Following an outbreak of Salmonella Typhimurium in Wales in July 2021 associated with sheep meat and offal, further genetically related cases were detected across the UK. Cases were UK residents with laboratory-confirmed Salmonella Typhimurium in the same 5-single-nucleotide polymorphism (SNP) single-linkage cluster with specimen date between 01/08/2021–2031/12/2022. We described cases using routine (UK) and enhanced (Wales only) surveillance data. Exposures in cases in Wales were compared with non-Typhimurium Salmonella case–controls. Environmental Health Practitioners and the Food Standards Agency investigated supply chains of food premises reported by ≥2 cases. Animal, carcass, and environmental samples taken for diagnostic or monitoring purposes for gastrointestinal pathogens were included in microbiological investigations. We identified 142 cases: 75% in England, 23% in Wales and 3% in Scotland. Median age was 32 years, and 59% were male. Direct contact with sheep was associated with becoming a case (aOR: 14, 95%CI: 1.4–145) but reported by few (6/32 cases). No single food item, premises, or supplier linked all cases. Multi-agency collaboration enabled the identification of isolates in the same 5-SNP single-linkage cluster from a sheep carcass at an English abattoir and in ruminant, wildlife, poultry, and environmental samples, suggesting multiple vehicles and pathways of infection.

Experimental procedures involving farm animals are often associated with stress due to restraining. Stress can be reduced through use of positive reinforcement training, which then serves as refinement according to the 3Rs principles. Trainer skills, however, may influence the feasibility and success of animal training. The potential influence of trainer skills as well as the education of animal trainers are rarely described in literature but are necessary information for the implementation of positive reinforcement training as a refinement measure. To investigate the effect of educational programmes on animal trainers, we compared the training success of two groups of participants in training goats to elicit a behaviour that would allow simulated venipuncture. One group was educated in a two-day workshop while the other was provided with specific literature for self-instructed learning. Training success was evaluated using an assessment protocol developed for this study. A greater training success in the WORKSHOP GROUP, reflected by objective and subjective measures, was clearly supported statistically. In addition, 73 versus only 13% of the participants of the WORKSHOP GROUP and the self-instructed BOOK GROUP, respectively, stated that they could completely implement the knowledge gained in the course of this study. Our results indicate that more intensively educated trainers can train animals more successfully. In conclusion, if animal training is implemented as refinement, animal caretakers should receive instruction for positive reinforcement training.

Understanding the transfer of polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs) as well as polychlorinated biphenyls (PCBs) from oral exposure into cow’s milk is not purely an experimental endeavour, as it has produced a large corpus of theoretical work. This work consists of a variety of predictive toxicokinetic models in the realms of health and environmental risk assessment and risk management. Their purpose is to provide mathematical predictive tools to organise and integrate knowledge on the absorption, distribution, metabolism and excretion processes. Toxicokinetic models are based on more than 50 years of transfer studies summarised in part I of this review series. Here in part II, several of these models are described and systematically classified with a focus on their applicability to risk analysis as well as their limitations. This part of the review highlights the opportunities and challenges along the way towards accurate, congener-specific predictive models applicable to changing animal breeds and husbandry conditions.

Polychlorinated dibenzo-para-dioxins (PCDDs) and dibenzofurans (PCDFs) (collectively and colloquially referred to as ‘dioxins’) as well as polychlorinated biphenyls (PCBs) are persistent and ubiquitous environmental contaminants that may unintentionally enter and accumulate along the food chain. Owing to their chronic toxic effects in humans and bioaccumulative properties, their presence in feed and food requires particular attention. One important exposure pathway for consumers is consumption of milk and dairy products. Their transfer from feed to milk has been studied for the past 50 years to quantify the uptake and elimination kinetics. We extracted transfer parameters (transfer rate, transfer factor, biotransfer factor and elimination half-lives) in a machine-readable format from seventy-six primary and twenty-nine secondary literature items. Kinetic data for some toxicologically relevant dioxin congeners and the elimination half-lives of dioxin-like PCBs are still not available. A well-defined selection of transfer parameters from literature was statistically analysed and shown to display high variability. To understand this variability, we discuss the data with an emphasis on influencing factors, such as experimental conditions, cow performance parameters and metabolic state. While no universal interpretation could be derived, a tendency for increased transfer into milk is apparently connected to an increase in milk yield and milk fat yield as well as during times of body fat mobilisation, for example during the negative energy balance after calving. Over the past decades, milk yield has increased to over 40 kg/d during high lactation, so more research is needed on how this impacts feed to food transfer for PCDD/Fs and PCBs.

Sepsis is a complex clinical syndrome triggered by an inflammatory host response to an infection. It is usually complicated to detect and diagnose, and has severe consequences in human and veterinary health, especially when treatment is not started early. Therefore, efforts to detect sepsis accurately are needed. In addition, its proper diagnosis could reduce the misuse of antibiotics, which is essential fighting against antimicrobial resistance. This case is a particular issue in farm animals, as antibiotics have been traditionally given massively, but now they are becoming increasingly restricted. When sepsis is suspected in animals, the most frequently used biomarkers are acute phase proteins such as C-reactive protein, serum amyloid A and haptoglobin, but their concentrations can increase in other inflammatory conditions. In human patients, the most promising biomarkers to detect sepsis are currently procalcitonin and presepsin, and there is a wide range of other biomarkers under study. However, there is little information on the application of these biomarkers in veterinary species. This review aims to describe the general concepts of sepsis and the current knowledge about the biomarkers of sepsis in pigs, horses, and cattle and to discuss possible advances in the field.

A data set of individual observations was compiled from 17 digestibility trials with sheep with the aim of evaluating the impact of the method of analysis and, within each method, the effect of dietary fibre content and trial on the faecal recovery rate (RR) of indigestible dry matter (iDM) and indigestible neutral detergent fibre (iNDF). Markers concentration in samples of diet and faeces were determined either in polyester filter bags of 40 μm of porosity incubated in situ for 144 h (method A; n = 257) or in bags of 16 μm of porosity incubated in situ for 288 h (method B; n = 321). Regardless of the incubation method, the intake of either iDM or iNDF was linearly (P < 0.05) related to the amount excreted in faeces and, for all linear relationships, the slopes were lower than 1 (i.e. between 0.53 and 0.71). Within both methods, the RR of both markers linearly decreased at increased NDF content in diet (P < 0.05). The root mean square error of the linear relationships varied from 0.147 to 0.189 which represented from 19% to 24% of the respective average RR of markers. In conclusion, regardless of the incubation method, the RR of both markers showed high individual variability and, thus, the use of average RR values obtained in controlled digestibility trials as an index to correct the individual digestibility values obtained with either marker in field trials has the potential to improve the accuracy but not the precision of the digestibility estimates.

Gastrointestinal parasite control has been a major challenge to livestock due to the failure of anthelmintic treatments. Monepantel (MNT) was introduced in 2009 as an alternative treatment option showing a new mechanism of action against nematode parasites. To study the response of MNT in a suppressive regime, 45-Suffolk and White Dorper naturally infected sheep were divided into one of three groups, G1: control – with no treatment, G2: MNT at 2.5 mg kg−1 live weight (LW) PO every 30 days, and G3: MNT at 4.0 mg kgLW−1 PO every 30 days for 6 months. Every 15 days, the animals were individually weighed (body weight, BW) and checked for Famacha (FMC) and body condition score (BCS). The efficacy of MNT was evaluated weekly by fecal egg count (FEC) every month. FEC showed >97% efficacy at the start of the experiment, revealing a significant reduction for G2 (28%) and G3 (39%) in the following months. There was no treatment, BW or BCS effect between treatments; however, there was a period (P < 0.0001) and a treatment vs period interaction (P < 0.0001) for BW. The data revealed that MNT at a therapeutic and suppressive dose had a non-linear polynomial efficacy regression (R2) of 0.988 and 0.992, respectively. This original experiment demonstrates how short-interval and suppressive MNT treatments would rapidly select Haemonchus contortus, showing a fast susceptible-resistance phenotypic population replacement. Therefore, it is suggested that MNT might be carefully used in parasite control programmes alongside other management strategies (i.e. FMC, BCS) to reduce treatment frequency and the selection process for resistance.

High yielding ruminant livestock require high nutritive value in forage for maintenance, growth and production. Climate change has been documented as impacting on the nutritive value of forage plants. Therefore, the aim of this study was to investigate the impact of increased temperature in combination with CO2-enhancement on the nutritive value of orchard grass (cocksfoot; Dactylis glomerata L.), as a C3 model plant, widespread in mountainous permanent grassland plant communities. Functional traits and forage quality of orchard grass were investigated both under ambient (C0T0) and under simulated, future climate conditions (C2T2) with increased temperature (+3°C) and enhanced CO2 concentration (+300 ppm) under field conditions. Plant samples were taken from each of the three growths over a period of three consecutive years and numerous functional properties and forage quality parameters were determined. Special attention was paid to the determination of water-soluble carbohydrates (WSC), crude protein (CP), non-protein N (NPN) and metabolizable energy (ME) as possible indicators for different climatic conditions. It is hypothesized that (i) functional traits and (ii) forage quality of orchard grass are altered by increased temperature and higher CO2 concentration. The results showed a negative impact of C2T2 compared to C0T0 on tiller height (54.4 v. 70.6 cm) and weight (2.42 v. 3.22 g) as average over cuts and years. The NPN content was lower in C2T2 (312 g/kg CP) compared to C0T0 (339 g/kg CP). In contrast, the WSC content was higher in C2T2 (90.3 g/kg DM) compared to C0T0 (82.5 g/kg DM). Both ME content and digestibility were increased in C2T2 (9.18 ME/kg DM and 68.2%) compared to C0T0 (8.86 ME/kg DM and 65.4%). Concluding, under increased temperature and enhanced CO2, both functional traits and certain nutrients and their fractions appear to change in orchard grass.

Lolium multiflorum, one of the most important temperate forage grasses in the world, is used in integrated crop-livestock systems and as a cover crop. However, it is also one of the main weeds in winter crops. The continuous use of glyphosate to manage this species has led to the selection of resistant biotypes (LOLMU-R), making it important to prevent the dispersal of these seeds. This study aimed to assess the recovery and germination of LOLMU-R that have passed through the digestive system of cattle. The experiments were carried out in metabolism cages, using a completely randomized design with six replications. The animals were given 12 112 seeds each, which were recovered from their faeces over a period of 6 days. Germination of the recovered seeds was assessed in a germination chamber and compared against a control (no animal passage). After germination, a glyphosate dose-response curve was constructed. The results obtained showed a total recovery of 1109 seeds (9.1%), with maximum recovery 2 days after ingestion, decreasing to almost zero on day 6. Germination declined linearly as a function of recovery time; however, 4 days after ingestion, germination potential was 18%. The dose-response curve proved the resistance of the recovered seeds. Cattle is a dispersal agent for LOLMU-R seeds, with animals requiring 7 days of quarantine before moving from one infested area to another.

The present study was conducted to evaluate the effect of a live culture of Aspergillus oryzae (A; CCT4359) and fibrolytic enzyme (E; Fibrozyme Alltech Inc.) on fibre digestibility by a gas production bioassay and in vitro degradation of maize silage and sugarcane silage. A completely randomized design trial was performed to evaluate: A doses (0, 20, 60 and 100 mg/l), E doses (0, 160, 320 and 480 mg/l) and roughage source (R; maize and sugarcane silage) in a 4 × 4 × 2 factorial arrangement. The inclusion of increasing doses of A and E increased dry matter and neutral detergent fibre in vitro digestibility linearly, but for E this effect occurred only in maize silage. There was a linear increase in the potential for gas production at the highest dose of A only in sugarcane silage, with no effect on lag time (L). Increasing doses of E increased the volume of gases produced linearly, and a trend of linear reduction of L, regardless of the roughage. There was a linear reduction in ammonia-nitrogen concentration in response to increasing doses of A and E, and an increase in acetic acid concentration at the highest dose of A, regardless of roughage. The additives had no synergistic effect on gas production and digestibility, but were efficient in altering the fermentative pattern, demonstrating the potential to increase fibre degradation.

Parabronema skrjabini is one of the most harmful nematodes to camels and is responsible for economic losses in animal husbandry industry. There is an urgent need for in-depth studies of potential vectors of the nematode due to its scant regarding information. As previous studies indicated that flies may be the vectors of P. skrjabini, we captured flies in the main camel-producing areas of Inner Mongolia. After autopsy of the specimens of two species of horn flies, we observed the morphology of the suspected nematode larvae found in them. Internal transcribed spacer ribosomal-DNA gene sequences were considered the best candidate to confirm the species of the larvae found. Our results showed that the homology compared with P. skrjabini was 99.5% in GenBank. Subsequently, we preliminarily identified two species of horn flies through morphological observation and then sequenced the mitochondrial-DNA-gene cytochrome oxidase subunit I obtained from two species of horn flies, with 100 and 99.2% similarity to sequences deposited in GenBank, respectively. Thus, we identified Haematobia titillans and Haematobia irritans and provided evidence for their potential role as vectors of parabronemosis. Our study provides reference for future research on the life history of the nematode and the vectors of parabronemosis.

Digitalisation is an integral part of modern agriculture. Several digital technologies are available for different animal species and form the basis for precision livestock farming. However, there is a lack of clarity as to which digital technologies are currently used in agricultural practice. Thus, this work aims to present for the first time the status quo in Swiss livestock farming as an example of a highly developed, small-scale and diverse structured agriculture. In this context, the article focuses on the adoption of electronic sensors and measuring devices, electronic controls and electronic data-processing options and the usage of robotics in ruminant farming, namely, for dairy cattle, dairy goats, suckler cows, beef cattle and meat-sheep. Furthermore, the use of electronic ear tags for pigs and the smartphone usage for barn monitoring on poultry farms was assessed. To better understand the adoption process, farm and farmer’s characteristics associated with the adoption of (1) implemented and (2) new digital technologies in ruminant farming were assessed using regression analyses, which is classified at a 10% adoption hurdle. The results showed clear differences in the adoption rates between different agricultural enterprises, with both types of digital technologies tending to be used the most in dairy farming. Easy-to-use sensors and measuring devices such as those integrated in the milking parlour were more widespread than data processing technologies such as those used for disease detection. The husbandry system further determined the use of digital technologies, with the result that farmers with tie stall barns were less likely to use digital technologies than farmers with loose housing systems. Additional studies of farmers’ determinants and prospects of implementation can help identify barriers in the adoption of digital technologies.

Reducing dietary CP content is an effective approach to reduce animal nitrogen excretion and save protein feed resources. However, it is not clear how reducing dietary CP content affects the nutrient digestion and absorption in the gut of ruminants, therefore it is difficult to accurately determine how much reduction in dietary CP content is appropriate. This study was conducted to investigate the effects of reduced dietary CP content on N balance, intestinal nutrient digestion and absorption, and rumen microbiota in growing goats. To determine N balance, 18 growing wether goats (25.0 ± 0.5 kg) were randomly assigned to one of three diets: 13.0% (control), 11.5% and 10.0% CP. Another 18 growing wether goats (25.0 ± 0.5 kg) were surgically fitted with ruminal, proximate duodenal, and terminal ileal fistulae and were randomly assigned to one of the three diets to investigate intestinal amino acid (AA) absorption and rumen microbiota. The results showed that fecal and urinary N excretion of goats fed diets containing 11.5% and 10.0% CP were lower than those of goats fed the control diet (P < 0.05). When compared with goats fed the control diet, N retention was decreased and apparent N digestibility in the entire gastrointestinal tract was increased in goats fed the 10% CP diet (P < 0.05). When compared with goats fed the control diet, the duodenal flow of lysine, tryptophan and phenylalanine was decreased in goats fed the 11.5% CP diet (P < 0.05) and that of lysine, methionine, tryptophan, phenylalanine, leucine, glutamic acid, tyrosine, essential AAs (EAAs) and total AAs (TAAs) was decreased in goats fed the 10.0% CP diet (P < 0.05). When compared with goats fed the control diet, the apparent absorption of TAAs in the small intestine was increased in goats fed the 11.5% CP diet (P < 0.05) and that of isoleucine, serine, cysteine, EAAs, non-essential AAs, and TAAs in the small intestine was increased in goats fed the 10.0% CP diet (P < 0.05). When compared with goats fed the control diet, the relative richness of Bacteroidetes and Fibrobacteres was increased and that of Proteobacteria and Synergistetes was decreased in the rumen of goats fed a diet with 10.0% CP. In conclusion, reducing dietary CP content reduced N excretion and increased nutrient utilization by improving rumen fermentation, enhancing nutrient digestion and absorption, and altering rumen microbiota in growing goats.

Technological and mathematical advances have provided opportunities to investigate new approaches for the holistic quantification of complex biological systems. One objective of these approaches, including the multi-inverse deterministic approach proposed in this paper, is to deepen the understanding of biological systems through the structural development of a useful, best-fitted inverse mechanistic model. The objective of the present work was to evaluate the capacity of a deterministic approach, that is, the multi-inverse approach (MIA), to yield meaningful quantitative nutritional information. To this end, a case study addressing the effect of diet composition on sheep weight was performed using data from a previous experiment on saccharina (a sugarcane byproduct), and an inverse deterministic model (named Paracoa) was developed. The MIA successfully revealed an increase in the final weight of sheep with an increase in the percentage of corn in the diet. Although the soluble fraction also increased with increasing corn percentage, the effective nonsoluble degradation increased fourfold, indicating that the increased weight gain resulted from the nonsoluble substrate. A profile likelihood analysis showed that the potential best-fitted model had identifiable parameters, and that the parameter relationships were affected by the type of data, number of parameters and model structure. It is necessary to apply the MIA to larger and/or more complex datasets to obtain a clearer understanding of its potential.

Meat and milk from ruminants provide an important source of protein and other nutrients for human consumption. Although ruminants have a unique advantage of being able to consume forages and graze lands not suitable for arable cropping, 2% to 12% of the gross energy consumed is converted to enteric CH4 during ruminal digestion, which contributes approximately 6% of global anthropogenic greenhouse gas emissions. Thus, ruminant producers need to find cost-effective ways to reduce emissions while meeting consumer demand for food. This paper provides a critical review of the substantial amount of ruminant CH4-related research published in past decades, highlighting hydrogen flow in the rumen, the microbiome associated with methanogenesis, current and future prospects for CH4 mitigation and insights into future challenges for science, governments, farmers and associated industries. Methane emission intensity, measured as emissions per unit of meat and milk, has continuously declined over the past decades due to improvements in production efficiency and animal performance, and this trend is expected to continue. However, continued decline in emission intensity will likely be insufficient to offset the rising emissions from increasing demand for animal protein. Thus, decreases in both emission intensity (g CH4/animal product) and absolute emissions (g CH4/day) are needed if the ruminant industries continue to grow. Providing producers with cost-effective options for decreasing CH4 emissions is therefore imperative, yet few cost-effective approaches are currently available. Future abatement may be achieved through animal genetics, vaccine development, early life programming, diet formulation, use of alternative hydrogen sinks, chemical inhibitors and fermentation modifiers. Individually, these strategies are expected to have moderate effects (<20% decrease), with the exception of the experimental inhibitor 3-nitrooxypropanol for which decreases in CH4 have consistently been greater (20% to 40% decrease). Therefore, it will be necessary to combine strategies to attain the sizable reduction in CH4 needed, but further research is required to determine whether combining anti-methanogenic strategies will have consistent additive effects. It is also not clear whether a decrease in CH4 production leads to consistent improved animal performance, information that will be necessary for adoption by producers. Major constraints for decreasing global enteric CH4 emissions from ruminants are continued expansion of the industry, the cost of mitigation, the difficulty of applying mitigation strategies to grazing ruminants, the inconsistent effects on animal performance and the paucity of information on animal health, reproduction, product quality, cost-benefit, safety and consumer acceptance.

Rumen sensors provide specific information to help understand rumen functioning in relation to health disorders and to assist in decision-making for farm management. This review focuses on the use of rumen sensors to measure ruminal pH and discusses variation in pH in both time and location, pH-associated disorders and data analysis methods to summarize and interpret rumen pH data. Discussion on the use of rumen sensors to measure redox potential as an indication of the fermentation processes is also included. Acids may accumulate and reduce ruminal pH if acid removal from the rumen and rumen buffering cannot keep pace with their production. The complexity of the factors involved, combined with the interactions between the rumen and the host that ultimately determine ruminal pH, results in large variation among animals in their pH response to dietary or other changes. Although ruminal pH and pH dynamics only partially explain the typical symptoms of acidosis, it remains a main indicator and may assist to optimize rumen function. Rumen pH sensors allow continuous monitoring of pH and of diurnal variation in pH in individual animals. Substantial drift of non-retrievable rumen pH sensors, and the difficulty to calibrate these sensors, limits their application. Significant within-day variation in ruminal pH is frequently observed, and large distinct differences in pH between locations in the rumen occur. The magnitude of pH differences between locations appears to be diet dependent. Universal application of fixed conversion factors to correct for absolute pH differences between locations should be avoided. Rumen sensors provide high-resolution kinetics of pH and a vast amount of data. Commonly reported pH characteristics include mean and minimum pH, but these do not properly reflect severity of pH depression. The area under the pH × time curve integrates both duration and extent of pH depression. The use of this characteristic, as well as summarizing parameters obtained from fitting equations to cumulative pH data, is recommended to identify pH variation in relation to acidosis. Some rumen sensors can also measure the redox potential. This measurement helps to understand rumen functioning, as the redox potential of rumen fluid directly reflects the microbial intracellular redox balance status and impacts fermentative activity of rumen microorganisms. Taken together, proper assessment and interpretation of data generated by rumen sensors requires consideration of their limitations under various conditions.

This review aims to explain the influence and characterization of the microbiome in the ruminant digestive system by presenting the knowledge collected so far. The knowledge presented in this work is focused on the main factors affecting the microbiome and the main dependencies that have been found in it so far. The microbiome in the rumen is the first to come into contact with the biomass of the forage and its main purpose is to decompose into smaller particles or compounds. With the gradual increase in knowledge about the microbiome, there is a chance to manipulate it so that the animal continues to live in a symbiotic relationship with it, while reducing greenhouse gas emissions to the environment as well as increasing feed efficiency. Therefore, understanding the influence of the ruminant microbiome is the main step to achieve such results. However, learning the relationship between microorganisms is only at an early stage, because research focuses mainly on taxonomy. Future research should focus on interactions in the ecosystem which is the microbiome, on explaining individual functions and on influence of environmental factors.

Eosinophils are important immune cells that have been implicated in resistance to gastrointestinal nematode (GIN) infections in both naturally and experimentally infected sheep. Proteins of particular importance appear to be IgA-Fc alpha receptor (FcαRI), C-C chemokine receptor type 3 (CCR3), proteoglycan 3 (PRG3, major basic protein 2) and EPX (eosinophil peroxidase). We used known human nucleotide sequences to search the ruminant genomes, followed by translation to protein and sequence alignments to visualize differences between sequences and species. Where a sequence was retrieved for cow, but not for sheep and goat, this was used additionally as a reference sequence. In this review, we show that eosinophil function varies among host species. Consequently, investigations into the mechanisms of ruminant immune responses to GIN should be conducted using the natural host. Specifically, we address differences in protein sequence and structure for eosinophil proteins.