to help minimise animal and human AMR exposures.
• Bayesian inference of on farm disease dynamics from mortality data: pathogens such as African swine fever virus (ASFV) are an increasing threat to global livestock production. Quantification of epidemiological parameters, such as within-farm transmission rates and latent and infectious periods is critical to inform efficient disease control. Routinely collected livestock mortality data is a potential source of readily available and representative information regarding disease transmission early in outbreaks. We develop methodology to make use of such data and test it by inferring epidemiological parameters for ASFV using data from outbreaks on 9 farms in the Russian Federation. Our methodology performs better than current methods, quantifies transmission within-farm and from external sources, and allows combination of data across multiple herds, improving inference. The approach could be applied to other outbreaks or pathogens.
• Advanced statistical methods were used to analyse data from the Scottish bovine viral diarrhoea (BVD) eradication programme to inform improved BVD Control. Farms close to each other are more likely to share staff, equipment, animals and grazing ground. There is an increased likelihood of the incidence of over the fence contact and mixing of animals from the different herds. The result of these and other management associated risk factors is that transmission of BVD virus is more likely across neighbouring farms resulting in clusters of farms with similar BVD infection status. Using data from the Scottish BVD eradication program, we investigated the existence of clusters of BVD positive farms and how the clusters developed and changed as the eradication program progressed. This has helped inform better targeted control.
• Difficulties arise for between farm trade because of the differences in disease status arising from non-European Union (EU) regulated national or regional disease-free programmes. The Pan European STOC FREE project uses bovine viral diarrhoea virus (BVDV) in cattle as an exemplar; and Scottish BVD eradication as a comparative case study. International trade in livestock is also hampered where informed comparison of animal BVD status by livestock traders is impossible. Variable eradication approaches have led to differences in definition of and in the way disease free status is assigned. STOC-FREE has explored these issues and aims to enable comparisons to be made between countries to facilitate trade. Statistical models using data from several European countries have been established and generated estimates for the confidence that trading herd might be truly free of BVD. The method is transferable to different diseases in multiple species
• Research demonstrates that some environmental E. coli associated with plants and soil contain virulence genes including antibiotic resistance and toxins that are encoded on mobile elements (plasmids; bacteriophage), which helps to explain the presence of zoonotic E. coli (STEC) on plants.
• Using a combination of fluke egg counting in faecal samples taken from sentinel sheep, and mud snail PCR screening to determine species identification and fluke infection status, we have been able to show that the liver fluke risk to livestock associated with conservation grazing around wader scrapes at SRUC Kirkton & Auchtertyre, is currently relatively low, compared to neighbouring in-bye fields. This research features as a case study on the SEFARI website and is included in a Fluke Risk & Conservation Grazing Guide, currently in production.
• Researching farmer behaviour in relation to the livestock disease control: farmers views can be useful to inform how the government can best influence and support policy driven behaviour change and support eradication of diseases such as Johne’s disease and BVD.  There is a lack of homogeneity on many topics (which reflects diversity within the sector), except for ‘advice and guidance’ which farmers want to be simple, concise, tailored, and respectful.  In relation to government funding, some farmers felt this should prioritise stability while others wanted it to be used for practical measures to increase productivity and profit, reduce waste, and benefit health. 

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.