Ovine Respiratory Disease: A Pathway to Prevention

Lead Research Organisation: Moredun Research Institute
Department Name: Vaccines and Diagnostics

Abstract

Lung infections are one of the main causes of death and illness in sheep and lambs despite there being a vaccine available against the bacteria believed to be the main causes of the disease. This disease impacts on the health and welfare of sheep but it also reduces productivity and potentially adds to the environmental impact of sheep farming through slowed growth, increased time to slaughter, and premature death.

This project aims to support farmers and vets to reduce lung disease in the sheep they care for. We will increase knowledge and understanding of the disease, allowing those working with sheep to make evidence-based decisions to reduce the number of cases. This will help improve animal welfare, farm profitability and efficiency and will reduce antimicrobial usage. In this 1-year project we will update the basic information needed to develop better solutions.
Sheep farmers will be involved in this project throughout via established farmer groups (grazing groups) and will work in partnership with researchers to assess the scientific findings and place them into context on their farms. In addition to information from farmers about their flocks and their vaccine usage, we will also collect lung samples from any sheep that die on the farms of the participating farmers. We will also collect samples from sheep submitted to the UK veterinary surveillance network of laboratories. The use of archived sheep lung samples from research studies which have been completed recently by the Moredun Research will allow the laboratory studies to begin right from the start of the project.
These sheep samples will be used to find out which organisms are currently the most important in causing lung disease in sheep. These organisms may directly cause the damage to the lung or may predispose the animal to disease by decreasing the effectiveness of their immune response. Increased understanding of the important organisms will show whether the current vaccines sold for sheep pneumonia target the correct pathogens.

Working together, the researchers and farmers will develop their understanding of respiratory disease in sheep. This partnership will allow co-development of practical, user-friendly interventions, leading to potentially rapid improvement for the health of sheep and lambs. This information will be shared with the wider sheep farming and veterinary community.
We envisage this 1-year study as the first step, answering the important questions necessary for immediate improvements and also to enable us to forge ahead with developing more ambitious and innovative approaches for control of lung disease in sheep in the future.

Technical Summary

Ovine respiratory disease (ORD) is one of the chief causes of morbidity and mortality in sheep and lambs. It is multifactorial with both environmental stressors and co-infections predisposing the sheep to long-term chronic or acute inflammatory bacterial lung infections. The vaccines introduced over 35 years ago reduced the incidence and severity, but unacceptably high levels of ORD remain. To address ORD with modern, innovative solutions we first need to establish the basics. We will determine the microbiota of diseased compared to healthy lungs using 16S rRNA gene amplicon nanopore sequencing (MinION). Analysis pipelines are already in place to transform the data into information on the bacterial species/genus present and estimate the relative abundance. PCR and sequencing will further define species, strains, and serotypes. The presence of co-infections will be assessed through PCR and serology.
This work will show whether the current vaccines used for sheep pneumonia target the correct pathogens. The use of well-suited lung samples stored in a biobank from previous projects will allow work to begin immediately, whilst prospective collection of samples and associated metadata will increase the range of clinical presentations to be assessed. This will allow interrogation of any difference, for example, by signalment, pathological presentation, or management systems.
Sheep farmers will work in partnership with researchers throughout the project to place the scientific findings into context on their farms. Facilitated qualitative interviews will allow description of current practice and barriers to action. This partnership will allow co-development of practical interventions which will be disseminated to the wider farming and veterinary community.
This study will build contextualised understanding of the disease to underpin and define the next steps towards improved ORD control, thus reducing the losses experienced within the UK sheep industry.

Publications

10 25 50
 
Title Prospective collection of samples from ovine lung 
Description Frozen and fixed lung tissue samples were collected from sheep at post mortem examination (fallen stock) alongside data about the age, farming system, geographical location etc of the sheep. To date 125 samples have been collected. 
Type Of Material Biological samples 
Year Produced 2022 
Provided To Others? No  
Impact This provides an archive of tissue to be used by the current project and potentially future projects to investigate sheep lung disease. 
 
Title Pipeline for analysis of 16S NGS data 
Description The entire analysis pipeline is based in R and uses DADA2 package for estimating Amplicon sequence variants and their annotation. Briefly, the sequences are trimmed to remove primers and sequencing linkers and then filtered to remove poor quality sequences. Subset of good sequences are then used to model the error profile which is in turn used to denoise entire data. The pairs of sequences are merged and chimeric/bimeric sequences are removed. Genome Taxonomy Database (GTDB) was used to annotate all the predicted variants. The downstream analysis is performed using Phyloseq package with additional functions from other packages and plotting with ggplot2 package. Phyloseq package allows creating a phyloseq object which stores multi-layered data for same samples including sequence variants and their abundances per sample, taxonomic annotation of each sequence variant, and other metadata information associated with each sample. This object is then used throughout for generating alpha diversity, beta diversity, taxonomic-level based profiles and comparisons using functions within the package. 
Type Of Material Data analysis technique 
Year Produced 2023 
Provided To Others? No  
Impact The analysis pipeline will enable more rapid analysis of the data that will be generated from the sequencing component of this project. 
 
Description Meeting with farmers group 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Farmers attending a "Grazing group" meeting discussed respiratory diseases in sheep, led by a sheep health specialist. They were also asked for their feedback on their own beliefs and practices around sheep respiratory disease.
Year(s) Of Engagement Activity 2023