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 (R² 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.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03248-x.

Unraveling the Complexity to Observe Associations Between Welfare Indicators and Hair Cortisol Concentration in Dairy Calves

Using levels of the stress hormone cortisol as an indicator for welfare is a common, but debated practice. In this observational study, hair cortisol concentration (HCC) of samples from 196 dairy calves from 7 to 302 days of age collected from 12 Swedish farms was determined using a commercially available ELISA. An assessment of animal welfare, assessed using animal-based indicators, was performed on the day of sampling. First, methodological factors with the potential to impact HCC and the effect of age were analyzed using generalized additive models. This revealed a significant peak in hair cortisol in young calves (around 50 days of age) and an association between fecal contamination of hair samples and the level of cortisol extracted. Second, associations between welfare indicators and HCC were explored using cluster analysis and regularized regression. The results show a complex pattern, possibly related to different coping styles of the calves, and indicators of poor welfare were associated with both increased and decreased hair cortisol levels. High cortisol levels were associated with potential indicators of competition, while low cortisol levels were associated with the signs of poor health or a poor environment. When running the regularized regression analysis without the contaminated hair samples and with the contaminated samples (including a contamination score), the results did not change, indicating that it may be possible to use a contamination score to correct for contamination.

Overview of Cattle Diseases Listed Under Category C, D or E in the Animal Health Law for Which Control Programmes Are in Place Within Europe

The COST action “Standardising output-based surveillance to control non-regulated diseases of cattle in the European Union (SOUND control),” aims to harmonise the results of surveillance and control programmes (CPs) for selected cattle diseases to facilitate safe trade and improve overall control of cattle infectious diseases. In this paper we aimed to provide an overview on the diversity of control for these diseases in Europe. A selected cattle disease was defined as an infectious disease of cattle with no or limited control at EU level, which is not included in the European Union Animal health law Categories A or B under Commission Implementing Regulation (EU) 2020/2002. A CP was defined as surveillance and/or intervention strategies designed to lower the incidence, prevalence, mortality or prove freedom from a specific disease in a region or country. Passive surveillance, and active surveillance of breeding bulls under Council Directive 88/407/EEC were not considered as CPs. A questionnaire was designed to obtain country-specific information about CPs for each disease. Animal health experts from 33 European countries completed the questionnaire. Overall, there are 23 diseases for which a CP exists in one or more of the countries studied. The diseases for which CPs exist in the highest number of countries are enzootic bovine leukosis, bluetongue, infectious bovine rhinotracheitis, bovine viral diarrhoea and anthrax (CPs reported by between 16 and 31 countries). Every participating country has on average, 6 CPs (min–max: 1–13) in place. Most programmes are implemented at a national level (86%) and are applied to both dairy and non-dairy cattle (75%). Approximately one-third of the CPs are voluntary, and the funding structure is divided between government and private resources. Countries that have eradicated diseases like enzootic bovine leukosis, bluetongue, infectious bovine rhinotracheitis and bovine viral diarrhoea have implemented CPs for other diseases to further improve the health status of cattle in their country. The control of the selected cattle diseases is very heterogenous in Europe. Therefore, the standardising of the outputs of these programmes to enable comparison represents a challenge.

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

Simple Summary

Pain scales are tools developed to improve pain assessment in horses. They are based on behaviors and/or facial expressions, and the observer allocates a score based on the character of the behavior or facial expression. Little is known about behaviors and facial expressions at rest in horses with orthopedic pain since pain is mainly assessed by lameness evaluation during movement. The aim of this study was to describe how closely equine behaviors and facial expressions are associated with movement asymmetry and to identify combinations of behavior and expressions present in horses with induced orthopedic pain. Orthopedic pain was induced in eight horses and assessed in two ways; using four existing equine pain scales at rest, and by measuring movement asymmetry during movement. The association of behavior and facial expression items in the pain scales with actual lameness was analyzed. Posture-related behavior showed the strongest association, while facial expressions varied between horses. These results show that pain scales for orthopedic pain assessment would benefit from including posture, head position, location in the box stall, focus, interactive behavior, and facial expressions. This could improve orthopedic pain detection in horses during rest with mild lameness.

Abstract

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.

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.

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.