Improve animal health to reduce livestock emissions: quantifying an open goal.

Greenhouse gas (GHG) emissions from livestock production must be urgently tackled to substantially reduce their contribution to global warming. Simply reducing livestock numbers to this end risks impacting negatively on food security, rural livelihoods and climate change adaptation. We argue that significant mitigation of livestock emissions can be delivered immediately by improving animal health and hence production efficiency, but this route is not prioritized because its benefits, although intuitive, are poorly quantified. Rigorous methodology must be developed to estimate emissions from animal disease and hence achievable benefits from improved health through interventions. If, as expected, climate change is to affect the distribution and severity of health conditions, such quantification becomes of even greater importance. We have therefore developed a framework and identified data sources for robust quantification of the relationship between animal health and greenhouse gas emissions, which could be applied to drive and account for positive action. This will not only help mitigate climate change but at the same time promote cost-effective food production and enhanced animal welfare, a rare win-win in the search for a sustainable planetary future.

Phase-specific outcmes of arginine or branched-chain amino acids supplementation in low crude protein diets on performance, nutrient digestibility, and expression of tissue protein synthesis and degradation in broiler chickens infected with mixed Eimeria spp.

A 35-d study investigated the impact of dietary supplementation with Arginine (Arg) or branched-chain amino acids (BCAA) of broilers receiving low-protein diets whilst infected with mixed Eimeria species. All birds were given the same starter (d0-10) and finisher (d28-35) diets. The 4 grower diets used were a positive control (PC) with adequate protein (18.5%), a low protein diet (NC;16.5% CP), or the NC supplemented with Arg or BCAA. Supplemental AA was added at 50% above the recommended levels. The treatments were in a 4 × 2 factorial arrangement, with 4 diets, with or without Eimeria inoculation on d14. Birds and feed were weighed after inoculation in phases: prepatent (d14-17), acute (d18-21), recovery (d22-28), and compensatory (d29-35). Ileal digesta, jejunum, and breast tissue were collected on d21, 28, and 35. There was no diet × Eimeria inoculation on growth performance at any phase. Infected birds weighed less and consumed less feed (P < 0.05) in all phases. In the prepatent and acute phases, birds on the Arg diets had higher weight gain (P < 0.05) and lower FCR, similar to PC, when compared to NC and BCAA-fed ones. Infection reduced AA digestibility on d21 and 28 (Met and Cys). However, birds that received supplemental AA had higher digestibility (P < 0.05) of their respective supplemented AA on d 21 only. Infected birds had lower (P < 0.05) BO + AT and higher PEPT1 expression on d21. There was a diet × Eimeria interaction (P = 0.004) on gene expression at d28; 4EBP1 genes were significantly downwardly expressed (P < 0.05) in birds fed Arg diet, irrespective of infection. Infected birds exhibited an upward expression (P < 0.05) of Eef2 on d21 and d28 but experienced a downward expression on d35. Supplemental Arg and BCAA had variable effects on growth performance, apparent ileal AA digestibility, and genes of protein synthesis and degradation, but the effect of Arg on promoting weight gain, irrespective of the Eimeria challenge, was more consistent.

Supplementing low protein diets with methionine or threonine during mixed Eimeria challenge.

We investigated the effects of supplementing low protein diets with methionine (Met) or threonine (Thr) during a mixed Eimeria (consisting of E. acervulina, E. maxima and E. tenella) challenge in broilers. All birds were fed the same starter diet (d1-9) and finisher diet (d28-35) which met Cobb 500 nutrient specifications. Birds were allocated to 1 of 4 dietary treatments from d9 to 28: a standard protein diet (19% CP); a low protein diet (16% CP); or the low protein diet supplemented with Met or Thr at 50% above recommendations. On d14, half of the birds were challenged, and half of the birds were unchallenged. From d14 to 28, feed intake was recorded daily and BW every 3 or 4 d. Oocyst excretion was measured daily from d18 to 27. On d21 and 28, 3 birds per pen were euthanized to assess nutrient digestibility, cytokine expression and intestinal histology. During the acute stage of the challenge, challenged birds reduced ADFI and ADG (P < 0.05). In the pre-patent and recovery stages, birds given the 16% CP diets increased ADFI (P < 0.05), meanwhile there were no differences in ADG in these stages (P > 0.05). Nutrient digestibility was reduced in challenged birds in the acute stage (P < 0.05) but tended to be greater than in unchallenged birds during the recovery stage. There was no significant effect of diet on oocyst excretion or intestinal histology (P > 0.05). Interactions were observed between diet and challenge on IL-10 and IL-21 expression in the cecal tonsils during the acute stage of the challenge (P < 0.05), due to reduced IL-10 expression in challenged Thr birds and greater IL-21 expression in challenged Met birds. Supplementation with Thr or Met had limited effects on the outcomes of a mixed Eimeria challenge but provides benefits to the host by enhancing their immune response.

Hotspots and bottlenecks for the enhancement of the environmental sustainability of pig systems, with emphasis on European pig systems.

Although pig systems start from a favourable baseline of environmental impact compared to other livestock systems, there is still scope to reduce their emissions and further mitigate associated impacts, especially in relation to nitrogen and phosphorous emissions. Key environmental impact hotspots of pig production systems are activities associated with feed production and manure management, as well as direct emissions (such as methane) from the animals and energy use. A major contributor to the environmental impacts associated with pig feed is the inclusion of soya in pig diets, especially since European pig systems rely heavily on soya imported from areas of the globe where crop production is associated with significant impacts of land use change, deforestation, carbon emissions, and loss of biodiversity. The "finishing" pig production stage contributes most to these environmental impacts, due to the amount of feed consumed, the efficiency with which feed is utilised, and the amount of manure produced during this stage. By definition therefore, any substantial improvements pig system environmental impact would arise from changes in feed production and manure management. In this paper, we consider potential solutions towards system environmental sustainability at these pig system components, as well as the bottlenecks that inhibit their effective implementation at the desired pace and magnitude. Examples include the quest for alternative protein sources to soya, the limits (perceived or real) to the genetic improvement of pigs, and the implementation of alternative manure management strategies, such as production of biogas through anaerobic digestion. The review identifies and discusses areas that future efforts can focus on, to further advance understanding around the potential sustainability benefits of modifications at various pig system components, and key sustainability trade-offs across the environment-economy-society pillars associated with synergistic and antagonistic effects when joint implementation of multiple solutions is considered. In this way, the review opens a discussion to facilitate the development of holistic decision support tools for pig farm management that account for interactions between the "feed * animal * manure" system components and trade-offs between sustainability priorities (e.g., environmental vs economic performance of pig system; welfare improvements vs environmental impacts).

The effects of arginine and branched-chain amino acid supplementation to reduced-protein diet on intestinal health, cecal short-chain fatty acid profiles, and immune response in broiler chickens challenged with Eimeria spp.

We investigated the effects of supplementing arginine (Arg) and branched-chain amino acids (BCAA) in broilers fed reduced-protein diets and challenged with Eimeria spp. All birds were fed the same starter diet meeting Cobb 500 nutrient specifications from d 1 to 9. Four grower diets: positive control (PC) with 20.0% crude protein (CP); reduced-protein negative control (NC) with 17.5% CP; or NC supplemented with Arg or BCAA at 50% above recommendations (ARG or BCAA) were fed to the birds from d 9 to 28. Birds were allocated in a 2 × 4 factorial arrangement (4 diets, each with or without challenge), with 8 replicates per treatment. On d 14, the challenge groups were orally gavaged with mixed Eimeria spp. Intestinal permeability was higher (P < 0.05) in NC than PC, whereas the permeability of ARG and BCAA groups did not differ significantly from PC. On d 28, a significant interaction (P < 0.01) was observed in CD8+: CD4+ ratios in cecal tonsils (CT), Eimeria challenge increased the ratios in all groups except for the ARG group. On d 21, a significant interaction was found for CD4+CD25+ percentages in CT (P < 0.01) that Eimeria challenge increased the percentages only in PC and NC groups. On d 21 and 28, significant interactions (P < 0.01) were found for macrophage nitric oxide (NO) production. In nonchallenged birds, NO was higher in the ARG group than other groups, but in challenged birds, NO was higher in both ARG and BCAA groups. On d 21, a significant interaction was found for bile anticoccidial IgA concentrations (P < 0.05) that Eimeria challenge increased IgA only in NC and ARG groups. The results suggest that a reduced-protein diet exacerbates the impact of the Eimeria challenge on intestinal integrity, but this could be mitigated by Arg and BCAA supplementations. Arginine and BCAA supplementations in reduced-protein diets could be beneficial for broilers against Eimeria infection by enhancing the immune responses. The beneficial effects of Arg supplementation tended to be more pronounced compared to BCAA supplementation.

Deep learning pose estimation for multi-cattle lameness detection.

The objective of this study was to develop a fully automated multiple-cow real-time lameness detection system using a deep learning approach for cattle detection and pose estimation that could be deployed across dairy farms. Utilising computer vision and deep learning, the system can analyse simultaneously both the posture and gait of each cow within a camera field of view to a very high degree of accuracy (94-100%). Twenty-five video sequences containing 250 cows in varying degrees of lameness were recorded and independently scored by three accredited Agriculture and Horticulture Development Board (AHDB) mobility scorers using the AHDB dairy mobility scoring system to provide ground truth lameness data. These observers showed significant inter-observer reliability. Video sequences were broken down into their constituent frames and with a further 500 images downloaded from google, annotated with 15 anatomical points for each animal. A modified Mask-RCNN estimated the pose of each cow to output 5 key-points to determine back arching and 2 key-points to determine head position. Using the SORT (simple, online, and real-time tracking) algorithm, cows were tracked as they move through frames of the video sequence (i.e., in moving animals). All the features were combined using the CatBoost gradient boosting algorithm with accuracy being determined using threefold cross-validation including recursive feature elimination. Precision was assessed using Cohen's kappa coefficient and assessments of precision and recall. This methodology was applied to cows with varying degrees of lameness (according to accredited scoring, n = 3) and demonstrated that some characteristics directly associated with lameness could be monitored simultaneously. By combining the algorithm results over time, more robust evaluation of individual cow lameness was obtained. The model showed high performance for predicting and matching the ground truth lameness data with the outputs of the algorithm. Overall, threefold lameness detection accuracy of 100% and a lameness severity classification accuracy of 94% respectively was achieved with a high degree of precision (Cohen's kappa = 0.8782, precision = 0.8650 and recall = 0.9209).

Tracking gastrointestinal nematode risk on cattle farms through pasture contamination mapping.

Gastrointestinal nematode (GIN) parasites in grazing cattle are a major cause of production loss and their control is increasingly difficult due to anthelmintic resistance and climate change. Rotational grazing can support control and decrease reliance on chemical intervention, but is often complex due to the need to track grazing periods and infection levels, and the effect of weather on larval availability. In this paper, a simulation model was developed to predict the availability of infective larvae of the bovine GIN, Ostertagia ostertagi, at the level of individual pastures. The model was applied within a complex rotational grazing system and successfully reproduced observed variation in larval density between fields and over time. Four groups of cattle in their second grazing season (n = 44) were followed throughout the temperate grazing season with regular assessment of GIN faecal egg counts, which were dominated by O. ostertagi, animal weight and recording of field rotations. Each group of cattle was rotationally grazed on six group-specific fields throughout the 2019 grazing season. Maps and calendars were produced to illustrate the change in pasture infectivity (density of L3 on herbage) across the 24 separate grazing fields. Simulations predicted differences in pasture contamination levels in relation to the timing of grazing and the return period. A proportion of L3 was predicted to persist on herbage over winter, declining to similar intensities across fields before the start of the following grazing season, irrespective of contamination levels in the previous year. Model predictions showed good agreement with pasture larval counts. The model also simulated differences in seasonal pasture infectivity under rotational grazing in systems that differed in temperature and rainfall profiles. Further application could support individual farm decisions on evasive grazing and refugia management, and improved regional evaluation of optimal grazing strategies for parasite control. The integration of weather and livestock movement is inherent to the model, and facilitates consideration of climate change adaptation through improved disease control.

Economic feasibility of interventions targeted at decreasing piglet perinatal and pre-weaning mortality across European countries.

BACKGROUND: Piglet perinatal and pre-weaning mortality is a welfare problem causing economic losses in pig production. In this study, the effects of housing and management interventions on the economic result of sow enterprises representing six European countries (Belgium, Denmark, Finland, Germany, The Netherlands and Spain) were tested. Interventions concerned: (1) installing mechanical ventilation, (2) re-designing of the gestation unit, (3) drying and warming newborn piglets, (4) providing enrichment for gestating sows, including high-fiber dietary supplementation and point-source objects, and (5) music provision and backscratching of sows in the farrowing unit. A bio-economic model was used to determine the effects of interventions on economic outcomes during the nursery phase and to calculate a maximum cost of 1%-point reduction in perinatal and pre-weaning mortality, irrespective of the intervention type. Biological parameters were set according to previous observational and experimental studies. Interventions 1-4 were expected to decrease perinatal mortality, defined as stillbirths and deaths occurring within the first 48 h of postnatal life. Intervention 5 was expected to decrease pre-weaning mortality. Interventions increased fixed (1-3) and variable costs (3-5). We hypothesized that housing and management interventions would have a positive economic effect. RESULTS: Piglet mortality can be decreased in various ways. Interventions concerning ventilation and re-designing of the gestation unit (1 and 2) were the most beneficial in countries with low housing costs and high perinatal mortality. Drying and warming newborn piglets (3) resulted in varying economic results, with the highest increase in profits obtained in a country with low labor costs and high litter size. Interventions providing sows with enrichment and human-animal interaction (4 and 5) were effective across varying conditions. Regardless of intervention type, policies aiming at 1%-point reduction in perinatal and pre-weaning mortality could cost from €0.2 to €0.5 (average €0.4) and from €0.4 to €0.5 (average €0.5) per piglet, respectively, depending on productions conditions. CONCLUSIONS: To decrease piglet mortality, farmers should consider low input interventions, such as those targeting appropriate behavior. Our results suggest that providing enrichment or increasing human-animal interaction pays off and brings positive economic result even when piglet mortality is marginally reduced.

Quantifying the effect of coccidiosis on broiler performance and infection outcomes in the presence and absence of control methods.

A systematic review and meta-analysis was conducted to investigate the role of Eimeria species, dose and inoculation time, on performance and infection outcomes of different broiler strains infected for different study durations. The meta-analysis addressed E. acervulina, E. maxima, E. tenella, and mixed species infections, and involved data from 72 peer-reviewed articles, corresponding to 521 treatments performed on 20,756 broilers. A secondary objective was to investigate the effects of synthetic anticoccidials, ionophores, and vaccination against Eimeria on the above outcomes. Performance during infection was scaled (%) to that of the uninfected birds. Infection reduced scaled ADFI and ADG (P < 0.001) and increased feed conversion ratio (FCR; P < 0.05); there was a significant interaction between dose and species on scaled ADFI and ADG, suggesting that different species affected these variables to different extents (P < 0.001). There was a tendency for an interaction between dose and broiler strain on scaled ADFI (P = 0.079), and a significant interaction between these variables on scaled ADG (P < 0.01). A tendency for an interaction between oocyst dose and Eimeria species (P = 0.067) on maximum number of oocysts excreted was observed. Lesion scores were significantly affected by dose, species, and their interaction (P < 0.05), the latter caused by an increase in the lesion scores during E. maxima and E. tenella infections. Control methods significantly affected scaled ADG and FCR (P < 0.05) and there was an interaction between dose and control methods on ADFI (P < 0.001). Synthetic anticoccidial use improved scaled ADG (P < 0.01), whereas ionophores improved FCR compared with untreated birds (P < 0.01). An interaction between dose and control method on scaled ADFI was caused by the higher ADFI of vaccinated compared to untreated birds, as dose increased. There was a significant effect of control methods on lesion scores (P < 0.01). All findings advance our understanding of the factors that influence the impact of coccidiosis and its controls in broilers.

Toward the automated detection of behavioral changes associated with the post-weaning transition in pigs.

We modified an automated method capable of quantifying behaviors which we then applied to the changes associated with the post-weaning transition in pigs. The method is data-driven and depends solely on video-captured image data without relying on sensors or additional pig markings. It was applied to video images generated from an experiment during which post-weaned piglets were subjected to treatments either containing or not containing in-feed antimicrobials (ZnO or antibiotics). These treatments were expected to affect piglet performance and health in the short-term by minimizing the risk from post-weaning enteric disorders, such as diarrhea. The method quantified total group feeding and drinking behaviors as well as posture (i.e., standing and non-standing) during the first week post-weaning, when the risk of post-weaning diarrhea is at its highest, by learning from the variations within each behavior using data manually annotated by a behavioral scientist. Automatically quantified changes in behavior were consistent with the effects of the absence of antimicrobials on pig performance and health, and manifested as reduced feed efficiency and looser feces. In these piglets both drinking and standing behaviors were increased during the first 6 days post-weaning. The correlation between fecal consistency and drinking behavior 6 days post weaning was relatively high, suggesting that these behaviors may have a diagnostic value. The presence or absence of in-feed antimicrobials had no effect on feeding behavior, which, however, increased over time. The approach developed here is capable of automatically monitoring several different behaviors of a group of pigs at the same time, and potentially this may be where its value as a diagnostic tool may lie.

Starving for nutrients: anorexia during infection with parasites in broilers is affected by diet composition.

In 2 experiments, we investigated whether diet composition plays a role in pathogen-induced anorexia, the voluntary reduction in ADFI during infection in broilers. We hypothesized that either energy or CP dietary content could influence the extent of anorexia in Ross 308 broilers and infection outcomes with Eimeria maxima. From d 13 of age, half of the birds were infected, and half were uninfected. ADFI was measured daily, and BW every 3 d until d 29. Oocyst excretion was measured daily from d 17 to 23. The impact of parasitism on the small intestine was assessed on d 19 and 25. In Experiment 1, 336 birds were offered diets progressively diluted with lignocellulose, starting from a diet with 3,105 (kcal ME/kg) and 20% CP. There was a significant interaction between infection and diet on ADFI during the acute stage of infection (d 17 to 21): for control birds diet dilution decreased ADFI and consequently reduced energy and CP intake. For infected birds, diet dilution increased ADFI, leading to the same energy and CP intake across diets. Oocyst excretion and villi length to crypt depth ratio (VCR) were constant across infected treatments. In Experiment 2, 432 birds were offered diets with constant ME (3,105 kcal/kg), but different CP contents (24, 20, 26, and 12%). Infection significantly reduced ADFI. Although there was no interaction between infection and diet on ADFI, there was an interaction on CP intake during the acute stage of infection. Infected birds on the 20% CP diet achieved the same CP intake as uninfected birds. There were no differences in the VCR and ADG of the infected birds on 24, 20 and 16% CP treatments, but birds on 12% had the lowest ADG and excreted more oocysts. We suggest that during infection, birds target a nutrient resource intake, which appears to be beneficial for infection outcomes, while at the same time they avoid excess protein intake. We conclude that different mechanisms regulate ADFI in infected and uninfected birds.

Towards the prediction of feed intake capacity of modern broilers on bulky feeds.

The use of alternative, often bulky ingredients is becoming widespread in poultry diets as the industry seeks to reduce its economic and environmental costs. Consequently, there is an increased need to accurately predict the performance of birds given such diets and identify their maximum capacity for bulk. We offered diets diluted with a range of bulky ingredients to male Ross 308 broilers to assess their capacity for bulk and identify a bulk characteristic responsible for limiting intake. Four hundred ninety-five day-old broilers allocated into 45 pens, were offered a common starter diet until day (d) 7, and 1 of 9 grower diets from d 8 to 29 (Period 1). Each of the grower diets was diluted with either 30 or 60% of oat hulls (OH), wheat bran (WB), or grass meal (GM), or a mixture of 2 bulky ingredients at an inclusion level of 30% each (OHWB, OHGM, WBGM). From d 29 to 43 (Period 2), all birds were offered the bulkiest diet (GM60). A number of bulk characteristics were measured on the diets. Feed intake was measured daily, and birds were dissected on d 29 and 43 for organ and carcass measurements. During d 8 to 14 diet water-holding capacity (WHC) was more consistent in predicting feed intake when scaled per unit of body weight than any other bulk characteristic. However, this was no longer the case during d 15 to 28. In Period 2, the response and adaptation to the bulkiest diet was determined by previous experience to bulk. Birds offered a bulkier diet during Period 1, were better able to adapt the size of their digestive organs and increase scaled feed intake, such that there were no differences between these birds and those offered the GM60; the converse was the case for birds on the least bulky diets. We conclude that WHC is able to predict maximum intake on bulky diets in unadapted birds. Adaptation to bulky diets can be very fast, so that their high bulk content no longer limits feed intake and performance.

A Novel Estimation of Unobserved Pig Growth Traits for the Purposes of Precision Feeding Methods.

Recent technological advances make it possible to deliver feeding strategies that can be tailored to the needs of individual pigs in order to optimise the allocation of nutrient resources and contribute toward reducing excess nutrient excretion. However, these efforts are currently hampered by the challenges associated with: (1) estimation of unobserved traits from the available data on bodyweight and feed consumption; and (2) characterisation of the distributions and correlations of these unobserved traits to generate accurate estimates of individual level variation among pigs. Here, alternative quantitative approaches to these challenges, based on the principles of inverse modelling and separately inferring individual level distributions within a Bayesian context were developed and incorporated in a proposed precision feeding modelling framework. The objectives were to: (i) determine the average and distribution of individual traits characterising growth potential and body composition in an empirical population of growing-finishing barrows and gilts; (ii) simulate the growth and excretion of nitrogen and phosphorus of the average pig offered either a commercial two-phase feeding plan, or a precision feeding plan with daily adjustments; and (iii) simulate the growth and excretion of nitrogen and phosphorus across the pig population under two scenarios: a two-phase feeding plan formulated to meet the nutrient requirements of the average pig or a precision feeding plan with daily adjustments for each and every animal in the population. The distributions of mature bodyweight and ratio of lipid to protein weights at maturity had median (IQR) values of 203 (47.8) kg and 2.23 (0.814) kg/kg, respectively; these estimates were obtained without any prior assumptions concerning correlations between the traits. Overall, it was found that a proposed precision feeding strategy could result in considerable reductions in excretion of nitrogen and phosphorus (average pig: 8.07 and 9.17% reduction, respectively; heterogenous pig population: 22.5 and 22.9% reduction, respectively) during the growing-finishing period from 35 to 120 kg bodyweight. This precision feeding modelling framework is anticipated to be a starting point toward more accurate estimation of individual level nutrient requirements, with the general aim of improving the economic and environmental sustainability of future pig production systems.

What are the limits to feed intake of broilers on bulky feeds?

The view that genetic selection for carcass yield has limited the size of the gastrointestinal tract (GIT) of modern broilers has sparked concerns that their capacity to cope with energy dilution or bulk is also limited. We investigated the capacity of male Ross 308 broilers to deal with increasing levels of bulk and aimed to identify a feed bulk dimension responsible for limiting feed intake (FI). About 528 day-old broilers were allocated to 48 pens and offered a common starter feed until day 8, and 1 of 7 feeds from day 8 to 36 of age: a basal control (B), which was diluted to 3 levels (15, 30, or 45%) with either oat hulls (OH) or sugar beet pulp (SBP). Feed intake was measured daily and birds were dissected for GIT measurements at day 15, 22, and 36. Feed intake increased in birds offered OH15 (135 g/d), OH30 (140 g/d), and SBP15 (138 g/d) compared with birds offered the B feed (106 g/d; SEM 2.4). By increasing FI, birds were able to compensate for the lower energy content of their feeds. The greatest increase in FI was seen on OH30: its energy content (2,273 kcal/kg) was 26% lower than the B feed (3,081 kcal/kg). There was evidence of adaptation on the bulky feeds, as during the last week only birds on SBP45 were limited in FI and performance. The relative weights of the GIT were greater in the SBP than OH series, suggesting that the former needed to accommodate a higher bulk intake. For the OH series the increase in the relative GIT weights was confined to the gizzard and small intestine; whereas for the SBP series, the increase was extended to proventriculus and large intestine. Because only SBP45 was limiting FI, we were unable to identify a bulk dimension to be used to predict FI. Our data reject the suggestion that modern broilers have a reduced ability to cope with reductions in feed energy content.

Financial Analysis of Herd Status and Vaccination Practices for Porcine Reproductive and Respiratory Syndrome Virus, Swine Influenza Virus, and Mycoplasma hyopneumoniae in Farrow-to-Finish Pig Farms Using a Bio-Economic Simulation Model.

This study aimed (1) to quantify the effects of positive status and vaccination practices for porcine reproductive and respiratory syndrome virus (PRRSv), swine influenza virus (SIV) and Mycoplasma hyopneumoniae (MHYO) on the profitability of farrow-to-finish pig farms and (2) to examine the financial impact of vaccination status in PRRSv and SIV positive farms. Data from 56 Irish farrow-to-finish pig farms were used for this study. Production effects associated with herd status for the three pathogens were incorporated into the Teagasc Pig Production Model (TPPM), a bio-economic stochastic simulation model for farrow-to-finish pig farms. In the analysis, farms negative (-) for either PRRSv, SIV or MHYO were assumed as baseline when presenting results for farms positive (+) for each pathogen. While all MHYO(+) farms used vaccination against the pathogen, not all PRRSv(+) or SIV(+) farms vaccinated against the disease. For all scenarios, a 728-sow farrow-to-finish farm with weekly farrowing batches was simulated. Financial risk analysis was conducted by Monte Carlo simulation within the TPPM using the Microsoft Excel add-in @Risk. Mortality rates, feedstuff costs and price per kg of meat produced were included as input stochastic variables and annual net profit was set as stochastic output variable. Positive farms sold fewer pigs and produced less kg of meat than negative farms and had increased feed usage during the weaner and finisher stages. Variable costs increased in positive farms due to increased feed costs, more dead animals for disposal and healthcare costs. Annual mean profit was lower by 24% in vaccinated PRRSv(+), 14.6% in unvaccinated PRRSv(+), 36.7% in vaccinating SIV(+), 12.8% in unvaccinated SIV(+), and 41% in MHYO(+) farms. Negative farms were first order stochastically dominant over positive farms, indicating that for a given level of profit, the financial risk is lower by avoiding respiratory pathogens. Similarly, unvaccinated farms were second order stochastically dominant over vaccinating farms suggesting that farms that do not vaccinate are less affected by the disease. Results from this study provide further evidence to encourage farmers to undertake improved disease control measures and/or to implement eradication programs.

Environment-, health-, performance- and welfare-related parameters in pig barns with natural and mechanical ventilation.

A multifactorial approach using environmental, performance, health and welfare parameters was used to investigate the numerous associations of ventilation throughout three consecutive fattening batches (08/2015 to 12/2016) in a farrow-to-finish commercial pig farm in Belgium. Two fattening pig units were used, unit A (1256 pigs) with mechanical ventilation and unit B (1264 pigs) with natural ventilation. Animal genetics, nutrition, stocking density and health management were the same for both units. Key environmental indicators were monitored in real-time (temperature, humidity, CO2 and NH3) and the daily prevalence of respiratory disease cases was recorded to monitor the temporal expression of disease over time within a farm environment. The welfare status of the animals was assessed twice per production round (batch) with a simplified version of the Welfare quality® protocol. Serological tests for the most prevalent respiratory infectious agents (Mycoplasma hyopneumonniae, swine influenza virus (subtypes H1N1, H1N2 and H3N2), Actinobacillus pleuropneumoniae serotypes 1-2-9-11 and porcine circovirus type 2) were performed during the first, second and final third of each fattening period. Finally, key performance parameters were calculated (average daily growth, feed conversion ratio) and upon slaughter lungs from pigs from unit A (n: 782) and from unit B (n: 544) were assessed for the presence of lung lesions, pleurisy and fissures. To identify the associations of ventilation on the aforementioned parameters, statistical models were run that also included other factors (when applicable) namely production batch, season, age and sampling. Overall, the use of natural ventilation was associated with a less optimal environment with regards to thermal comfort (p < 0.001), CO2 (p < 0.001) and NH3 (p < 0.001). A higher daily prevalence of respiratory disease cases was seen in the naturally-ventilated unit (p < 0.001). Concerning the sero-prevalence of the infectious agents tested, the odds to have a positive H1N1 sample were 3.17 higher in the naturally-ventilated unit (p = 0.003). From the visual assessment of the lungs no statistically significant associations were seen between ventilation type and the presence of lesions, fissures or pleuritis. Yet, the lung lesion score was expected to be lower in the naturally-ventilated unit (p = 0.010). Regarding performance parameters, feed conversion ratio and average daily gain were overall better in the mechanically-ventilated unit (descriptive results). Finally, a better welfare score was seen in the mechanically-ventilated unit in all three production batches (descriptive results). In conclusion, the mechanically-ventilated farm was associated with better environmental conditions for the fattening pigs. Yet, further research is needed to reach definite causal claims.

Automated recognition of postures and drinking behaviour for the detection of compromised health in pigs.

Changes in pig behaviours are a useful aid in detecting early signs of compromised health and welfare. In commercial settings, automatic detection of pig behaviours through visual imaging remains a challenge due to farm demanding conditions, e.g., occlusion of one pig from another. Here, two deep learning-based detector methods were developed to identify pig postures and drinking behaviours of group-housed pigs. We first tested the system ability to detect changes in these measures at group-level during routine management. We then demonstrated the ability of our automated methods to identify behaviours of individual animals with a mean average precision of [Formula: see text], under a variety of settings. When the pig feeding regime was disrupted, we automatically detected the expected deviations from the daily feeding routine in standing, lateral lying and drinking behaviours. These experiments demonstrate that the method is capable of robustly and accurately monitoring individual pig behaviours under commercial conditions, without the need for additional sensors or individual pig identification, hence providing a scalable technology to improve the health and well-being of farm animals. The method has the potential to transform how livestock are monitored and address issues in livestock farming, such as targeted treatment of individuals with medication.

Risk factors for poor health and performance in European broiler production systems.

BACKGROUND: Conventional broilers are currently one of the most efficient protein converters. Although decades of progress in genetic selection and feed formulation have lead to high standards of efficient broiler production, still a lot of variability is found between farms and between successive flocks. The aim of this study was to investigate risk- and/or protective factors for poor health and performance in conventional broiler-farms in Europe by developing eight multivariable linear mixed models. Three different models were used to investigate mortality (overall, first week, after first week), three models for performance variables (growth, feed conversion, European production index) and two models were related to slaughterhouse data (i.e. dead on arrival and condemnation rate). RESULTS: Several factors related to management and housing were significantly associated with health and performance of broilers. The following factors were associated with increased mortality: floor quality, neonatal septicemia, ventilation type and other professional activities of the farmer. The factors associated with performance were chick sex, coccidiosis infections, necrotic enteritis, dysbacteriosis, light intensity adaptations, ventilation type, comparing daily flock results with previous flock results by farmer, daily check of feed and water system and type of feed. For dead on arrival three risk factors were identified i.e. daily growth, type of light adaptation and type of drinkers system. For condemnation rate seven risk factors were found, i.e. type of drinking system, daily growth, feed withdrawal time, type of ventilation, house size, septicemia after seven days and type of feed. CONCLUSIONS: These results imply that a multifactorial approach is required with adaptations involving both improvements in management, housing, health programs and an increasing level of professionalism of the farmer in order to improve broiler performance and health.

Changes in Faecal Microbiota Profiles Associated With Performance and Birthweight of Piglets.

The gastrointestinal tract microbiota interacts with the host to modulate metabolic phenotype. This interaction could provide insights into why some low birthweight pigs can exhibit compensatory growth whilst others remain stunted. This study aimed to identify microbiota markers associated with birthweight [low birthweight (n = 13) or normal birthweight pigs (n = 13)] and performance ["good" or "poor" average daily gain (ADG) class]. Furthermore, the study determined whether the taxonomic markers were longitudinal, or time point specific in their ability to identify low birthweight pigs who could exhibit compensatory growth. Faecal samples were collected and liveweight recorded at 10 different time points from birth to 56 days of age. No consistent associations between birthweight, performance and gut microbiota were found across all time points. However, there was a significant (P < 0.05) effect of birthweight on microbiota richness at 21, 27, 32 and 56 days of age. Significant differences (P < 0.05) in genera abundance according to birthweight and performance were also identified. Low birthweight pigs had a significantly (P < 0.05) lower abundance of Ruminococcaceae UCG-005, but a significantly (P < 0.05) higher abundance of Ruminococcaceae UCG-014 on days 21 and 32, respectively. Piglets classified as having a "good" ADG class had a significantly (P < 0.05) higher abundance of Lactobacillus, unclassified Prevotellaceae and Ruminococcaceae UCG-005 on days 4, 8 and 14, respectively. Furthermore, Ruminococcaceae UCG-005 was significantly more abundant at 14 days of age in normal birthweight pigs with a "good" ADG class compared to those classified as "poor." The results of this study indicate that there are time point-specific differences in the microbiota associated with birthweight and performance, corresponding to the period in which solid feed intake first occurs. Identifying early-life microbiota markers associated with performance emphasises the importance of the neonatal phase when considering intervention strategies aimed at promoting performance.