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Improving animal health and welfare in livestock systems depends on reliable proxies for assessment and monitoring. The aim of this project was to develop a novel method that relies on animal-based indicators and data-driven metrics for assessing health and welfare at farm level for the most common livestock species in Switzerland. Method development followed a uniform multi-stage process for each species. Scientific literature was systematically reviewed to identify potential health and welfare indicators for cattle, sheep, goats, pigs and poultry. Suitable indicators were applied in the field and compared with outcomes of the Welfare Quality® scores of a given farm. To identify farms at risk for violations of animal welfare regulations, several agricultural and animal health databases were interconnected and various supervised machine-learning techniques were applied to model the status of farms. Literature reviews identified a variety of indicators, some of which are well established, while others lack reliability or practicability, or still need further validation. Data quality and availability strongly varied among animal species, with most data available for dairy cows and pigs. Data-based indicators were almost exclusively limited to the categories “Animal health” and “Husbandry and feeding”. The assessment of “Appropriate behavior” and “Freedom from pain, suffering, harm and anxiety” depended largely on indicators that had to be assessed and monitored on-farm. The different machine-learning techniques used to identify farms for risk-based animal welfare inspections reached similar classification performances with sensitivities above 80%. Features with the highest predictive weights were: Participation in federal ecological and animal welfare programs, farm demographics and farmers' notification discipline for animal movements. A common method with individual sets of indicators for each species was developed. The results show that, depending on data availability for the individual animal categories, models based on proxy data can achieve high correlations with animal health and welfare assessed on-farm. Nevertheless, for sufficient validity, a combination of data-based indicators and on-farm assessments is currently required. For a broad implementation of the methods, alternatives to extensive manual on-farm assessments are needed, whereby smart farming technologies have great potential to support the assessment if the specific monitoring goals are defined.

The feeding of waste milk containing antibiotic residues (WMA) to calves has been associated with the shedding of antibiotic-resistant bacteria by calves. However, little is known regarding farmers' intrinsic factors affecting this practice, and on which it would be relevant to intervene in order to change this practice. The objectives of this study were (1) to describe the farmers' intrinsic factors, such as perceived benefits, risks, and social norms related to the feeding of WMA to calves, antibiotic resistance, and antibiotic use, and (2) to evaluate how the feeding of WMA to calves is related to farmers' personal values and perceptions related to WMA feeding and antibiotic resistance. Answers to an online survey were collected from 233 Swiss dairy producers (38.3% response rate). The proportion of respondents who fed WMA to calves was 48.3%. In a hierarchical logistic regression model, only perception factors extracted by factor analysis were associated with the feeding of WMA to calves, namely (in decreasing order of magnitude): farm-level benefits of WMA feeding, the interaction of farm-level benefits with support from governmental authorities, and causes and threats of antibiotic resistance. The results suggest that, in order to reduce the feeding of WMA to calves, communications to dairy producers should focus on changing the perceived benefits of this practice in comparison to those of alternative WMA disposal methods carrying a lower risk of antibiotic resistance. The involvement of veterinarians and governmental authorities in these communications and in supporting producers may increase the successful adoption of alternative WMA disposal methods.

The prevention of bovine respiratory disease is important, as it may lead to impaired welfare, economic losses, and considerable antimicrobial use, which can be associated with antimicrobial resistance. The aim of this study was to describe the prevalence of respiratory viruses and to identify risk factors for their occurrence. A convenience sample of 764 deep nasopharyngeal swab samples from veal calves was screened by PCR for bovine respiratory syncytial virus (BRSV), bovine parainfluenza-3 virus (BPI3V), bovine coronavirus (BCoV), influenza D virus (IDV), and influenza C virus (ICV). The following prevalence rates were observed: BRSV, 2.1%, BPI3V, 3.3%, BCoV, 53.5%, IDV, 4.1%, ICV, 0%. Logistic mixed regression models were built for BCoV to explore associations with calf management and housing. Positive swab samples were more frequent in younger calves than older calves (&gt, 100 days, p &lt, 0.001). The probability of detecting BCoV increased with increasing group size in young calves. Findings from this study suggested that young calves should be fattened in small groups to limit the risk of occurrence of BCoV, although an extended spectrum of risk factors for viral associated respiratory disorders such as nutritional aspects should be considered in future studies.

BACKGROUND Cryptosporidiosis is a parasitic disease associated with potentially fatal diarrhea. The most used method in Cryptosporidium subtyping is based on the glycoprotein gene gp60. Each infection can represent a parasite population, and it is important to investigate the influence on transmission and virulence, as well as any impact on public health investigations. However, an easy-to-use method for detection is lacking. METHODS Here we report on the use of the bioinformatic program TIDE for deconvolution of gp60 chromatograms. A combination of single oocyst analysis and cloning successfully confirmed the within-sample parasite population diversity. Retrospective sample analysis was conducted on archived chromatograms. RESULTS For C. parvum, 8.6% multi-strain infections (13 out of 152) obscured by currently used consensus base calling were detected. Importantly, we show that single oocysts can harbor a mixed population of sporozoites. We also identified a striking dominance of unappreciated polymerase stutter artefacts in all 218 chromatograms analyzed, challenging the uncritical use of gp60 typing. DISCUSSION We demonstrate the value of a new easy-to-use analytical procedure for critical characterization of C. parvum and C. hominis in epidemiological investigations, also applicable in retrospect. Our findings illuminate the hidden parasite diversity with important implications for tracing zoonotic and person-to-person transmissions.

Feeding waste milk containing antimicrobial residues (WMA) to calves has been associated with increased antimicrobial resistance in calves' commensal bacterial flora. The objectives of this study were (1) to document practices related to the disposal of WMA on Swiss dairy farms and (2) to evaluate the association between farm characteristics and the feeding of WMA to calves. A web-based questionnaire on practices surrounding waste milk disposal was completed by 1,625 dairy producers (10.9% of solicited producers). Logistic regression models were built to evaluate the association between herd characteristics and the practice of feeding WMA. Waste milk produced during and up to the first milking after completion of antimicrobial treatment or during the withdrawal period was fed to at least some of the calves on 47.3% of respondents' farms. Farms in organic production had lower odds of feeding WMA to calves than nonorganic farms [odds ratio (OR) 0.59]. Farms located in the eastern region of Switzerland, as opposed to those in the western region, had increased odds of feeding WMA to calves (OR 2.01). A yearly average bulk tank somatic cell count ≥150,000 cells/mL was associated with increased odds of feeding WMA to calves compared with the reference category of

BACKGROUND Genetic skin diseases in cattle are rare. CLINICAL SUMMARY A 7-week-old female Holstein calf was presented with epidermal lesions and alopecia in the caudal region of the ears and on the neck, as well as deep bilateral ulcerative lesions on the palmar aspect of the metacarpi and dorsal aspect of the right metacarpus. Clinical, pathological and histopathological examination of the calf was suggestive of a subepidermal vesicular dermatosis. Genetic analysis identified a de novo non-sense variant affecting the aspartate dehydrogenase domain containing (ASPDH) gene, which might be associated with the formation of subepidermal vesicles in this case. CONCLUSION AND CLINICAL IMPORTANCE The observed phenotype in the calf may represent a novel form of a vesicular skin disorder. Haploinsufficiency of the ASPDH gene might be considered as a possible cause.

In 2015, cholesterol deficiency (CD) was reported for the first time as a new recessive defect in Holstein cattle. After GWAS mapping and identification of a disease-associated haplotype, a causative loss-of-function variant in APOB was identified. CD-clinically affected APOB homozygotes showed poor development, intermittent diarrhea and hypocholesterolemia and, consequently, a limited life expectation. Herein, we present a collection of 18 cases clinically diagnosed as CD-affected APOB heterozygotes. CD-clinically affected heterozygotes show reduced cholesterol and triglyceride blood concentrations. The differences in total blood cholesterol and triglycerides between nine CD-clinically affected and 36 non-affected heterozygotes were significant. As only some APOB heterozygotes show the clinical CD phenotype, we assume that the penetrance is reduced in heterozygotes compared to the fully penetrant effect observed in homozygotes. We conclude that APOB-associated CD represents most likely an incomplete dominant inherited metabolic disease with incomplete penetrance in heterozygotes.

Dieser Fallbericht beschreibt eine neue Erbkrankheit beim Braunvieh in der Schweiz. Diese auch beim Deutschen Fleckvieh als FH2 vorkommende Krankheit entspricht einer beim Menschen als Fanconi-Bickel-Syndrom bekannten Glykogenspeicherkrankheit. Sie wird durch Mutationen im SLC2A2 Gen verursacht, das für den Glukosetransporter GLUT2 kodiert. Ein Original Braunviehkalb mit homozygotem Genotyp für die FH2-assoziierte SLC2A2 Leserasterverschiebung wird vorgestellt. Die klinische Untersuchung des Kalbes zeigte ein verzögertes Wachstum, Polyurie und Polydipsie sowie schlechte Fell- und Klauenhornqualität. Die pathologische Untersuchung der Nieren zeigte makroskopisch eine unilaterale Hypoplasie sowie eine Aufhellung der Rinde. Histologisch war eine Tubulonephrose der proximalen Tubuli sowie Protein- und Glukosehaltiger Inhalt sichtbar. Eine übermässige Glykogenspeicherung war in keinem Organ feststellbar. Diese histopathologischen Befunde unterscheiden sich von den zuvor beim Fleckvieh beschriebenen Veränderungen. Beim beschriebenen Fall scheint primär eine Nierenfunktionsstörung die Wachstumsretardierung zu erklären. Den Züchtern steht ein direkter Gentest zur Ausmerzung des Defektallels zur Verfügung., INTRODUCTION This case report describes a new genetic disease of the Braunvieh breed in Switzerland. The bovine disorder also occurs in German Fleckvieh, and corresponds to human Fanconi-Bickel syndrome which is an inherited glycogen storage disease caused by mutations of the SLC2A2 gene encoding the glucose transporter GLUT2. This case report describes a single affected Original Braunvieh calf genotyped as homozygous for the FH2-associated SLC2A2 frame shift mutation. The clinical examination showed stunted growth, polyuria and polydipsia, as well as poor claw horn and coat quality. Necropsy revealed a pale cortex of the kidneys and a unilateral renal hypoplasia. Histology showed tubulonephrosis of the proximal tubules with protein- and glucose-rich contents. Glycogen accumulation was not evident in any organ. This finding is different from the reported lesions in two previously described GLUT2-deficient Fleckvieh heifers. In the presented case, growth retardation mainly seems to be associated with renal dysfunction. A direct gene test is available to eliminate the mutant allele from the population.

Nach einer Häufung von Fällen der bovinen dilatativen Kardiomyopathie (BDCMP) in den 1980er-Jahren nahm deren Prävalenz dank klassischer zuchthygienischer Ausschlussmassnahmen stetig ab. Die hier beschriebenen Fälle zeigen, dass die rezessiv vererbte Krankheit in der Schweizer Rinderpopulation, wenn auch selten, nach wie vor vorhanden ist. Mittels eines vor einigen Jahren entwickelten direkten Gentests kann eine klinische Verdachtsdiagnose eindeutig bestätigt werden. Seit Ende 2016 werden Anlageträger in der Schweiz offiziell gekennzeichnet. Zur Zeit tragen rund 2% aller Besamungsstiere der Rassen Holstein, Red Holstein und Swiss Fleckvieh die ursächliche Mutation im OPA3- Gen. Durch eine erhöhte Aufmerksamkeit und einen vermehrten Einsatz des Gentests stehen heute die nötigen Instrumente zu Verfügung, um die Krankheit in der Schweizer Rinderpopulation zu eliminieren., Numerous cases of bovine dilatative cardiomyopathy (BDCMP) were registered in the nineteen-eighties, but the prevalence decreased steadily thanks to classical selection measures, i.e. excluding putative carrier animals from breeding. The cases described here show that the recessively inherited disease is still present in the Swiss cattle population. By use of a direct gene test developed a few years ago, a clinical tentative diagnosis can be confirmed. Since the end of the year 2016, carriers are officially labelled as such in Switzerland. Currently, about 2% of the insemination sires of the Holstein, Red Holstein and Swiss Fleckvieh breeds carry the causative mutation in the OPA3 gene. A combination of increased awareness of the disease and use of the gene test should allow for complete elimination of the disease from the Swiss cattle population., La cardiomyopathie dilatative bovine: Presqu’oubliée mais toujours présente De nombreux cas de cardiomyopathie dilatative bovine (CMPDB) ont été rapportés dans les années 1980. Leur prévalence a ensuite fortement diminué grâce à des mesures classiques de sélection, à savoir l’exclusion de l’élevage des porteurs potentiels. Les cas décrits ici montrent que cette maladie héréditaire récessive, quoique rare, est toujours bien présente dans la population bovine suisse. Un test génétique direct développé il y a quelques années permet de confirmer définitivement un diagnostic de suspicion clinique. Depuis fin 2016, les porteurs de la mutation sont signalés officiellement en Suisse: environ 2% des taureaux d’insémination des races Holstein, Red Holstein et tachetée rouge sont porteurs de la mutation causative du gène OPA3. Une attention augmentée et un usage accru du test génétique rendent possible pour la première fois une éradication complète de la maladie du cheptel bovin suisse., Cardiomiopatia dilatativa nei bovini: quello che si sapeva e si sa Dopo un aumento di casi di cardiomiopatia dilatativa bovina (BDCMP) negli anni 1980, la prevalenza è diminuita grazie all’applicazione di misure igieniche negli allevamenti. I casi descritti qui di seguito dimostrano che la malattia è recessiva nella popolazione bovina in Svizzera ma ancora presente, anche se di rado. Grazie allo sviluppo di un test genetico qualche anno fa, si è potuto confermare chiaramente la diagnosi clinica dei casi sospetti. Dalla fine del 2016, in Svizzera, i portatori genetici sono ufficialmente identificabili. Attualmente, circa il 2% di tutti i tori per fecondazione delle razze Holstein, Red Holstein e Swiss Fleckvieh sono portatori della mutazione sul gene OPA3. Con una maggiore attenzione e un maggiore utilizzo dei test genetici al giorno d’oggi abbiamo a disposizione gli strumenti necessari per eliminare la malattia dalla popolazione di bovini in Svizzera.

Diese Arbeit beschreibt die Befunde der klinischen, hämatologischen, blutchemischen und ultrasonographischen Untersuchungen bei einem Simmentaler Rind mit caeco-caecaler Invagination. Das Rind präsentierte sich in mittelgradig reduziertem Allgemeinzustand mit leichter Kolik. In der rechten Flanke war eine unter der Bauchwand verschiebliche Masse sicht- und tastbar. Rektaluntersuchung, Kotmenge und -absatz waren unauffällig. Die Ultraschalluntersuchung der Masse ergab typische Befunde für eine Invagination. Aufgrund der langsamen Entwicklung der Krankheit, des erhaltenen Kotabsatzes und der Ultraschallbefunde wurde die Diagnose einer caeco-caecalen Invagination gestellt. Der veränderte Darm wurde in Vollnarkose über einen Zugang in der rechten Flanke reseziert, und es wurde eine End-zu-Seit-Anastomose zwischen dem Jejunum und dem proximalen Colon durchgeführt. Die Heilung verlief ohne Komplikationen., This report describes the clinical, laboratory and ultrasonographic findings in a Simmental heifer with a ceco-cecal intussusception. The general condition of the heifer was moderately reduced and it showed mild colic signs. Physical examination revealed a firm longish mass visible and palpable in the right flank. Findings upon rectal examination, fecal output und defecation were normal. Ultrasound examination of the mass revealed features typical for an intussusception. Based on the slow development of symptoms, normal fecal output and ultrasonography findings, a ceco-cecal intussusception was diagnosed. Right flank laparatomy was performed under general anaesthesia, and an end-to-side anastomosis between the jejunum and the spiral colon was made after resection of the intussuscepted intestines. Recovery was uneventful.