A Transdisciplinary Approach Supporting the Implementation of a Big Data Project in Livestock Production: An Example From the Swiss Pig Production Industry.

Big Data approaches offer potential benefits for improving animal health, but they have not been broadly implemented in livestock production systems. Privacy issues, the large number of stakeholders, and the competitive environment all make data sharing, and integration a challenge in livestock production systems. The Swiss pig production industry illustrates these and other Big Data issues. It is a highly decentralized and fragmented complex network made up of a large number of small independent actors collecting a large amount of heterogeneous data. Transdisciplinary approaches hold promise for overcoming some of the barriers to implementing Big Data approaches in livestock production systems. The purpose of our paper is to describe the use of a transdisciplinary approach in a Big Data research project in the Swiss pig industry. We provide a brief overview of the research project named "Pig Data," describing the structure of the project, the tools developed for collaboration and knowledge transfer, the data received, and some of the challenges. Our experience provides insight and direction for researchers looking to use similar approaches in livestock production system research.

Variables of initial examination and clinical management associated with survival in small ruminants with obstructive urolithiasis.

BACKGROUND: Obstructive urolithiasis is a common disease associated with a guarded prognosis in small ruminants. HYPOTHESIS/OBJECTIVE: The results of physical examination, laboratory analyses, and clinical management of male small ruminants presented to 2 referral clinics were investigated to identify variables significantly associated with disease outcome, so as to provide better recommendations to animal owners regarding the management of these patients. ANIMALS: Two-hundred ten small ruminants (130 sheep and 80 goats) with confirmed diagnosis of obstructive urolithiasis. METHODS: Clinical findings (including diagnostic imaging) and laboratory results of the 210 animals were reviewed, and relevant information regarding clinical and laboratory variables recorded upon admission and clinical management was retrieved. The association of the different variables with nonsurvival was investigated by univariable and multivariable logistic regression models. RESULTS: Only 39% of all patients considered for treatment and 52% of those undergoing tube cystostomy survived to be released from the clinic. Nonsurvival was strongly associated with a very poor clinical condition upon presentation, obesity, castration, and evidence of uroperitoneum. Among blood variables, abnormal PCV, severely increased serum creatinine concentrations, and increased activity of the creatine kinase were associated with increased risk of nonsurvival. Presence of signs of colic or macroscopic appearance of urine was not significantly associated with outcome. CONCLUSIONS AND CLINICAL IMPORTANCE: The prognosis of obstructive urolithiasis was guarded with survival rates of 39% (overall) to 52% (after tube cystostomy). Intact young males with normal body condition presented early in the course of disease had the best chances of survival.

Cross-sectional study on risk factors for Porcine Reproductive and Respiratory Syndrome virus sow herd instability in German breeding herds.

BACKGROUND: Porcine Reproductive and Respiratory Syndrome virus (PRRSV) stability, besides meeting production targets, is also a requirement for several control options of PRRS in pig breeding farms. This study aimed to investigate the frequency of, and risk factors associated with, PRRSV instability in pig breeding farms in northern Germany. In 120 sow herds, a questionnaire on production and management parameters was filled, and blood samples from 30 suckling pigs from 10 different litters were taken and examined using real-time polymerase chain reaction (PCR). RESULTS: PRRSV was detected in 32 herds (27%), thus classified as PRRSV-unstable. According to multivariable logistic regression analysis, a suckling period ≤ 21 days, a low distance between the cadaver collection site and the actual sow barn, ≥ 2 pig herds in a 1000 m radius, presence of external employees, a time interval between purchase of gilts of ≤ 9 weeks and a 1- or 2-weekly farrowing rhythm were associated with a higher risk of PRRSV instability. CONCLUSIONS: External and internal biosecurity as well as management factors were associated with PRRSV instability, which could be targeted by farmers and veterinarians to help them to achieve PRRSV PCR-negative status and in the control of PRRS.

Brachyspira hyodysenteriae detection in the large intestine of slaughtered pigs.

Detection of subclinical Brachyspira hyodysenteriae infection in pig herds using feces is challenging. However, the ability to detect the pathogen in intestinal samples of slaughtered pigs has not been investigated, to our knowledge. Therefore, we determined the detection of B. hyodysenteriae in the colon, cecum, and rectum from slaughtered pigs. We analyzed the correlation between detection rates and intestinal lesions, ingesta or fecal consistency, and time from sample collection until processing. A total of 400 ingesta-mucosal (colon, cecum) and 200 fecal (rectum) samples from 200 pigs originating from 20 different herds were bacteriologically examined using selective culture followed by Brachyspira spp. identification by PCR and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Ingesta or fecal consistency and intestinal lesions were scored. Brachyspira hyodysenteriae was detected in 23 samples from 16 intestines originating from 7 herds. Brachyspira spp. were detected in 96 samples. More intestinal (16) than fecal (7) samples tested positive for B. hyodysenteriae. For Brachyspira spp., this difference was significant (69 vs. 27; p < 0.01). In particular, colon samples tested positive ( n = 42, p = 0.06). Most (91%) of the intestines showed no lesions typical for clinical B. hyodysenteriae infection, and median ingesta or fecal consistency was "soft and formed," indicating subclinical infection, colonization, or absence of infection. Ingesta from slaughtered pigs, in particular from the colon and sites with lesions, is useful material for detection of B. hyodysenteriae.

Provision of straw by a foraging tower -effect on tail biting in weaners and fattening pigs.

BACKGROUND: Straw is one of the most effective rooting materials to reduce tail biting in pigs. A so-called foraging-tower (FT) provides only small quantities of straw compatible with liquid manure systems. The focus of the present study was on the effect of providing straw by FT in order to prevent tail biting in tail docked pigs. Four consecutive batches of 160 pigs, randomly divided into a straw (SG) and a control group (CG) were followed up from weaning to slaughter. RESULTS: Tail wounds (Score ≥ 2) were detected in 104 out of 12,032 single observations (SG n = 48; CG n = 56) in 9 pens (SG n = 4/32; CG n = 5/32) mainly focused on the fattening period of batch 2 due to a failure in the ventilation system. No significant differences concerning the distribution of Score ≥ 2 in pens of the SG and CG could be identified. Bite marks (Score 1) were documented in 395 observations at animal level (SG n = 197, CG n = 198) in all batches. In the nursery period, the air velocity significantly increased the chance that at least one pig per pen and week showed a tail lesion score ≥1 (p = 0.024). In the fattening period ammonia concentration was positively associated with tail lesions (p = 0.007). The investigation of blood samples revealed infections with Mycoplasma hyopneumoniae in all batches and a circulation of Porcine Reproductive and Respiratory Syndrome Virus (NA-vaccine strain) and Porcine Circovirus Type 2 in two batches each. The average daily straw consumption was 3.5 g/pig (standard deviation (SD) = 1.1) during the rearing period and 31.9 g/pig (SD = 7.7) during the fattening period. CONCLUSION: Due to the low prevalence of tail biting in all batches the effect of the FT tower could not be evaluated conclusively. The operation of the FT with an average daily straw consumption of 3.5 g/pig (SD = 1.1) during the rearing period and 31.9 g/pig (SD = 7.7) during the fattening period did not affect the weight gain. Exploratory behaviour seems to cause bite marks (score 1), which do not necessarily result in tail biting. The main outbreak of tail biting was probably triggered by a failure of the ventilation system, which resulted in a number of climatic and air quality changes including higher ammonia concentrations and sudden temperature changes.

Authorization of Animal Experiments Is Based on Confidence Rather than Evidence of Scientific Rigor.

Accumulating evidence indicates high risk of bias in preclinical animal research, questioning the scientific validity and reproducibility of published research findings. Systematic reviews found low rates of reporting of measures against risks of bias in the published literature (e.g., randomization, blinding, sample size calculation) and a correlation between low reporting rates and inflated treatment effects. That most animal research undergoes peer review or ethical review would offer the possibility to detect risks of bias at an earlier stage, before the research has been conducted. For example, in Switzerland, animal experiments are licensed based on a detailed description of the study protocol and a harm-benefit analysis. We therefore screened applications for animal experiments submitted to Swiss authorities (n = 1,277) for the rates at which the use of seven basic measures against bias (allocation concealment, blinding, randomization, sample size calculation, inclusion/exclusion criteria, primary outcome variable, and statistical analysis plan) were described and compared them with the reporting rates of the same measures in a representative sub-sample of publications (n = 50) resulting from studies described in these applications. Measures against bias were described at very low rates, ranging on average from 2.4% for statistical analysis plan to 19% for primary outcome variable in applications for animal experiments, and from 0.0% for sample size calculation to 34% for statistical analysis plan in publications from these experiments. Calculating an internal validity score (IVS) based on the proportion of the seven measures against bias, we found a weak positive correlation between the IVS of applications and that of publications (Spearman's rho = 0.34, p = 0.014), indicating that the rates of description of these measures in applications partly predict their rates of reporting in publications. These results indicate that the authorities licensing animal experiments are lacking important information about experimental conduct that determines the scientific validity of the findings, which may be critical for the weight attributed to the benefit of the research in the harm-benefit analysis. Similar to manuscripts getting accepted for publication despite poor reporting of measures against bias, applications for animal experiments may often be approved based on implicit confidence rather than explicit evidence of scientific rigor. Our findings shed serious doubt on the current authorization procedure for animal experiments, as well as the peer-review process for scientific publications, which in the long run may undermine the credibility of research. Developing existing authorization procedures that are already in place in many countries towards a preregistration system for animal research is one promising way to reform the system. This would not only benefit the scientific validity of findings from animal experiments but also help to avoid unnecessary harm to animals for inconclusive research.

Binding studies on isolated porcine small intestinal mucosa and in vitro toxicity studies reveal lack of effect of C. perfringens beta-toxin on the porcine intestinal epithelium.

Beta-toxin (CPB) is the essential virulence factor of C. perfringens type C causing necrotizing enteritis (NE) in different hosts. Using a pig infection model, we showed that CPB targets small intestinal endothelial cells. Its effect on the porcine intestinal epithelium, however, could not be adequately investigated by this approach. Using porcine neonatal jejunal explants and cryosections, we performed in situ binding studies with CPB. We confirmed binding of CPB to endothelial but could not detect binding to epithelial cells. In contrast, the intact epithelial layer inhibited CPB penetration into deeper intestinal layers. CPB failed to induce cytopathic effects in cultured polarized porcine intestinal epithelial cells (IPEC-J2) and primary jejunal epithelial cells. C. perfringens type C culture supernatants were toxic for cell cultures. This, however, was not inhibited by CPB neutralization. Our results show that, in the porcine small intestine, CPB primarily targets endothelial cells and does not bind to epithelial cells. An intact intestinal epithelial layer prevents CPB diffusion into underlying tissue and CPB alone does not cause direct damage to intestinal epithelial cells. Additional factors might be involved in the early epithelial damage which is needed for CPB diffusion towards its endothelial targets in the small intestine.

Estimating diagnostic test accuracies for Brachyspira hyodysenteriae accounting for the complexities of population structure in food animals.

For swine dysentery, which is caused by Brachyspira hyodysenteriae infection and is an economically important disease in intensive pig production systems worldwide, a perfect or error-free diagnostic test ("gold standard") is not available. In the absence of a gold standard, Bayesian latent class modelling is a well-established methodology for robust diagnostic test evaluation. In contrast to risk factor studies in food animals, where adjustment for within group correlations is both usual and required for good statistical practice, diagnostic test evaluation studies rarely take such clustering aspects into account, which can result in misleading results. The aim of the present study was to estimate test accuracies of a PCR originally designed for use as a confirmatory test, displaying a high diagnostic specificity, and cultural examination for B. hyodysenteriae. This estimation was conducted based on results of 239 samples from 103 herds originating from routine diagnostic sampling. Using Bayesian latent class modelling comprising of a hierarchical beta-binomial approach (which allowed prevalence across individual herds to vary as herd level random effect), robust estimates for the sensitivities of PCR and culture, as well as for the specificity of PCR, were obtained. The estimated diagnostic sensitivity of PCR (95% CI) and culture were 73.2% (62.3; 82.9) and 88.6% (74.9; 99.3), respectively. The estimated specificity of the PCR was 96.2% (90.9; 99.8). For test evaluation studies, a Bayesian latent class approach is well suited for addressing the considerable complexities of population structure in food animals.