Detecting genetic signals of selection in heavily bottlenecked reindeer populations by comparing parallel founder events.

Founder populations are of special interest to both evolutionary and conservation biologists, but the detection of genetic signals of selection in these populations is challenging due to their demographic history. Geographically separated founder populations likely to have been subjected to similar selection pressures provide an ideal but rare opportunity to overcome these challenges. Here we take advantage of such a situation generated when small, isolated founder populations of reindeer were established on the island of South Georgia, and using this system we look for empirical evidence of selection overcoming strong genetic drift. We generated a 70 k ddRADseq single nucleotide polymorphism database for the two parallel reindeer founder populations and screened for signatures of soft sweeps. We find evidence for a genomic region under selection shared among the two populations, and support our findings with Wright-Fisher model simulations to assess the power and specificity of interpopulation selection scans-namely Bayescan, OutFLANK, PCadapt and a newly developed scan called Genome Wide Differentiation Scan (GWDS)-in the context of pairwise source-founder comparisons. Our simulations indicate that loci under selection in small founder populations are most probably detected by GWDS, and strengthen the hypothesis that the outlier region represents a true locus under selection. We explore possible, relevant functional roles for genes in linkage with the detected outlier loci.

The tales of contradiction: A thematic analysis of British sheep farmers' perceptions of managing sheep scab in their flocks.

Sheep scab is endemic in Great Britain with an estimated national herd-level prevalence of 10.9% from a surveyed population of sheep farms. Previous studies have investigated how sheep farmers manage sheep scab on their farms in Great Britain, but there have not been any qualitative studies investigating sheep farmers perceptions on the roles different stakeholders have in the management of sheep scab. This qualitative study aims to explore how sheep farmers perceive their role and the different stakeholders' roles in the management of sheep scab, and how they would like sheep scab to be managed going forward. Semi-structured interviews were conducted with 43 sheep farmers from England, Scotland, and Wales. The data were analysed using reflexive thematic analysis, through the theoretical lens of Foucault's notion of 'biopower'. Two themes were generated: 'The feeling of powerlessness leads to a need of rules and regulations', with sub-themes: 'The need for governmental rules and regulations' and 'The need for rules and regulation at livestock markets', and 'An apparent lack of sheep scab surveillance', with sub-themes: 'The farmers perceive that the veterinarians have control over surveillance' and 'The farmers have control over surveillance on their farms'. In the first theme, the respondents suggested that more rules and regulations to control the management of sheep scab was required. This included reinstating of sheep scab as a notifiable disease in England and Wales, as well as more regulations at livestock markets to prevent the trading of infested sheep; both of which would subject the farmers to regulatory power mechanisms. The second theme centred around who has the control of surveillance on the farms. Most of the respondents perceived that the veterinarians had knowledge and expertise of the local area on sheep scab, which they were able to relay to the farmers. Thus, veterinarians exerted disciplinary power by creating 'docile' bodies. However, it also appeared that veterinarians were not regularly called onto farms. Although disciplinary power flows through the interactions between the farmer and veterinarian, the techniques currently used are not always having their desired effect. The study demonstrated that how sheep farmers want sheep scab to be managed is, at times, conflicting and contradictory, which highlights the complexity of sheep scab as a disease to manage.

Antibiotic use in the Northern Irish sheep flock: What lessons can be learnt from medicine records and farmer attitudes to improve stewardship of these essential medicines?

Stewardship of antibiotics used in livestock production has come under increasing scrutiny, from both the animal welfare point of view and due to concerns that antibiotic use in livestock may pose a risk to human health through selection pressure to drive development of antibiotic resistant strains of bacteria. Despite this concern, however, antibiotic consumption in the sheep sector is currently poorly described. This study determines the range and quantities of antibiotics used in the Northern Irish (NI) sheep flock as well as exploring drivers for their use. A mixed-methods approach was utilised, with an anonymous online scoping survey, analysis of the medicine records from 52 NI sheep farms and semi-structured interviews undertaken with 27 farmers. Eighteen farmers contributed both records and participated in interviews. Veterinary medicine records were derived from two sources: on-farm medicine books (seven) or veterinary practice sales data (51). As six of these farmers provided information from both sources a total of 52 unique farms participated. Overall, antibiotic use in sheep on the 52 farms sampled was low, with a median value of 11.35 mgPCU-1 (mean 13.63 mgPCU-1, sd 10.7; range 0-45.29 mgPCU-1), with all farms below 50 mgkg-1. Critically important antibiotics accounted for 0.21% of all antibiotics purchased. Lameness was the main driver of antibiotic use identified by this study. Others included a range of prophylactic treatments such as oral antibiotics to prevent watery mouth, injectable antibiotics to prevent abortion and following assisted lambing. Farmers acknowledged some of these uses had become habitual over time. The veterinary medicine sales records demonstrated significant sales of antibiotics not authorised for use in sheep, on an ongoing, rather than case-by-case, basis. Farmers were positive about their veterinarian's ability and knowledge to improve flock welfare and productivity, but were unwilling to pay for this advice. However, veterinarians may have facilitated weak medicine stewardship through a failure to adequately challenge farmers seeking antibiotics. Farmers did not maintain accurate or up-to-date on farm medicine or production records in the majority of cases. Despite this lack of on-farm recording, veterinary sales records can be studied in consultation with farmers to provide veterinarians with a farm-specific insight into antibiotic use and related attitudes and behaviours. Farmers and veterinarians can then identify areas and behaviours to target collaboratively, improving antibiotic and wider medicine stewardship, whilst simultaneously improving flock health and productivity.

Identifying veterinary surgeons' barriers to, and potential solutions for, improving antimicrobial stewardship among sheep farmers in Northern Ireland.

Background: In order to improve antimicrobial stewardship (AMS), including changes in antimicrobial prescribing and use, an enhanced understanding is needed of the barriers that veterinary surgeons (vets) encounter to institute such change. Methods: A qualitative approach, using grounded theory, was followed. Interviews and discussion groups, with vets and farm industry stakeholders in Northern Ireland (NI), were undertaken to identify and explore attitudes and behaviours surrounding AMS, with a particular emphasis on the barriers vets encountered and the context within which they were working. Results: Seven inter-related themes associated with improving AMS among their sheep farming clients were identified. The first six addressed barriers were working under commercial and practical constraints, farmer behaviour, multiple medicine sources, poor prescribing practice, a perceived lack of incentive or facilitation to improve AMS and a perceived lack of action by regulators to challenge poor AMS. The seventh theme revealed suggestions vets considered that may improve AMS in NI, including greater state intervention in recording and regulating medicine sales. Conclusions: Improving AMS will require vets and their client farmers to change behaviour. This will involve concerted effort over an extended period of time to enact and embed change. Veterinary surgeons believe that further action by the industry and state to develop centralised antimicrobial sales recording and by the state to enforce prescribing regulations will aid their efforts. However, critical to achieving this is the development of a sustainable and funded mechanism to create more meaningful farmer-vet consultation around flock health prior to every prescription to improve AMS and sheep welfare.

Longitudinal study of antimicrobial use patterns, vaccination and disease prevalence in British sheep flocks.

BACKGROUND: The aim of the study was to describe the longitudinal dynamics of antimicrobial use (AMU) on sheep farms and explore associations between AMU and management factors, vaccination strategies, reproductive performance and prevalence of lameness. METHODS: Antimicrobial supply data were collected for 272 British sheep farms for 3-6 consecutive years between 2015 and 2021. These data were obtained from the farms' veterinary practices. RESULTS: Annual median AMU ranged from 8.1 to 11.8 mg/kg population corrected unit. AMU was skewed in each year with a small proportion of very high users. AMU within farms varied substantially between years. High AMU farms in 1 year were not necessarily high in other years. No associations between AMU and either vaccine usage or lameness prevalence were found. LIMITATIONS: The study design requires veterinarians and farmers to volunteer their data. This unavoidably introduces the potential for a participation bias. CONCLUSIONS: AMU on sheep farms is generally low, with a small number of farms being responsible for high usage. Targeting antimicrobial stewardship effort towards the small minority of persistently high users may be more appropriate than a focus on generic, industry-wide attempts to reduce overall AMU.

Moxidectin use in Scottish sheep flocks suggests a need for clearer product labelling and communication of updated SCOPS guidelines.

BACKGROUND: Guidelines for sustainable use of moxidectin were established in 2020. This study aimed to identify how Scottish sheep farmers are using this key endectocide and estimate its effectiveness against gastrointestinal nematodes. METHODS: Questionnaires were distributed to sheep farmers across Scotland, and analysis focused on moxidectin use in relation to Sustainable Control of Parasites in Sheep (SCOPS) guidelines. Farmers using moxidectin in their flock volunteered to submit post-treatment sheep faecal samples, which were analysed for the presence of gastrointestinal nematodes using faecal egg counts with polymerase chain reaction to determine species. RESULTS: Despite 70% of farmers using moxidectin in 2020, knowledge levels varied: 24% of farmers included other anthelmintics when asked about moxidectin use. Moxidectin was used for a wide variety of reasons, and most farmers did not consistently follow SCOPS guidelines. Despite only 2 of 76 farmers reporting failure of moxidectin treatment, gastrointestinal nematodes were found following moxidectin treatment on five out of six farms tested and included Teladorsagia circumcincta, Cooperia curticei, Haemonchus contortus and Nematodirus sp. CONCLUSION: Findings from this project indicate the need for improved anthelmintic product labelling and farmer support to encourage sustainable use. The presence of nematodes in treated animals is suggestive of anthelmintic resistance.

A survey of British sheep farmers: Practices, opinions and knowledge surrounding the management of sheep scab.

Ovine psoroptic mange (commonly known as sheep scab) is, arguably, one of the most important ectoparasitic diseases of sheep in the UK. Although research has been conducted on the practices and knowledge of British sheep farmers regarding the management of sheep scab, recent data is limited. During October 2021 an online survey was completed by 725 British sheep farmers. Most respondents farmed in England (63.0%, 457/725), followed by Wales (20.6%, 149/725) and Scotland (16.4%, 119/725). Over half (53.0%, 384/725) of the respondents had experienced sheep scab in their flocks before, and 38.3% (147/384) of respondents experienced sheep scab twice or more in the previous ten years. The estimated prevalence of sheep scab from these surveyed farmers was 10.9% (79/725). Of the farmers who had experienced sheep scab before, only 36.2% (139/384) reported using skin scrapes and 12.5% (48/384) reported using blood tests for diagnosis. Over three-quarters of farmers quarantined all new sheep (76.6%; 498/650), but fewer quarantined returning sheep (28.6%; 83/290). Many of the respondents (43.7%, 252/577) did not quarantine new sheep for the suggested minimum 21 days. In addition, only 53.0% (384/725) of respondents answered all three of the knowledge questions regarding sheep scab correctly. The analysis illustrates that there is scope to improve the use of diagnostics, which suggests that misdiagnosis of sheep scab may be high and thus inappropriate treatments may be used, or treatments may not be used at all. It also demonstrated that there is scope for improvement in farmers' knowledge regarding sheep scab, particularly that sheep scab could be detected via a blood test and that the disease could present without visible signs. Our results further support that sheep scab is a large-scale endemic issue, potentially with an increasing prevalence in Great Britain. Future control interventions need to focus on improving knowledge exchange, raising awareness of best practice controls to ensure that better management strategies are employed by farmers, including improved control at livestock markets to reduce the national transmission and thus focus on coordinated control interventions.

Methods to develop and evaluate attitudinal scales to measure farmer perceptions: Using sheep scab as an example.

There is limited information on the attitudes and opinions of British sheep farmers when preventing and managing sheep scab in their flocks. Attitudes are examples of latent traits, which are not directly observable. They must be measured indirectly which can be achieved using measurement scales. Attitudinal measurement scales are used frequently in research, but are seldom evaluated prior to use, particularly in veterinary research. Therefore, the aim of this study was to identify and assess latent traits which influence the control of sheep scab with the use of exploratory factor analysis, and then further evaluate these factors with the use of item response theory to determine how they perform as scales. An online survey was completed by 726 British sheep farmers during October 2021 (725 useable responses), which included a section with 37 belief statements related to the opinions and attitudes of sheep farmers around the management of sheep scab. These belief statements were developed and adapted from previous research. During the analysis, they were subjected to exploratory factor analysis, which suggested that the scales performed reasonably well. The scales were then evaluated further by item response theory. The graded response models for each attitudinal scale were assessed by graphical evaluation. They demonstrated that the scales were able to distinguish those respondents with low perceptions of control, responsibility, and trust, and those who had high perceptions of luck. This study provides insights into some of the factors influencing the management of sheep scab, and how well these scales perform. Additionally, it further highlights the importance of evaluating attitudinal scales for use in research, and that exploratory factor analysis alone does not provide enough information on how well they perform.

Improving analgesia provision for sheep: An analysis of farm medicine records and attitudes towards pain relief on sheep farms in Northern Ireland.

Background: Management of pain is critical to improve the welfare of farmed livestock and meet consumer expectations. There is limited published information about the use of analgesic drugs in the sheep sector. Methods: A mixed-method approach was followed. The range of analgesic drugs used on 52 Northern Irish sheep farms was determined through analysis of medicine purchase records. Through interview and discussion groups, with both farmer and veterinarian participants, attitudes towards the use and adoption of such medicines were explored. Results: The use of non-steroidal anti-inflammatory drugs (NSAIDs) was widespread and highly variable. One-third of farmers in the sample did not purchase any NSAID. Meloxicam was the most commonly purchased NSAID by mass (72%) and standardised dose (73%). During interviews and discussions, farmers outlined the benefits they saw in using NSAIDs and how veterinarians influenced their uptake of these medicines. Use of corticosteroid was evidenced on 50% of the farms that supplied medicine records for analysis. Conclusions: Veterinarians can influence farmers to adopt NSAIDs for the provision of analgesia in their sheep and farmers observed the benefits they delivered. However, many farmers are still to be reached with this message, perhaps due to being largely self-sufficient and rarely engaging with veterinarians. Veterinarians have the opportunity to challenge farmers about the provision of analgesia, especially when farmers seek antibiotics for painful conditions such as lameness. Currently, the lack of an authorised product in the UK, with associated treatment guidance and industry promotion, may limit veterinarians' confidence in prescribing drugs for pain control in sheep.

To scan or not to scan? The economics of transthoracic ultrasonography for 'whole-flock' ovine pulmonary adenocarcinoma screening in UK sheep flocks.

BACKGROUND: Transthoracic ultrasonography (TTUS) is currently the only widely used method to diagnose suspected preclinical or subclinical cases of ovine pulmonary adenocarcinoma/Jaagsiekte (OPA) in live sheep. However, the economic impact of using TTUS as a screening test has not been described previously. METHODS: Test characteristics for TTUS in a low-prevalence situation were obtained from a previous study of 1074 breeding ewes that underwent TTUS with an experienced operator. The economic impact was modelled using a 10,000-iteration partial budget simulation and probability sensitivity analysis to explore the relative influence of model variables. RESULTS: In flocks of this size, culling true-positive and false-positive cases resulted in an estimated median net loss of £4647 (interquartile range: £3537-£6006), determined primarily by replacement ewe value and the cost of TTUS per ewe. CONCLUSION: The results of this study emphasise that great caution should be exercised by practitioners when determining if TTUS is appropriate as a screening test for OPA in low-prevalence flocks or subpopulations within a flock, such as younger age groups, where the losses incurred through the inadvertent culling of healthy sheep may significantly exceed any benefit derived from culling preclinical/subclinical cases.

Sheep scab in Northern Ireland: Its distribution, costs and farmer knowledge about prevention and control.

Sheep scab (psoroptic mange), which is endemic in the United Kingdom (UK) flock, has a significant, negative impact on sheep welfare. Nothing has previously been published about the distribution of sheep scab in Northern Ireland (NI), nor about Northern Irish farmers' knowledge and behaviours relating to the disease, its treatment, prevention and control. Between March and June 2021 an online questionnaire on the disease was completed by sheep farmers in NI. Forty-four respondents out of a total of 122 valid returns (36%) indicated that they had at least one outbreak of sheep scab in their flock within the previous five years. These flocks were spread throughout NI and included flocks grazing on common land. Farmers reporting sheep scab in their flock considered movements of sheep between flocks to be the main cause of flock infestation. Respondents demonstrated knowledge gaps in relation to the parasite biology, disease transmission, prevention and treatment options, as well as a lack of awareness of some of the relevant industry guidelines. We highlight that some farmers rely on clinical signs alone to rule out the possibility that newly purchased sheep are infested with sheep scab before mixing them with their flock. This activity poses a high risk for the introduction of sheep scab into previously uninfested flocks. The inadequacy of some farmers' quarantine rules, or their inability to follow them, was also reported by farmers as being the cause of their flock infestation. Sheep scab outbreaks were shown to result in significant financial cost, with some farmers reporting their most recent outbreak had cost over £2500 ($3329). The paper also highlights that in addition to the animal health and welfare impact and financial cost, sheep scab was reported to have a social cost: 94 respondents (79%) agreed that a sheep scab outbreak caused emotional stress to affected farmers. These findings have provided evidence of the widespread nature of sheep scab in the NI flock, and of the knowledge gaps and behaviours which need to be addressed to improve sheep scab control. This will require a combination of focused research, knowledge exchange between farmers, advisors, policy makers and regulators, and co-developed disease control plans at a flock and national level.

Putting sheep scab in its place: A more relational approach.

Since the reintroduction of sheep scab within the UK, its prevalence has increased despite several industry-led initiatives to control and manage the disease. Some studies have suggested that initiatives or policies should instead focus on specific places, such as geographically high-risk areas for sheep scab, which could allow for a more targeted approach. However, this risk of sheep scab has been measured in set geographical areas, without the reference to the interplay of topography, host, pathogen and the way in which humans socially and culturally define risk and place, potentially limiting the effectiveness of preventative initiatives. Therefore, the aim of the current study was to understand how place influences sheep farmers' approaches to the identification and management of the risk of sheep scab in their flocks. Qualitative data was collected from 43 semi-structured interviews with sheep farmers from England, Scotland, and Wales and was analysed by using the constant comparative approach. The codes were grouped into four concepts that influenced farmers' decision-making strategies for sheep scab control: perception of place; risk identification; risk categorisation; and risk management. These concepts were used as an analytical framework to identify three different 'places': 'uncontrollable places', 'liminal places' and 'protective places'. Each place reflects a different sheep scab control strategy used by farmers and shaped by their perceptions of place and risk. The 'uncontrollable places' category represented farmers who were located in areas that were geographically high-risk for sheep scab and who experienced a high frequency of sheep scab infestations in their flocks. The risk posed by their local landscape and neighbouring farmers, who neglected to engage in preventative behaviours, led them to feel unable to engage in effective risk management. Thus, they viewed scab as uncontrollable. The farmers within the 'liminal places' category were characterised as farmers who were located in high-risk areas for sheep scab, but experienced low levels of sheep scab infestations. These farmers characterised the risks associated with sheep scab management in terms of needing to protect their reputation and felt more responsibility for controlling sheep scab, which influenced them to engage in more protective measures. The farmers within the 'protective places' category were characterised as farming within low-risk areas and thus experienced a low level of sheep scab infestations. These farmers also described their risk in terms of their reputation and the responsibility they held for protecting others. However, they sought to rely on their low geographical risk of sheep scab as a main source of protection and therefore did not always engage in protective measures. These results suggest that place-based effects have significant impacts on sheep farmers' beliefs and behaviours and thus should be considered by policymakers when developing future strategies for sheep scab control.

Failure to detect Schmallenberg virus RNA in ram semen in the UK (2016-2018).

Background: Schmallenberg virus (SBV) is a midge-borne arbovirus that first emerged in the European ruminant population in 2011 and has since settled to an endemic pattern of disease outbreaks on an approximately 4-year cycle when herd immunity from the previous circulation drops to a point allowing renewed widescale virus circulation. The impacts of trade restrictions on genetic products (semen, embryos) from affected areas were severe, particularly after the discovery that the virus is intermittently shed in the semen of a small number of bulls. The trade in small ruminant (ram and goat) semen is less than that of bulls; nonetheless, there has been no study into the shedding rate of SBV in ram semen. Methods: Semen samples (n = 65) were collected as part of UK ram trials and artificial insemination studies around the period of the 2016-2018 SBV recirculation. Semen was preserved in RNAlater for shipping, and RNA extraction with RNeasy and S gene RT-quantitative PCR performed for SBV nucleic acid detection. Results: No SBV RNA was detected in any samples. Conclusions: While larger numbers of animals would be needed to completely exclude the possibility of SBV shedding in ram semen, this trial nonetheless highlights that this is likely a rare event if it occurs at all and is unlikely to play a role in disease transmission.

The impact of glutaraldehyde based footbaths on Dichelobacter nodosus prevalence and the antimicrobial resistant community of the ovine interdigital skin.

Ovine footrot, is a highly contagious polymicrobial bacterial infection, primarily caused by Dichelobacter nodosus. Preventative bactericidal footbaths are commonly used in the sheep industry to reduce the spread of bacteria. However, their effect on the bacterial community is poorly understood. This is the first study to investigate the impact of 2% Digicur (ProGiene,UK) footbath on the bacterial community of the ovine interdigital skin following a common UK footbathing routine. Swab samples were analysed by qPCR to determine prevalence and load of D. nodosus and numerated on MacConkey agar in the presence or absence of tetracycline and ampicillin to determine phenotypic antimicrobial resistance. Metagenomics were used to determine the impact of a single footbath on the bacterial community and genotypic antimicrobial resistance. The results suggest 2% Digicur is ineffective at reducing the load of D. nodosus when applied as a one off or weekly footbath, however sheep may act as a reservoir for multi-drug resistant bacteria creating opportunities to spread antimicrobial resistance to other sheep and their environment.

Understanding farmers' naturalistic decision making around prophylactic antibiotic use in lambs using a grounded theory and natural language processing approach.

The routine use of antibiotics for prevention of disease in neonatal lambs has been highlighted as inappropriate, yet research suggests that many farmers in the UK still carry out this practice. The aim of the study was to understand farmers' naturalistic decision-making around prophylactic antibiotic use in lambs. Data from 431 posts by 133 different users of an online discussion forum were analysed quantitatively using natural language processing and qualitatively using a grounded theory approach. Results from the qualitative analysis identified five categories that influenced farmers risk perceptions around prophylactic antibiotic use in lambs: anticipated regret, negative emotions and experiential avoidance; economic considerations; farmer identity; perception of capability; and perception of social judgement. Natural language processing analysis of the posts by the study group were compared to posts on topics unrelated to antibiotic use by control groups from the same forum to understand the underlying style and tone within the text. Analytical thinking and authenticity scores were significantly lower in the study group compared to the control groups (P < 0.01). Words relating to cognitive processes were significantly higher in the study group compared to the control groups (P < 0.01). Results of the qualitative and quantitative analysis were integrated to assess the fit of the data and enhance findings from either method alone. The key findings were the identification of reasons why farmers used antibiotics prophylactically in neonatal lambs. Farmers disassociated the use of oral antibiotics in neonatal lambs from other types of antibiotics within sheep farming. Farmers used the concept of luck and uniqueness to justify their prophylactic antibiotic use. This may explain farmers' low analytical thinking scores as this reflects a more personal style of thinking as farmers express their thoughts on antibiotic use on an individual basis. Farmers' felt that they did not have the capabilities to control neonatal disease without antibiotics during busy periods and this was exacerbated by external economic constraints. For farmers' who used antibiotics for therapeutic use, fear of social judgement was an important factor in their perceptions of risk around antibiotic use. The high frequency of negations and conjunctions suggested feelings of moral duty. As such, antibiotic use has developed into a symbol of their good farming identity which conflicted with the identity held by those who used antibiotics prophylactically. These results can be used to inform knowledge exchange around prophylactic antibiotic use in lambs to improve antibiotic stewardship in the sheep farming sector.

Evaluation of the use of antibiotic waste bins and medicine records to quantify antibiotic use on sheep, beef, and mixed species farms: A mixed methods study.

There is a lack of robust data on antibiotic use on sheep and beef farms in the UK, particularly for farms with mixed species. On mixed farms, quantification of antibiotic use is reliant on accurate farmers' records as veterinary prescription data does not provide information at the species level. Previous studies that have investigated multiple antibiotic use collection methods were conducted on single species farms and failed to collect data on the reasons why differences in methods may exist. This study aimed to evaluate sheep and beef farmers' antibiotic recording practices by comparing quantities of antibiotics measured from medicine records and empty antibiotic packaging collection bins, and identify barriers and facilitators of the antibiotic use collection methods. Thirty-five farms were followed for a year period. Farmers were asked to record their antibiotic treatments and deposit empty antibiotic packaging used in sheep or beef cattle into a bin. Semi-structured qualitative interviews were conducted to understand the experiences of farmers taking part in the study and explore the possible differences in methods. Bins and medicine records were collected and the mass of active ingredient (mg) was calculated. The level of agreement between the two antibiotic use collection methods was measured using rank parameters of Kendall's Ta. The bins were 67 % (CI = 29-87 %) more likely to measure more antibiotic use than the medicine records. The scale of variability of the measurements between two random farms was 33 % (CI = 6-56 %) larger for the antibiotic waste bins than the scale of variability between the medicine records. Sheep farmers often missed neonatal lamb treatments off their medicine records, with a median of 32.5 missing treatments per farm (IQR = 18-130). Of the mixed species farms, 28 % of treatment entries were missing the species the antibiotic was used in. Farmers reported that the bin was easy to use but they also reported that there was a tendency to under-report actual use where there were multiple workers on the farm or where treatments were administered by the veterinarian. The qualitative analysis identified contextual barriers to accurate medicine recording, such as difficulties with animal identification, with recording in the field, and with recording during lambing time. This study demonstrated that there were significant differences in antibiotic use measured by the bins and the medicine records. The mixed-methods approach provided an understanding of the contextual barriers that impacted farmers' medicine recording and use of the bin. This information on the contextual barriers can be used to inform the design of data collection methods to improve antibiotic consumption data in the sheep and beef sectors.

From the other perspective: Behavioural factors associated with UK sheep farmers' attitudes towards antibiotic use and antibiotic resistance.

Research suggests that many sheep farmers continue to carry out traditional antibiotic use practices despite new 'good practice' recommendations. The aim of this study was to group farmers depending on their attitudes around antibiotic use and antibiotic resistance, and determine the behaviours that are associated with the farmers in these groups. In 2017, a flock health survey was sent to British sheep farmers. K-means cluster analysis was used to identify groups of farmers with similar attitudes towards antibiotic use and resistance. A multivariable logistic regression model was built to determine the associations between farmers' past behaviours and their antibiotic attitude group. There were 461 responses. Two groups of farmers were identified based on their antibiotic attitudes. Cluster 1 were defined as the "discordant" group who had positive views of using antibiotics prophylactically and negative views of reducing antibiotic use. Cluster 2 were defined as the "concordant" group who were positive about reducing antibiotic use and had negative views about using antibiotics prophylactically. Using antibiotics in all lambs (OR = 2.689, CI = 1.571, 4.603), using antibiotics in all ewes (OR = 3.388, CI = 1.318, 8.706), always trimming diseased feet over the past three years (OR = 2.487, CI = 1.459, 4.238), not using a computer to record information over the past three years (OR = 1.996, CI = 1.179, 3.381), not changing worming practices over the past three years (OR = 1.879, CI = 1.144, 3.087), and farmers' perceptions that their sheep flock did not make a financial loss in the past three years (OR = 2.088, CI = 1.079, 4.040) were significantly associated with belonging to the discordant group. Talking to their veterinarian about antibiotic use or the frequency of veterinary visits were not associated with antibiotic attitude group. These results suggest that farmers who had attitudes relating to antibiotic use that did not align with current recommendations carried out more traditional practices, which were strengthened by their positive perceptions of profitability.

Variable selection for inferential models with relatively high-dimensional data: Between method heterogeneity and covariate stability as adjuncts to robust selection.

Variable selection in inferential modelling is problematic when the number of variables is large relative to the number of data points, especially when multicollinearity is present. A variety of techniques have been described to identify 'important' subsets of variables from within a large parameter space but these may produce different results which creates difficulties with inference and reproducibility. Our aim was evaluate the extent to which variable selection would change depending on statistical approach and whether triangulation across methods could enhance data interpretation. A real dataset containing 408 subjects, 337 explanatory variables and a normally distributed outcome was used. We show that with model hyperparameters optimised to minimise cross validation error, ten methods of automated variable selection produced markedly different results; different variables were selected and model sparsity varied greatly. Comparison between multiple methods provided valuable additional insights. Two variables that were consistently selected and stable across all methods accounted for the majority of the explainable variability; these were the most plausible important candidate variables. Further variables of importance were identified from evaluating selection stability across all methods. In conclusion, triangulation of results across methods, including use of covariate stability, can greatly enhance data interpretation and confidence in variable selection.

Use of bootstrapped, regularised regression to identify factors associated with lamb-derived revenue on commercial sheep farms.

The profitability of UK sheep farms is variable with many farms making a net loss. For economic sustainability, farms have to be profitable, therefore it is important to maximise income whilst controlling costs. The most important source of income in sheep flocks is from lamb production but there is little information on factors that explain variability between farms in revenue from lamb sales. The aim of this research was to identify farm, farmer and management factors likely to have the largest, most reliable associations with lamb-derived revenue. From a population of 830 sheep farms, 408 farmers completed an online questionnaire comprising over 300 variables. Total lamb-derived revenue was calculated for each farm using abattoir information including carcass classification. The median flock size was 560 ewes, median land size 265 acres, median revenue per acre from lambs sold was £197 (IQR = 120-296) and median revenue per ewe £95 (IQR = 72-123). A robust analytic approach using regularised (elastic net) regression with bootstrapping was implemented to account for multicollinearity in the data and to reduce the likelihood of model over-fitting. To provide model inference and allow ranking of variables in terms of relevance, covariate stability and coefficient distributions were evaluated. Factors with high stability and relatively large positive associations with revenue per acre were (median effect size (£); 95 % bootstrap probability interval); an increased stocking rate of 0.2 ewe/acre (13; 6-17), fertilizer being used on most of the grazing land (18; 0.1-37), the use of rotational grazing (13; 0.3-34), decreased proportion of ewes with prolapses (4; 0.3-9), separation of lame sheep from the rest of the flock (16; 0.9-37), selecting ewes for culling based on prolapses (20; 0.2-55) and infertility (20; 2-46), conducting body condition scoring of ewes at lambing (28; 3-58), early lactation (21; 1-54) or weaning (25; 2-70), increased farmer education (20; 2-54) and farmers with a positive business attitude (15; 0.2-38). Additional factors with a high stability and relatively large associations with increased revenue per ewe were; never trimming diseased feet of lame ewes (9; 0.8-22) and making use of farm records (5; 0.3-12). This is the first study in animal health epidemiology to use bootstrapped regularised regression to evaluate a wide dataset to provide a ranking of the importance of explanatory covariates. We conclude that the relatively small set of variables identified, with a potentially large influence on lamb-derived revenue, should be considered prime candidates for future intervention studies.

Sustainable lamb production: Evaluation of factors affecting lamb growth using hierarchical, cross classified and multiple memberships models.

In light of current concerns about the sustainability of red meat production in a world with increasing global demand for food from animal origin there is a need for a better understanding of factors that influence the growth rate and feed conversion efficiency of animals on commercial farms. The primary objective of this observational study was to use longitudinal data to quantify the simultaneous effects of multiple ewe and lamb factors on lamb growth rate. A secondary aim was to evaluate model structures that specifically account for lamb grouping effects during the growth period and compare these to classical hierarchical growth rate models. A total of 4172 weight recordings from 805 lambs and data on disease events were collected over a 6-month period from a commercial pedigree sheep flock. Three mixed model structures were compared, hierarchical, cross classified and multiple membership, and final estimates determined within a Bayesian framework. The multiple membership structure provided the best model fit and was used for final inference; taking account of the effect of lamb grouping over time provided the best estimates of lamb growth rate. Ewe lameness and mastitis cases had a deleterious impact on lamb growth. Lambs from ewes identified with mastitis during lactation were on average 3.0 (standard error (SE) 1.6) kg lighter during the four month growth period than lambs from unaffected ewes. Lambs from ewes that were not lame during pregnancy were 3.0 (SE 1.2) kg heavier at eight weeks of age than lambs from ewes with a least one lameness case during the same period. Lambs from ewes lame either during the first 4 weeks or between 4-8 weeks of a lamb's life (but not lame during pregnancy) were also significantly heavier at 56 days of age, than lambs reared by ewes that were lame during pregnancy (2.8 (SE 1.2) and 3.4 (SE 1.2) kg respectively). Cases of pneumonia and bacterial arthritis in lambs had a significant negative impact on lamb growth with affected lambs being on average 5.5 (SE 1.1) kg and 2.2 (SE 1.2) kg less than non-affected lambs respectively after the disease event. Prior to a case of lameness or pneumonia, lambs were significantly heavier than unaffected lambs suggesting a possible trade-off between growth and immune function. Overall, the study provides evidence that that a combination of ewe and lamb characteristics and disease events play an important role in determining lamb growth rate and that heavier lambs may be more susceptible to disease.