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In the present study, relationships between the intestinal microbiota and innate immunity response, acute cryptosporidiosis, and weight gain in female dairy calves were investigated. A total of 112 calves born during a natural outbreak of cryptosporidiosis on one dairy farm was included in the study. Microbiota composition was analysed by means of 16S ribosomal RNA gene amplicon sequencing from faecal samples collected during the second week of life, while the status of Cryptosporidium spp. infection was determined using immunofluorescence. Serum samples from the second week of life were colourimetrically analysed for the following markers of acute inflammation: acute-phase proteins (serum amyloid A and haptoglobin) and pro-inflammatory cytokines (interleukin-1 beta, interleukin-6, and tumour necrosis factor-alpha). Statistical analyses were performed using random forest analysis, variance-partitioning, and negative binomial regression. The faecal microbiota of the two-week old calves was composed of the phyla Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, and Actinobacteria (in order of decreasing abundance). Microbial diversity, measured in terms of the Shannon index, increased with the age of the calves and decreased if a high count of Cryptosporidium spp. oocysts was found in the faeces. Fusobacterium was positively associated with Cryptosporidium spp. oocyst count and serum amyloid A concentration. Peptostreptococcus was positively associated with haptoglobin and serum amyloid A concentrations, and negatively associated with average daily weight gain at 9 months of age. The markers of innate immunity, in combination with age, explained 6% of the microbial variation. These results suggest that some components of the intestinal microbiota may have a long-lasting negative effect on animal growth through the stimulation of the systemic innate immune response.

Simple Summary Biosecurity breaches have been shown to play a major role in the introduction and spread of African swine fever (ASF) in domestic pig populations. The aim of the study was to describe the biosecurity levels and management practices of ASF outbreak and uninfected herds and to identify potential risk factors for ASF introduction. The biosecurity score of ASF outbreak herds was significantly lower compared to uninfected herds. This may reflect general improvement in the application of biosecurity measures over time in Estonian pig farms as the data on uninfected herds were collected later, at a time when intensified official controls may have had their effect. Larger herds were more at risk of being ‘outbreak herds’ compared to smaller herds. The biosecurity parameters significantly associated with ‘outbreak herd’ status in statistical analysis were mostly related to indirect contacts with the outside farm environment. The biosecurity barriers applied in Estonian pig farms have not been sufficient to avoid the introduction of ASF and need critical evaluation and improvement. Reduction of all contacts between the farm and the external environment should be emphasized in a situation where ASF is circulating in wild boar populations close to pig farms. Abstract Risk factors related to external biosecurity have been considered to play a major role in the introduction and spread of African swine fever (ASF) in domestic pig populations. The aim of the study was to describe the biosecurity levels and management practices of ASF outbreak and uninfected herds and to identify potential risk factors for ASF introduction. Data collected from the outbreak herds during outbreak investigations and from the randomly selected uninfected herds were analyzed. The biosecurity score in ASF outbreak herds was significantly lower compared to uninfected herds. However, this may reflect general improvement in the application of biosecurity measures in pig farms over time as the data on uninfected herds were collected later, at a time when intensified official controls may have had their effect. Larger herds were more at risk of being outbreak herds compared to smaller herds. The biosecurity parameters significantly associated with the outbreak herd status in multiple correspondence analysis were mostly related to indirect contacts with the outside farm environment. The biosecurity barriers applied in Estonian pig farms have not been sufficient to avoid ASF introduction and need critical evaluation and improvement. Reduction of all contacts between the farm and the external environment should be emphasized in a situation where ASF is circulating in wild boar populations close to pig farms.

The present study aimed to reveal the culling-related metrics, identify the culling reason patterns for cows by developing and implementing the cow culling form (CCF), and analyse the concordance of farmers' stated culling reasons with those identified based on the CCF. A CCF was developed to register the disease history and conditions of cows that were related to culling. CCFs were completed by farm managers and veterinarians in eight dairy herds over a one-year period for slaughtered (n = 686) and dead (n = 250) cows. Completed CCFs were interpreted by the study authors to identify underlying, intermediate, influential, and immediate culling reasons. The identified culling reasons were compared to those reported by producers. The mean annual cow culling rate of the study farms was 31.8%, and the average on-farm mortality was 9.3%. Of the 250 cows that died on the farms, 43.6% were euthanised. Only 2% of the cows were slaughtered due to low milk yield. In total, 260 and 119 unique three-reason culling codes were created for slaughtered and dead cows, respectively. Single disease or condition causing slaughter or death of cows was identified in 44.8% and 52.0% of the cases, respectively. Producers' reported culling reasons concurred with the underlying culling reason in 72.6% and 63.6% of slaughtered and dead cows, respectively. A high variety of agreements between the farmers' reported and CCF-based culling codes was identified across single culling reasons. Improved registration of culling reasons is required to support informed herd-based decisions.

This is the deliverable D-JRP21-WP2.8 "Quantified biosecurity effectiveness from applied biosecurity protocol at slaughterhouses" of the OHEJP BIOPIGEE project produced in WP2 T3.

This is the deliverable D-JRP21-WP6.15 "Biosecurity protocol on slaughterhouse provided" of the OHEJP BIOPIGEE project produced in WP6.1.2b.

In neonatal period, lamb's immune system goes through rapid adaptation to the extra-uterine environment. Success of this process can influence the animal's future performance and, thus, the quantitative assessment of it would greatly benefit sheep producers. The current study was conducted to investigate the acute phase response (APR) (measured through serum amyloid A (SAA), haptoglobin (Hp) and albumin (ALB)) in relation to later life growth (measured at 122 days of age), and naturally occurring Cryptosporidium and Giardia infections in neonatal lambs grown in organic farm. Serum (n = 692) and faecal (n = 141) samples were collected from 269 lambs in their first 3 weeks of life. The ewes' colostrum (n = 181) SAA concentrations were positively associated with the lambs' serum SAA and Hp concentrations at 2 to 4 days of age. Hp and ALB concentrations at the second week of age were positively associated with the growth rate at 122 days of age. Lamb serum globulin (GLOB) concentrations and Cryptosporidium-positive faecal samples were negatively associated at the second and third weeks of life. These findings suggest the importance of interactions between the immune system and environmental factors at the second week of the lambs' lives and its association with future performance.

After the extensive spread of the African swine fever virus (ASFV) genotype II in Eastern Europe, the first case of African swine fever (ASF) in Estonia was diagnosed in September 2014. By the end of 2019, 3971 ASFV-positive wild boars were found, and 27 domestic pig outbreaks were reported. A selection of ASFV isolates from wild boar and domestic pigs (during the period of September 2014&ndash, 2019) was molecularly characterized using standardized genotyping procedures. One of the proven markers to characterize this virus is the central variable region (CVR) within the B602L gene. In summer 2015, a new ASFV genotype II CVR variant 2 (GII-CVR2) was confirmed in Estonia. The results suggest that the GII-CVR2 variant was only confirmed in wild boar from a limited area in southern Estonia in 2015 and 2016. In addition to GII-CVR2, a single nucleotide polymorphism (SNP) that resulted in amino acid change was identified within the genotype II CVR variant 1 (GII-CVR1). The GII-CVR1/SNP1 strain was isolated in Estonia in November 2016. Additional GII-CVR1/SNP1 cases were confirmed in two neighbouring counties, as well as in one outbreak farm in June 2017. Based on the available data, no GII-CVR2 and GII-CVR1/SNP1 have been reported by other affected European countries. The spread of variant strains in Estonia has been limited over time, and restricted to a relatively small area.

Cryptosporidium spp. infections in neonatal dairy calves can cause diarrhoea and, in rare cases, death. The infection is usually self-limiting, but halofuginone lactate (HL) can be used prophylactically. Calves (n = 144) in the study were born during a 2-month period on one farm. A total of 901 serum and 767 faecal samples were collected. Based on HL treatment, the calves were divided into 3 groups: I) not treated, II) treated incorrectly (treatment started > 48 h after birth, or lasted, Highlights • Acute phase response was affected by halofuginone lactate treatment. • Haptoglobin concentration was more affected than serum amyloid A by Cryptosporidium. • Gamma-glutamyltransferase activity after birth had a positive association with survival. • Halofuginone lactate treatment had a negative effect on weight gain.

The herd on-farm mortality rate is an indicator of herd animal health and welfare status. The aim of the present study was to describe herd-level on-farm mortality rates and to identify risk factors that contribute to high herd mortality rates. Online or postal questionnaires were sent to 676 Estonian beef farms, and the response rate was 25.4%. The calf (ear-tagged) and cow within-herd mortality rates for the years 2014-2016 ranged from 0.00 to 5.45 per 100 calf-months and 0.00-12.15 per 100 cow-years, respectively. The risk factors for a higher calf within-herd mortality rate in the negative binomial regression analysis were the following: calvings not being monitored at nighttime, bedding not being added daily, a low proportion of calvings occurring during summer, lack of using a consultancy service and conventional herd type compared to organic. Failure to separate sick animals and failure to use new pastures for cow-calf pairs were risk factors for cow mortality. Mortality rate was generally higher in larger herds. In order to lower the mortality rate, it is essential to ensure good calving management, a clean environment, and isolation of sick animals.

African swine fever (ASF) was first detected in the Estonian wild boar population in September 2014, while the first domestic pig farm was affected in July 2015. In the present study, we aimed to analyse, retrospectively, the epidemiology of the disease in all 26 outbreaks in domestic pig herds that occurred in Estonia during the period 2015–2017. Formal interviews were conducted to estimate the high-risk period for every farm, and to identify the possible origin of the ASF virus and the mode of virus introduction. Furthermore, the clinical manifestation of the disease as well as the course of the disease within the farm were investigated. Survival analysis was used to calculate herd incidence and to estimate outbreak risk. A hierarchical Bayesian space–time model was used to analyse the associations between outbreaks and ASF occurrence in wild boar. The spatial and temporal distribution of outbreaks was analysed to characterise the ASF epidemic in the Estonian domestic pig population from 2015 to 2017. The estimated high-risk period varied from seven to 20 days with a median of 11 days. On most of the affected farms, the first clinical signs were mild and not specific to ASF despite the high virulence of the circulating virus. Morbidity and mortality were often limited to a single pen or unit of the farm. The highest mortality (29.7%) was seen on backyard farms with 1–10 pigs and the lowest (0.7%) on large commercial farms (>1000 pigs). The spread of the virus within affected farms has been slow and the contagiousness of the virus has been relatively low. Farms of all sizes and types have been at risk, including large commercial farms operating at a high biosecurity level. In none of the affected farms could the specific route of introduction be verified. However, the findings suggested that virus introduction occurred via indirect transmission routes due to insufficient biosecurity. The total herd incidence of outbreaks was similar across all three years, being 2.4% in 2015 and 2016, and 2.0% in 2017. All outbreaks occurred from June to September, during the warmest period of the year. The results suggest that the increase in ASF cases in local wild boar populations is the main risk factor leading to the infection of farms; 88% of outbreaks occurred in areas where ASF virus was detected in wild boar prior to the outbreak, within a radius of 15 km from the outbreak farm.

This longitudinal observational study was conducted to investigate the spontaneous effect of Giardia and Cryptosporidium infections on acute phase response (APR) in reindeer calves (Rangifer tarandus tarandus) in Finnish Lapland. Serum (n = 609) and faecal samples (n = 366) were collected from 54 reindeer calves aged zero to 33 days. The samples were analysed for Giardia, Cryptosporidium, acute phase proteins (APP) and gamma-globulins. Linear regression models were used to investigate associations of early Giardia infection (before 12 days of life) with the response of APPs and acquiring of passive immunity. Giardia was detected in 100% and Cryptosporidium in 23% of calves. There was a negative association between early Giardia infection and gamma-globulin concentrations (p = 0.032) and a positive association with serum amyloid A (SAA) concentrations (p = 0.042). The results suggest a protective effect of colostrum against Giardia infection and that early infection may induce activation of APR.