3D pose estimation to detect posture transition in free-stall housed dairy cows.

Free stall comfort is reflected in various indicators, including the ability for dairy cattle to display unhindered posture transition movements in the cubicles. To ensure farm animal welfare, it is instrumental for the farm management to be able to continuously monitor occurrences of abnormal motions. Advances in computer vision have enabled accurate kinematic measurements in several fields such as human, equine and bovine biomechanics. An important step upstream to measuring displacement during posture transitions is to determine that the behavior is accurately detected. In this study, we propose a framework for detecting lying to standing posture transitions from 3D pose estimation data. A multi-view computer vision system recorded posture transitions between Dec. 2021 and Apr. 2022 in a Swedish stall housing 183 individual cows. The output data consisted of the 3D coordinates of specific anatomical landmarks. Sensitivity of posture transition detection was 88.2% while precision reached 99.5%. Analyzing those transition movements, breakpoints detected the timestamp of onset of the rising motion, which was compared with that annotated by observers. Agreement between observers, measured by intra-class correlation, was 0.85 between 3 human observers and 0.81 when adding the automated detection. The intra-observer mean absolute difference in annotated timestamps ranged from 0.4s to 0.7s. The mean absolute difference between each observer and the automated detection ranged from 1.0s to 1.3s. There was a significant difference in annotated timestamp between all observer pairs but not between the observers and the automated detection, leading to the conclusion that the automated detection does not introduce a distinct bias. We conclude that the model is able to accurately detect the phenomenon of interest and that it is equatable to an observer.

Farmers´ sense of the biological impact of extreme heat and seasonality on Swedish high-yielding dairy cows - A mixed methods approach.

Supporting dairy farmers in becoming resilient towards extreme weather requires a broad understanding of the experiences and perceived risks associated with these events from those who undergo them. We used a mixed methods approach to explore national trends of biological consequences on dairy cow udder health and fertility, combined with in-depth farmer conversations around extreme weather events, focusing on heat. The aim is to provide a comprehensive picture of how dairy farmer perceptions, priorities and decision-making are related to the season and extreme weather to identify preventive pathways that can reduce biological costs of heat stress on Swedish dairy cattle during summer. Data collected monthly at cow and farm level between 2016-2019 as part of the Swedish milk and disease recording system confirm seasonal trends and show increased somatic cell counts (SCC) and negatively impacted fertility during summers. In addition, transcriptions of 18 interviews with dairy farmers across the country and seasonal variations of SCC and fertility were thematically analysed. The results suggest that farmers have a broad definition of extreme weather and are aware of the negative impacts. Yet handling of extreme weather events can mainly be classified as reactive. Nevertheless, there are long-term effects on the farm economy, health and herd dynamics. Swedish dairy farmers are currently showing resilience, albeit a fragile one. The capability to ensure sufficient feed production in extreme weather is critical for farm self-perceived resilience. However, acknowledging the long-term biological costs related to fertility, currently not perceived by farmers, has the potential to support proactive planning and improve farm resilience and profitability.

Performance of four equine pain scales and their association to movement asymmetry in horses with induced orthopedic pain.

Objective: This study investigated the relationship between orthopedic pain experienced at rest, and degree of movement asymmetry during trot in horses with induced reversible acute arthritis. Orthopedic pain was assessed with the Horse Grimace Scale (HGS), the Equine Utrecht University Scale of Facial Assessment of Pain (EQUUS-FAP), the Equine Pain Scale (EPS), and the Composite Orthopedic Pain Scale (CPS). Reliability and diagnostic accuracy were evaluated with intraclass correlation coefficients (ICC) and area under the curve (AUC). Study design and animals: Eight healthy horses were included in this experimental study, with each horse acting as its own control. Methods: Orthopedic pain was induced by intra-articular lipopolysaccharide (LPS) administration. Serial pain assessments were performed before induction and during pain progression and regression, where three observers independently and simultaneously assessed pain at rest with the four scales. Movement asymmetry was measured once before induction and a minimum of four times after induction, using objective gait analysis. Results: On average 6.6 (standard deviation 1.2) objective gait analyses and 12.1 (2.4) pain assessments were performed per horse. The ICC for each scale was 0.75 (CPS), 0.65 (EPS), 0.52 (HGS), and 0.43 (EQUUS-FAP). Total pain scores of all scales were significantly associated with an increase in movement asymmetry (R 2 values ranging from -0.0649 to 0.493); with CPS pain scores being most closely associated with movement asymmetry. AUC varied between scales and observers, and CPS was the only scale where all observers had a good diagnostic accuracy (AUC > 0.72). Conclusions and clinical relevance: This study identified significant associations between pain experienced at rest and degree of movement asymmetry for all scales. Pain scores obtained using CPS were most closely associated with movement asymmetry. CPS was also the most accurate and reliable pain scale. All scales had varying linear and non-linear relations between total pain scores and movement asymmetry, illustrating challenges with orthopedic pain assessment during rest in subtly lame horses since movement asymmetry needs to be rather high before total pain score increase.

Clinical features and treatment response to differentiate idiopathic peritonitis from non-strangulating intestinal infarction of the pelvic flexure associated with Strongylus vulgaris infection in the horse.

BACKGROUND: Peritonitis in horses secondary to non-strangulating infarction (NSII) has a guarded prognosis, even after intestinal resection. In contrast, horses with idiopathic peritonitis respond well to medical treatment. Affected horses in both cases often show signs of both colic and systemic inflammation, but early diagnosis is crucial for optimal treatment and an accurate prognosis. One cause of NSII is thrombus formation secondary to Strongylus vulgaris larval migration. There has been a documented increase in S. vulgaris prevalence in Sweden since the implementation of selective anthelmintic treatment in 2007, which subsequently could result in a rise in NSII cases. In a retrospective clinical study, medical records from cases diagnosed with NSII of the pelvic flexure or idiopathic peritonitis from three equine referral hospitals in Sweden during 2017-2020 were reviewed. Information including demographic data, relevant medical history, and clinical- and laboratory parameters were obtained from patient records. To facilitate the differentiation between cases of idiopathic peritonitis and cases with confirmed NSII of the pelvic flexure, the aim of the study was to compare clinical and laboratory parameters, clinical progression and initial response to antimicrobial treatment. A secondary aim was to compare survival-rates. RESULTS: Horses with NSII (n = 20) were significantly more likely to present during the winter months with a poorer response to medical treatment within 48 h. Cases of idiopathic peritonitis (n = 107) had a 100% survival rate with medical treatment, although one case required surgical correction of a colon displacement. In comparison, all confirmed NSII cases were non-responsive to antimicrobial treatment, with a survival rate to discharge of 50% after colon resection. Specific rectal findings and peripheral blood neutropenia were strongly associated with NSII. CONCLUSIONS: In Sweden, idiopathic peritonitis cases still predominate over S. vulgaris associated NSII cases and have an excellent survival rate with antimicrobial treatment. However, horses presenting with septic peritonitis during the winter months with a palpable rectal mass and displaying fever and colic signs beyond 48 h of medical treatment are likely to suffer from NSII of the pelvic flexure and should be considered for abdominal surgery.

Existence and Quality of Data on Control Programs for EU Non-regulated Cattle Diseases: Consequences for Estimation and Comparison of the Probability of Freedom From Infection.

Some European countries have successfully implemented country-specific control programs (CPs) for infectious cattle diseases that are not regulated or are regulated only to a limited extent at the European Union (EU) level. Examples of such diseases include bovine viral diarrhea (BVD), infectious bovine rhinotracheitis (IBR), and Johne's disease (JD). The CPs vary between countries in the design and quality of collected data as well as methods used to detect infection and estimate prevalence or probability of freedom from infection. Differences in disease status between countries and non-standardized approaches to assess freedom from infection pose a risk for countries with CPs for non-regulated diseases as infected animals may influence the progress of the disease control or eradication program. The implementation of output-based standards allows estimation and comparison of the probability of freedom for non-regulated cattle diseases in European countries. The aim of the current study was to assess the existence and quality of data that could be used for estimating freedom from infection in European countries. The online data collection tool was sent to 32 countries participating in the SOUND control COST Action and was completed by 24 countries. Data on cattle demographics and data from CPs of IBR and BVD exist in more than 50% of the response countries. However, data describing risk factors and CP of JD was reported as existing in <25% of the countries. The overall quality of data in the sections on demographics and CPs of IBR and BVD were evaluated as "good", but risk factors and JD data were mostly evaluated as "fair." Data quality was considered less good mainly due to two quality criteria: accessibility and accuracy. The results of this study show that the quantity and quality of data about cattle populations and CPs are relatively similar in many surveyed countries. The outcome of this work provides an overview of the current situation in the European countries regarding data on EU non-regulated cattle diseases and will further assist in the development and implementation of output-based standards.

Identification of Body Behaviors and Facial Expressions Associated with Induced Orthopedic Pain in Four Equine Pain Scales.

Equine orthopedic pain scales are targeted towards horses with moderate to severe orthopedic pain. Improved assessment of pain behavior and pain-related facial expressions at rest may refine orthopedic pain detection for mild lameness grades. Therefore, this study explored pain-related behaviors and facial expressions and sought to identify frequently occurring combinations. Orthopedic pain was induced by intra-articular LPS in eight horses, and objective movement asymmetry analyses were performed before and after induction together with pain assessments at rest. Three observers independently assessed horses in their box stalls, using four equine pain scales simultaneously. Increase in movement asymmetry after induction was used as a proxy for pain. Behaviors and facial expressions commonly co-occurred and were strongly associated with movement asymmetry. Posture-related scale items were the strongest predictors of movement asymmetry. Display of facial expressions at rest varied between horses but, when present, were strongly associated with movement asymmetry. Reliability of facial expression items was lower than reliability of behavioral items. These findings suggest that five body behaviors (posture, head position, location in the box stall, focus, and interactive behavior) should be included in a scale for live assessment of mild orthopedic pain. We also recommend inclusion of facial expressions in pain assessment.

Socially engaged calves are more likely to be colonised by VTEC O157:H7 than individuals showing signs of poor welfare.

In cattle herds, the transmission and persistence of VTEC O157:H7 (a serotype of verotoxin-producing Escherichia coli - known for its life threatening complications in humans) is dependent on a small proportion of cattle who become colonised and shed high numbers of the bacteria. Reducing the proportion of these animals is considered key for decreasing the prevalence of VTEC O157:H7. In this study, observations of calf behaviour and animal-based welfare indicators were used to explore individual risk factors and underlying drivers of colonisation in Swedish dairy calves. Interdependencies between variables led to three different approaches being used to visualize and explore the associations. Combining the results of all methods revealed similar patterns and suggest that healthy animals, actively grooming and interacting with others calves in the group have a higher risk of colonisation than small dairy calves in poor condition (diarrhoea, poor ruminal fill, poor body condition score and nasal discharge). This lends no support to the hypothesis that reduced welfare is a risk factor for VTEC O157:H7, but implies that individual differences in calf behaviour affect oral exposure to the bacteria so driving the risk of colonisation. This new finding has important implications for understanding of VTEC O157:H7 transmission within farms.

Risk factors and dynamics of verotoxigenic Escherichia coli O157:H7 on cattle farms: An observational study combining information from questionnaires, spatial data and molecular analyses.

The increasing number of human cases infected with a highly virulent type of verotoxigenic Escherichia coli (VTEC) O157:H7 in Sweden is the result of domestic transmission originating in regional clusters of infected cattle farms. To control the spread of the bacteria a comprehensive picture of infection dynamics, routes of transmission between farms and risk factors for persistence is urgently needed. The aim of the study was to investigate different aspects of the epidemiology of VTEC O157:H7 on the Swedish island of Öland by combining information from environmental sampling of VTEC O157:H7 from 80 farms with information from farmer questionnaires, spatial and molecular analyses. The farms were sampled in the spring and fall of 2014 and on four of them additional samples were collected during summer and winter. The results show a high prevalence of VTEC O157:H7 and a high proportion of strains belonging to the virulent clade 8. Farms that became infected between samplings were all located in an area with high cattle density. The most important risk factors identified are generally associated with biosecurity and indicate that visitors travelling between farms may be important for transmission. In addition, whole genome sequencing of a subset of isolates from the four farms where additional sampling was performed revealed ongoing local transmission that cannot be observed with a lower resolution typing method. Our observations also show that VTEC O157:H7 may persist in the farm environment for extended periods of time, suggesting that specific on-farm measures to reduce environmental prevalence and spread between groups of animals may be required in these cases.

Systematic Review of Phytotherapeutic Treatments for Different Farm Animals Under European Conditions.

The emergence and spread of antibiotic resistance is a growing global threat and has aroused a global interest in limiting antibiotic use in animal agriculture. As we are entering the post-antibiotic era, there is a growing need for identifying alternatives to antibiotics for prevention and treatment. Although phytotherapeutic remedies are available and are used in Europe, evidence of their efficacy is currently very limited but is nevertheless still necessary. A systematic review of phytotherapy used for the treatment and prevention of infectious diseases in farm animals has been conducted using the PICOS approach. Analysis and extraction of information from studies was performed according to a protocol, and included: publication year and source, research body, species, farming system, purpose of application, disease in focus, diagnostic method, remedy used (origin and ingredients of the remedy), producer of remedy, way of administration, study design, and control groups, measure of effect, and outcome of the study. A total of 1,705 papers were screened, but only 44 (comprising 53 independent studies) met the inclusion criteria. The majority of the scientific studies identified show limitations in the study design as well as in presentation and standardization of the botanical remedies studied, which limits the possibilities of drawing firm conclusions. Preventive effect was investigated in 89% of the studies. Half of the studies reported uncertain effects of the botanical remedies on subclinical measures in comparison to a control group. The review highlights unresolved questions such as the need for standardized controlled trials and for improved standardization of the botanical products by analytical methods, such as high-performance liquid chromatography. It is necessary to consider this in order to achieve replicable outcomes and establish efficacy and safety of phytotherapy in farm practice. The manageability of alternative medicine in farm animals also warrants further investigation so as to ascertain whether all necessary preconditions for their use are being granted.

Effect of on-farm interventions in the aftermath of an outbreak of hypervirulent verocytotoxin-producing Escherichia coli O157:H7 in Sweden.

In 2007, human infections with a hypervirulent strain of verocytotoxin-producing Escherichia coli O157:H7 increased in Sweden and especially in the Halland County. A connection between the cases and a local beef cattle farm with an on-farm abattoir and meat processing plant was established. In this observational study the control measures implemented on the infected farm and the dynamics of infection in the herd are described. In May 2008, when measures were initiated and animals put to pasture, the prevalence of positive individuals was 40 per cent and 18 carcasses out of 24 slaughtered animals were contaminated. During summer the monthly prevalence of positive carcasses varied between 8 and 41 per cent and at turning-in 22 out of 258 individually sampled animals were shedding the pathogen. After January 2009 no positive carcasses were found at slaughter and follow-up samplings of environment and individuals remained negative until the study period ended in May 2010. The results indicate that on-farm measures have potential to reduce the prevalence of the pathogen in a long-term perspective. However, as self-clearance cannot be excluded the effectiveness of the suggested measures needs to be confirmed.

Priorities and Future Actions for an Effective Use of Phytotherapy in Livestock-Outputs from an Expert Workshop.

This study reflects on the recognised need for more joined-up, high-quality research on phytotherapy that addresses the current societal challenges in finding alternatives to the use of antibiotics. The study applied a multidisciplinary participatory approach in an expert workshop exercise within the FP7 EU IMPRO project. Prior to this study, a literature review was elaborated on research in the field of phytotherapy as applied to farm animals, cooperation between research bodies and initiatives to reduce the use of antibiotics by using phytotherapeutic remedies. The review was delivered to the participants of the workshop so as to receive feedback on it and enrich the discussion. Different expertise, background in research or veterinary practice, and varying positions regarding phytotherapy were the criteria in targeting participants. A structured workshop was subsequently organised, with questions to experts addressing scientific validation of phytotherapy, effective treatment under farm conditions and necessary developments for the future. Challenges identified by the experts were as follows: poor study designs, lack of reproducibility of studies, poor standardisation of products, cost-benefit concerns, lack of veterinarian training and poor data availability. To overcome obstacles, the need for improved study designs for clinical trials was given priority in order to prove the efficacy of remedies and to implement a monitoring system which enables the assessment of the effectiveness of treatments in farm practice. Reflections in this report are intended to be a resource for scientists, policy makers and end users for an effective use of phytotherapy at farm level.