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Knowledge of pathogenic potential, frequency and antimicrobial resistance patterns of porcine Streptococcus (S.) spp. other than S. suis is scarce. Between 2016 and 2020, altogether 553 S. spp. isolates were recovered from clinical specimens taken from Austrian swine stocks and submitted for routine microbiological examination. Antimicrobial susceptibility testing towards eight antimicrobial substances was performed using disk diffusion test. All isolates from skin lesions belonged to the species S. dysgalactiae subspecies equisimilis (SDSE). S. hyovaginalis was mainly isolated from the upper respiratory tract (15/19) and S. thoraltensis from the genitourinary tract (11/15). The majority of S. suis isolates were resistant to tetracycline (66%), clindamycin (62%) and erythromycin (58%). S. suis isolates from the joints had the highest resistance rates. S. suis and SDSE isolates resistant to tetracycline were more likely to be resistant to erythromycin and clindamycin (p &lt, 0.01). Results show that different species of Streptococcus tend to occur in specific body sites. Nevertheless, a statement whether these species are colonizers or potential pathogens cannot be given so far. High resistance rates of S. suis towards tetracyclines and erythromycin and high recovery rates of S. suis from lung tissue should be considered when treating pigs with respiratory diseases.

Assessing the effectiveness of non-pharmaceutical interventions (NPIs) to mitigate the spread of SARS-CoV-2 is critical to inform future preparedness response plans. Here we quantify the impact of 6,068 hierarchically coded NPIs implemented in 79 territories on the effective reproduction number, R

Biofilms are suggested to be a source of contamination in the food producing environment leading to food spoilage or the transmission of food-borne pathogens. However, to date, research has mainly focused on the presence of (biofilm-forming) bacteria within food processing environments, without analysing the associated biofilm matrix components. The aim of this study was to identify biofilm hotspots in a meat processing environment by analysing the presence of microorganisms (by cultivation and targeted quantitative real-time PCR based on 16S rRNA) and the major matrix components carbohydrates, extracellular DNA and proteins. Sampling included 47 distinct food contact surfaces and 61 distinct non-food contact surfaces from eleven rooms within an Austrian meat processing plant, either during operation or after cleaning and disinfection. Additionally, we isolated and characterized bacteria found in biofilms. The biofilm forming capacity of eleven isolates, was tested, using a static biofilm model. Additionally, two different multi-species settings were tested combining three strains, each. Biofilms were grown on stainless-steel slides for seven days at 10 °C, to mimic conditions found in the food producing environment. Overall, we identified ten biofilm positive sites, among them seven of which were sampled during operation and three after cleaning and disinfection. Five biofilms were detected on food contact surfaces (cutters and associated equipment and a screw conveyor) and five on non-food contact surfaces (drains and water hoses) resulting in 9.3 % of the sites being classified as biofilm positive. From these sites we cultivated bacteria of 29 different genera. The most prevalent bacteria belonged to the genera Brochothrix, Pseudomonas and Psychrobacter. From each biofilm we isolated bacteria from four to 12 different genera, indicating the presence of multi-species biofilms. Culturing of eleven isolates of different species (all detected in the mentioned biofilms, representing typical residential and spoilage bacteria in the meat processing environment) showed that there are differences of individual strains to produce matrix components and biomass on stainless steel slides. Brochothrix, Carnobacterium and Kocuria produced only detectable amounts of carbohydrates but neither eDNA nor proteins. The Acinetobacter and the Flavobacterium isolates were able to produce two of the measured components and six strains were capable of producing all types of analysed matrix components, among them a Pseudomonas fragi isolate. The minimal mean bacterial load detected was 5.4 log CFU/cm2 formed by the Psychrobacter strain. Different isolates showed differences in matrix formation ability, possible contributing in different amounts to the matrix production in multi-species biofilms, indicating that multi-species biofilms are a key survival mechanism for microorganisms within the food processing environment. Currently, we are testing two different multi-species biofilms in our model. Hereby we cultivate three species detected in the cutter-associated biofilms and other three species detected in the water hose-associated biofilms together to mimic these biofilms. This work ultimately showed the presence of multi-species biofilms within the meat processing environment, thereby identifying various sources of potential contamination. Data on the presence, formation and composition of biofilms (i.e. chemical and microbiological) will help to prevent and reduce biofilm formation within food processing environments.

Non-pharmaceutical interventions (NPIs) to mitigate the spread of SARS-CoV-2 were often implemented under considerable uncertainty and a lack of scientific evidence. Assessing the effectiveness of the individual interventions is critical to inform future preparedness response plans. Here we quantify the impact of 4,579 NPIs implemented in 76 territories on the effective reproduction number, Rt, of COVID-19. We use a hierarchically coded data set of NPIs and propose a novel modelling approach that combines four computational techniques, which together allow for a worldwide consensus rank of the NPIs based on their effectiveness in mitigating the spread of COVID-19. We show how the effectiveness of individual NPIs strongly varies across countries and world regions, and in relation to human and economic development as well as different dimensions of governance. We quantify the effectiveness of each NPI with respect to the epidemic age of its adoption, i.e., how early into the epidemics. The emerging picture is one in which no one-fits-all solution exists, and no single NPI alone can decrease Rt below one and that a combination of NPIs is necessary to curb the spread of the virus. We show that there are NPIs considerably less intrusive and costly than lockdowns that are also highly effective, such as certain risk communication strategies and voluntary measures that strengthen the healthcare system. By allowing to simulate “what-if” scenarios at the country level, our approach opens the way for planning the most likely effectiveness of future NPIs.

SummaryThe goal of this analysis is to estimate the effects of the diverse government intervention measures implemented to mitigate the spread of the Covid-19 epidemic. We use a process model based on a compartmental epidemiological framework Susceptible-Infected-Recovered-Dead (SIRD). Analysis of case data with such a mechanism-based model has advantages over purely phenomenological approaches because the parameters of the SIRD model can be calibrated using prior knowledge. This approach can be used to investigate how governmental interventions have affected the Covid-19-related transmission and mortality rate during the epidemic.

Bovine mastitis, an inflammation of the udder usually caused by bacteria, is the most common disease in dairy cattle worldwide with a negative economic impact on the dairy industry. In this study 3020 quarter milk samples from 647 dairy cows on 166 Austrian farms were collected and microbial species, spa type for Staphylococcus (S.) aureus and antimicrobial susceptibility were analysed. A multinomial logistic regression model was applied to investigate the effect of possible categorical influencing covariates on the microbiological findings. Additionally, a generalized linear model was used to analyse the effects of genotype and pathogen species on the occurrence of antimicrobial resistance. Staphylococci were the most common (17% of samples) udder pathogens including 32 different S. aureus spa types. The occurrence of pathogen groups was significantly associated with the clinical mastitis score. Enterobacteriaceae isolates had a significantly higher probability of being present in severe mastitis cases compared to streptococci. Benzylpenicillin and tetracycline were the most common resistance in S. aureus including 14% and 11% resistant isolates. Whereas 16% and 13% of coagulase-negative staphylococci (CNS) isolates were resistant to tetracycline and clindamycin. Overall the proportion of Enterobacteriaceae isolates resistant to at least one antibiotic agents was high (55% of isolates), whereas only 3% benzylpenicillin resistant streptococci were detected. Associations were detected between antimicrobial resistance and particular species of Enterobacteriaceae, CNS and specific S. aureus spa types. In conclusion we present in this study data on causative udder pathogen species and their antimicrobial resistance, which are of great importance for mastitis management and prevention.

The significant economic impacts of bovine viral diarrhoea (BVD) virus have prompted many countries worldwide to embark on regional or national BVD eradication programmes. Unlike other infectious diseases, BVD control is highly feasible in cattle production systems because the pathogenesis is well understood and there are effective tools to break the disease transmission cycle at the farm and industry levels. Coordinated control approaches typically involve directly testing populations for virus or serological screening of cattle herds to identify those with recent exposure to BVD, testing individual animals within affected herds to identify and eliminate persistently infected (PI) cattle, and implementing biosecurity measures such as double-fencing shared farm boundaries, vaccinating susceptible breeding cattle, improving visitor and equipment hygiene practices, and maintaining closed herds to prevent further disease transmission. As highlighted by the recent DISCONTOOLS review conducted by a panel of internationally recognized experts, knowledge gaps in the control measures are primarily centred around the practical application of existing tools rather than the need for creation of new tools. Further research is required to: (a) determine the most cost effective and socially acceptable means of applying BVD control measures in different cattle production systems; (b) identify the most effective ways to build widespread support for implementing BVD control measures from the bottom-up through farmer engagement and from the top-down through national policy; and (c) to develop strategies to prevent the reintroduction of BVD into disease-free regions by managing the risks associated with the movements of animals, personnel and equipment. Stronger collaboration between epidemiologists, economists and social scientists will be essential for progressing efforts to eradicate BVD from more countries worldwide.

16S rRNA amplicon sequencing is frequently used to investigate and compare microbiomes. This study focuses on the potential, applicability and limits of 16S rRNA amplicon sequencing for comparing the microbiomes of two dairy production plants, one of which experienced recurrent contamination with Listeria monocytogenes. During preceding in vitro studies, DNA extraction of Listeria monocytogenes and Salmonella enterica ser. Typhimurium with two extraction kits (PowerSoil and NucleoSpin) revealed differences between these exemplary bacteria and both extraction methods. When equivalent samples of the companies were processed independently with both methods, sequencing results demonstrated also bacterium specific variances. These variances do not reflect a direct correlation between Gram-positive or -negative bacteria and the performance of both kits. Despite these differences, the analysis with a non-metric multi-dimensional scaling plot showed grouping of respective samples independent of the DNA extraction method. Some operational taxonomic units (OTUs) occurred predominantly in one of the companies, but none of them generated a clear hypothesis why one of the plants had recurrent contamination with L. monocytogenes. This work provides insights into the microbiomes of the two dairy companies but advises cautions in over-interpreting sequencing results as selective DNA extraction and sampling only reflect components of prevalent bacterial communities.

Bovine viral diarrhoea virus (BVDV) is an important infectious agent of cattle worldwide that affects herd productivity and reproduction. In this systematic review of the impact of BVDV, studies were analysed with a particular focus on the monetary implications and types of direct losses, the initial infection status of herds, production systems, time periods of assessment, calculation level, study types and whether or not country-specific assessments were published. A linear mixed model was applied to analyse factors that influence the level of monetary direct losses due to BVDV infection. The 44 studies included in this review covered 15 countries and assessed direct monetary losses due to BVDV incurred over the past 30 years. Direct losses between and within countries were largely heterogeneous with respect to the monetary level and types of direct losses, ranging from 0.50 to 687.80 US dollars (USD) per animal.1 Average direct losses per naive dairy cow were USD24.85 higher than per beef cow. Country-specific assessments of direct losses due to BVDV were provided in 38/44 (86.4%) studies. Mortality, morbidity, premature culling, stillbirths, abortion, reinfection, country and study type had a significant influence on the monetary level of direct losses (r2 = 0.69). Countries recording direct losses were more likely to carry out voluntary or compulsory control and eradication programmes (odds ratio = 10.2; 95% confidence interval 1.7-81.9; P = 0.004).

European ungulates such as the roe deer face seasonally varying climatic conditions as well as food availability and quality. In some European countries, including Austria, it is common practice to provide game animals with supplemental feeding in winter. In this study we investigated if supplemental feeding significantly affects the composition of the bacterial rumen community. The rumen microbial composition of eight adult female roe deer was analysed by Illumina MiSeq 16S rRNA gene amplicon sequencing. Animals from a study area with supplemental feeding sites were compared to individuals relying on natural feed. Furthermore, the microbial community composition of different ruminal compartments (liquid phase, solid phase and wall) was compared. Our results revealed a significant qualitative difference between the microbiota composition of the two populations studied. Easily fermentable supplemental feeding promoted the proliferation of phylotypes correlated with conditions of acidosis in domestic ruminants, suggesting a possible similar adaptation and a hypothetical negative effect on health status also in roe deer. The results furthermore confirmed that in roe deer, like in other ruminant species, the most represented phyla are Firmicutes (63.2%) and Bacteroidetes (23.5%), and that the ruminal microenvironments influence the microbial community composition, with the lowest species richness and variation in the epimural microbiota.

Microbial food spoilage is responsible for a considerable amount of waste and can cause food-borne diseases in humans, particularly in immunocompromised individuals and children. Therefore, preventing microbial food spoilage is a major concern for health authorities, regulators, consumers, and the food industry. However, the contamination of food products is difficult to control because there are several potential sources during production, processing, storage, distribution, and consumption, where microorganisms come in contact with the product. Here, we conduct the first study that uses high-throughput full-length 16S rRNA gene sequencing to provide novel insights into bacterial community structure throughout a pork processing plant. Specifically, we investigated what proportion of bacteria on meat are not animal-associated and are therefore transferred during cutting via personnel, equipment, machines, or the slaughter environment. We then created a facility-specific transmission map of bacterial flow which revealed previously unknown sources of bacterial contamination. This allowed us to pinpoint specific taxa to particular environmental sources and provide the facility with essential information for targeted disinfection. For example,Moraxellaspp., a prominent meat spoilage organism which was one of the most abundant amplicon sequence variants (ASVs) detected on the meat, was most likely transferred from the gloves of employees, a railing at the classification step, and the polishing tunnel whips. Finally, we provide evidence that 1000 sequences per sample provides a reasonable sequencing depth for microbial source tracking in food processing, suggesting that this approach could be implemented in regular monitoring systems.

Antimicrobial use in livestock production is a controversial subject. While antimicrobials should be used as little as possible, it is still necessary, from both an animal health and welfare point of view, to treat infected animals. The study presented here aimed to analyse antimicrobial use on Austrian dairy farms by calculating the number of Defined Course Doses (DCDvet) administered per cow and year for dry cow therapy. Antimicrobial use was analysed by production system and whether farmers stated that they used blanket dry cow therapy (i.e., all cows in the herd were treated) or selective dry cow therapy (i.e., only cows with a positive bacteriological culture or current/recent history of udder disease were treated). A statistically significant difference (p &lt, 0.001) was determined between antimicrobial use for blanket (median DCDvet/cow/year: 0.88) and selective dry cow therapy (median DCDvet/cow/year: 0.41). The difference between antimicrobial use on conventional and organic farms for dry cow therapy as a whole, however, was not statistically significant (p = 0.22) (median DCDvet/cow/year: 0.68 for conventional, 0.53 for organic farms). This analysis demonstrates that selective dry cow therapy leads to a lower overall use of antimicrobials and can assist in a more prudent use of antimicrobials on dairy farms.

International audience; Infection with bovine viral diarrhoea virus (BVDV) is associated with a loss in productivity in cattle farms. Determining which factors influence monetary losses due to BVDV could facilitate the implementation of mitigation measures to reduce the burden of BVDV. Mixed-effect meta-analysis models were performed to estimate the extent to which the costs of mean annual BVDV production losses per animal may be influenced by epidemiological factors such as BVDV introduction risk, initial prevalence, viral circulation intensity and circulation duration (trial 1). Additionally, changes in mean annual BVDV production losses per animal due to specific mitigation measures (i.e., biosecurity, vaccination, testing and culling, cattle introduction or contact with neighbouring cattle herds) were analysed (trial 2). In total, 19 studies were included in the meta-analysis to assess mean annual BVDV production losses. The mean annual direct losses were determined to be euro42.14 per animal (trial 1). The multivariate meta-regression showed that four of the previously mentioned epidemiological factors significantly influenced the mean annual BVDV production losses per animal. Indeed, the per animal costs increased to euro67.19 when these four factors (trial 1) were considered as "high or moderate" compared to "low". The meta-regression analysis revealed that implementation of vaccination and biosecurity measures were associated with an 8%-12% and 28%-29% decrease in BVDV production losses on average, respectively, when simulated herds were compared with or without such mitigation measures (trial 2). This reduction of mean annual BVDV production losses per animal due to mitigation measures was partially counteracted when farmers brought new cattle on to farm or allowed contact with neighbouring cattle herds. The influencing mitigation factors presented here could help to guide farmers in their decision to implement mitigation strategies for the control of BVDV at farm level.

Diseases of the gastrointestinal tract due to changes in the bacterial flora have been described with increasing incidence in the European brown hare. Despite extensive demographic and phylogeographic research, little is known about the composition of its gut microbiota and how it might vary based on potential environmental or host factors. We analysed the intestinal and faecal microbiota of 3 hare populations by Illumina MiSeq 16S rRNA gene amplicon sequencing. The phyla and OTU abundance composition differed significantly between intestinal and faecal samples (PERMANOVA: P = 0.002 and P = 0.031, respectively), but in both sample types Firmicutes and Bacteroidetes dominated the microbial community composition (45.51% and 19.30% relative abundance). Intestinal samples contained an enrichment of Proteobacteria compared with faecal samples (15.71-fold change, P Escherichia-Shigella group, Eubacterium limosum, Sphingomonas kyeonggiensis, Flintibacter butyricus and Blautia faecis were detected in intestinal samples (P Enterobacteriaceae, regularly associated with intestinal dysbiosis in hares, in faecal samples. Our study is the first to describe the microbiota in brown hares and provides a foundation to generate hypothesis aiming to test the role of gut health in population fluctuations of the species.

The castor bean tick Ixodes ricinus (L.) is the principal vector for a variety of viral, bacterial, and protozoan pathogens causing a growing public-health issue over the past decades. However, a national density map of I. ricinus is still missing. Here, I. ricinus nymphs in Germany were investigated by compiling a high-resolution map depicting the mean annually accumulated nymphal density, as observed by monthly flagging an area of 100 m2. Input data comprise ticks collected at 69 sampling sites. The model domain covers an area of about 357,000 km2 (regional scale). Two negative binomial regression models were fitted to the data to interpolate the tick densities to unsampled locations using bioclimatic variables and land cover, which were selected according to their significance by the Akaike information criterion (AIC). The default model was fitted to the complete dataset resulting in AIC = 842. An optimized model resulted in a significantly better value of AIC = 732. Tick densities are very low in urban (green) areas. Maximum annual densities up to 1,000 nymphs per 100 m2 are observed in broad-leaved forests. The tick maps were verified by leave-one-out cross-validation. Root mean square errors of RMSE = 137 and RMSE = 126 nymphs per 100 m2 were estimated for the two models, respectively. These errors are of the order of the interannual variation of the tick densities. The compilation of a high-resolution density map of unfed nymphal I. ricinus for Germany provides a novel, nationwide insight into the distribution of an important disease vector.

The aim of this study was to disentangle the microbial diversity on porcine musculature. The hypervariable V1-V2 region of the 16S rRNA gene was amplified from DNA samples of clinically healthy slaughter pigs (n=8). Pyrosequencing yielded 37,000 quality-controlled reads and a diverse microbiome with 54-159 OTUs per sample was detected. Interestingly, 6 out of 8 samples were strongly dominated by 1-2 highly abundant OTUs (best hits of highly abundant OTUs: Serratia proteamaculans, Pseudomonas syringae, Aeromonas allosaccharophila, Brochothrix thermosphacta, Acidiphilium cryptum and Escherichia coli). In 1g musculature scraping, 3.20E+06 16S rRNA gene copies and 4.45E+01 Enterobacteriaceae rRNA gene copies were detected with qPCR. We conclude that i.) next-generation sequencing technologies help encompass the full content of complex, bacterial contamination, ii.) psychrophile spoilers dominated the microbiota and iii.) E. coli is an effective marker species for pork contamination, as it was one of very few abundant species being present in all samples.

Increasing numbers of multi-resistant Escherichia (E.) coli from clinical specimens emphasize the importance of monitoring of their resistance profiles for proper treatment. Furthermore, knowledge on the presence of virulence associated genes in E. coli isolates from European swine stocks is scarce. Consequently, a total of 694 E. coli isolated between 2016 and 2018 from diarrheic piglets of Austrian swine herds were investigated. The isolates were tested for their susceptibility to twelve antibiotics using agar disk diffusion test and for the presence of 22 virulence associated genes via PCR. Overall, 71.9, 67.7, and 49.5% of all isolates were resistant to ampicillin, tetracycline, and trimethoprim-sulfamethoxazole, while resistance levels to gentamicin and fosfomycin were 7.7 and 2.0%, respectively. Resistance frequency to ciprofloxacin was higher than in previous studies. Isolates were more likely to be resistant to ampicillin if they were also resistant to ciprofloxacin. No isolate was resistant to meropenem or amikacin. Virulence genes were detected more frequently in isolates expressing hemolytic activity on blood agar plates. The detection rate of faeG was increased in fimH negative isolates. We assume, that hemolytic activity and absence of fimH could be considered as potential indicators for the virulence of E. coli in piglets.

A random effect meta-analysis was performed to estimate the worldwide pooled bovine viral diarrhoea virus (BVDV) prevalences of persistently infected (PI), viraemic (VI) and antibody-positive (AB) animals and herds. The meta-analysis covered 325 studies in 73 countries that determined the presence or absence of BVDV infections in cattle from 1961 to 2016. In total, 6.5 million animals and 310,548 herds were tested for BVDV infections in the global cattle population. The worldwide pooled PI prevalences at animal level ranged from low (≤0.8% Europe, North America, Australia), medium (>0.8% to 1.6% East Asia) to high (>1.6% West Asia). The PI and AB prevalences in Europe decreased over time, while BVDV prevalence increased in North America. The highest mean pooled PI prevalences at animal level were identified in countries that had failed to implement any BVDV control and/or eradication programmes (including vaccination). Our analysis emphasizes the need for more standardised epidemiological studies to support decision-makers implementing animal health policies for non-globally-regulated animal diseases.

Microorganisms are translocated from the gut to lymphatic tissues via immune cells, thereby challenging and training the mammalian immune system. Antibiotics alter the gut microbiome and consecutively might also affect the corresponding translocation processes, resulting in an imbalanced state between the intestinal microbiota and the host. Hence, understanding the variant effects of antibiotics on the microbiome of gut-associated tissues is of vital importance for maintaining metabolic homeostasis and animal health. In the present study, we analyzed the microbiome of (i) pig feces, ileum, and ileocecal lymph nodes under the influence of antibiotics (Linco-Spectin and Colistin sulfate) using 16S rRNA gene sequencing for high-resolution community profiling and (ii) ileocecal lymph nodes in more detail with two additional methodological approaches, i.e., cultivation of ileocecal lymph node samples and (iii) metatranscriptome sequencing of a single lymph node sample. Supplementation of medicated feed showed a local effect on feces and ileal mucosa-associated microbiomes. Pigs that received antibiotics harbored significantly reduced amounts of segmented filamentous bacteria (SFB) along the ileal mucosa (p = 0.048; 199.17-fold change) and increased amounts of Methanobrevibacter, a methanogenic Euryarchaeote in fecal samples (p = 0.005; 20.17-fold change) compared to the control group. Analysis of the porcine ileocecal lymph node microbiome exposed large differences between the viable and the dead fraction of microorganisms and the microbiome was altered to a lesser extent by antibiotics compared with feces and ileum. The core microbiome of lymph nodes was constituted mainly of Proteobacteria. RNA-sequencing of a single lymph node sample unveiled transcripts responsible for amino acid and carbohydrate metabolism as well as protein turnover, DNA replication and signal transduction. The study presented here is the first comparative study of microbial communities in feces, ileum, and its associated ileocecal lymph nodes. In each analyzed site, we identified specific phylotypes susceptible to antibiotic treatment that can have profound impacts on the host physiological and immunological state, or even on global biogeochemical cycles. Our results indicate that pathogenic bacteria, e.g., enteropathogenic Escherichia coli, could escape antibiotic treatment by translocating to lymph nodes. In general ileocecal lymph nodes harbor a more diverse and active community of microorganisms than previously assumed.

Dairy farms were identified, which can be included in a contingency plan set up to prevent or mitigate the consequences of deliberate contamination of a food supply chain. The deliberate introduction of a contamination into the supply chain of milk was simulated in a scenario where milk producers serve as the entry sources and consumers of milk represent the target to be affected by the contamination. It is shown that the entry sources have an impact on the damage caused, i.e. in terms of the number of consumers reached. A contingency plan is provided that contains a list of entry sources ranked according to their impact on the damage to consumers. To generate this list, a computer program was developed that simulates the impact of the contaminations on consumers via the trade of contaminated milk. Possible variations in the trade links between milk producers, dairies and consumers as well as between dairies are considered. It is investigated how these trade links alter the generated list of entry sources.The results indicate that, regardless of the actual milk trade flow, control measures should be introduced on 39% of the milk producers in order to minimize the damage. The identification of suitable entry sources may help risk managers to focus on these farms in a contingency plan that improves the sensitivity of control activities related to deliberate contamination.

This study was designed to evaluate the costs between 2005 and 2013 of the national bluetongue virus (BTV) surveillance and vaccination programmes before, during and after the BTV serotype 8 (BTV-8) outbreak in Austria commencing in 2008. In addition to an assessment of the temporal development of costs, a spatial cost analysis was performed. Within the context of this study, the term ‘costs’ refers to actual financial expenditure and imputed monetary costs for contributions in-kind. Costs were financed directly by the private–public sectors, by the European Commission (EC), and (in-kind) by responsible national institutions and individuals (e.g. blood sampling by veterinarians).The total net cost of the BTV-8 surveillance and vaccination programmes arising from the outbreak amounted to €22.8 million (0.86% of the national agricultural Gross Value Added), of which 32% was allocated to surveillance and 68% to the vaccination programme. Of the total programme costs, the EC supplied €4.9 million, while the remaining costs (€18 million) were directly financed from national resources. Of the latter, €14.5 million was classed as public costs, including €2 million contributions in-kind, and €3.4 million as private costs. The assessment of the costs revealed heterogeneous temporal and spatial distributions. The methodology of this analysis might assist decision makers in calculating costs for other surveillance and intervention programmes. The assessment of contributions in-kind is of importance to public authorities as it increases visibility of the available resources and shows how they have been employed. This study also demonstrates the importance of tracking changing costs per payer over time.

Aims Ileocaecal lymph nodes (ICLNs) of pigs, the key immune inductive site for bacterial systemic invasion, were examined in this study with emphasis on viable and cultivable bacteria. Methods and Results Asymptomatic and pathologically altered ICLNs of slaughter pigs (n = 16) with hyperplasia, purulence or granulomatous formations were aerobically and anaerobically cultivated. In total, 209 isolates were collected and the near full-length 16S rRNA gene from each isolate was sequenced. Taxonomic classification revealed that 68% of the isolates belonged to Proteobacteria, 27% to Firmicutes and 5% to Actinobacteria. Purulent and granulomatous ICLNs generally tended to contain more Proteobacteria than asymptomatic and enlarged ICLNs (P = 0·061). The isolates could be assigned to 25 species belonging to 17 genera including Escherichia, Carnobacterium, Lactobacillus, Staphylococcus and Acinetobacter. Furthermore, pathogens such as Streptococcus suis and Salmonella enterica were detected. The most abundant isolate (57%) was most similar (>99%) to Escherichia coli. Random amplified polymorphic DNA (RAPD) profiling revealed a high genetic diversity among E. coli isolates and 24% of these isolates were positive for at least one gene associated with enterohemorrhagic disease (eae, fliC, stx1 or hlyA). Compared with a recently published DNA-based high-throughput sequencing data set including the same ICLNs, 4% of species detected were cultivable. Conclusions The presence of viable, commensal and pathogenic bacterial phylotypes could be proven in ICLNs with Proteobacteria being dominant. Significance and Impact of the Study This is the first study that broadly characterizes viable bacteria from ICLNs of pigs. The presence of bacteria in lymph nodes of farm animals has practical relevance for host colonization and possible chronic infection. It is also of great interest for basic research investigating translocation of bacteria from the gastrointestinal tract to ICLNs.

Bovine viral diarrhoea (BVD) is a significant drain on efficient and successful cattle production in both dairy and beef systems around the world. Several countries have achieved eradication of this disease, but always through the motivation of stakeholders who accept the benefits of eradication. These include increased cattle welfare and fitness of cattle to withstand other diseases, and decreased costs of production, the latter resulting from both decreased costs spent on managing the disease and decreased losses. This paper provides a systematic review of 31 papers, published between 1991 and 2015, that address the economic impact of BVD. Each paper takes a different approach, in either beef or dairy production or both. However with the breadth of work collated, a stakeholder engaged in BVD eradication should find an economic figure of most relevance to them. The reported economic impact ranges from £0 to £552 per cow per year (£2370 including outliers). This range represents endemic or subclinical disease situations seen in herds with stable BVD virus infection, and epidemic or severe acute situations, most often seen in naïve herds. The outcome of infection is therefore dependent on the immune status of the animal and severity of the strain. The variations in figures for the economic impact of BVD relate to these immune and pathogenicity factors, along with the variety of impacts monitored.

This study evaluated the voluntary and compulsory implementation of a bovine viral diarrhoea virus (BVDV) eradication programme in the Austrian Federal State of Styria, Austria, from an economic point of view using ex-post assessment of costs and benefits (disease losses avoided). An economic net benefit (benefit:cost ratio, BCR = 1.18) of the programme was demonstrated during the voluntary programme phase (January 1998–July 2004). The break-even point was reached in 2003. If investments in the compulsory programme (August 2004–December 2016) were taken into account, a net economic loss (BCR = 0.16) was demonstrated. In contrast to on-going annual testing of all cattle herds, annual testing in accordance with a revised sampling scheme could reduce total surveillance costs by more than 77%. A Bayesian structural time series model was applied to analyse a hypothesised positive impact of the compulsory BVDV programme on the Styrian cattle export market. The average number of exported cows and bulls increased significantly by 42% (P = 0.03) and 47% (P = 0.01), respectively, and the producer price increased by 14% (P = 0.00) and 5% (P = 0.16), respectively, during the compulsory programme period compared with the period prior to intervention. This equates to an average revenue increase of €29,754 for cows and €137,563 for bulls per month. These results justify the implementation of eradication programmes, which initially may not appear to be economically viable, particularly if trade effects are not included in the calculations.

Bluetongue virus (BTV) is an emerging transboundary disease in Europe, which can cause significant production losses among ruminants. The analysis presented here assessed the costs of BTV surveillance and vaccination programmes in Austria and Switzerland between 2007 and 2016. Costs were compared with respect to time, type of programme, geographical area and who was responsible for payment. The total costs of the BTV vaccination and surveillance programmes in Austria amounted to €23.6 million, whereas total costs in Switzerland were €18.3 million. Our analysis demonstrates that the costs differed between years and geographical areas, both within and between the two countries. Average surveillance costs per animal amounted to approximately €3.20 in Austria compared with €1.30 in Switzerland, whereas the average vaccination costs per animal were €6.20 in Austria and €7.40 in Switzerland. The comparability of the surveillance costs is somewhat limited, however, due to differences in each nation’s surveillance (and sampling) strategy. Given the importance of the export market for cattle production, investments in such programmes are more justified for Austria than for Switzerland. The aim of the retrospective assessment presented here is to assist veterinary authorities in planning and implementing cost-effective and efficient control strategies for emerging livestock diseases.

The aim of this study was to collect information on the global distribution of the prevalence of bovine viral diarrhoea virus (BVDV) and respective mitigation programmes, using a questionnaire and literature review to provide as complete a picture of the worldwide BVDV situation as possible. This study collated information on 107 countries with respect to mitigation activities and 88 countries regarding BVDV infections during the observation period (1960-2017). A heterogeneous epidemiological situation for both BVDV prevalence and the presence of mitigation programmes was observed. The results of this analysis could be used to increase the visibility of the distribution of BVDV, to provide supporting data for global animal disease databases and to assist veterinary public health authorities in the decision-making processes to establish mitigation activities.

The trade of livestock is an important and growing economic sector, but it is also a major factor in the spread of diseases. The spreading of diseases in a trade network is likely to be influenced by how often existing trade connections are active. The activity α is defined as the mean frequency of occurrences of existing trade links, thus 0

Subacute ruminal acidosis (SARA) is a prevalent metabolic disorder in cattle, characterized by intermittent drops in ruminal pH. This study investigated the effect of a gradual adaptation and continuously induced long-term SARA challenge diet on the epimural bacterial community structure in the rumen of cows. Eight rumen-cannulated nonlactating Holstein cows were transitioned over 1 wk from a forage-based baseline feeding diet (grass silage-hay mix) to a SARA challenge diet, which they were fed for 4 wk. The SARA challenge diet consisted of 60% concentrates (dry matter basis) and 40% grass silage-hay mix. Rumen papillae biopsies were taken at the baseline, on the last day of the 1-wk adaptation, and on the last day of the 4-wk SARA challenge period; ruminal pH was measured using wireless sensors. We isolated DNA from papillae samples for 16S rRNA gene amplicon sequencing using Illumina MiSeq. Sequencing results of most abundant key phylotypes were confirmed by quantitative PCR. Although they were fed similar amounts of concentrate, cows responded differently in terms of ruminal pH during the SARA feeding challenge. Cows were therefore classified as responders (n = 4) and nonresponders (n = 4): only responders met the SARA criterion of a ruminal pH drop below 5.8 for longer than 330 min/d. Data showed that Proteobacteria, Firmicutes, and Bacteroidetes were the most abundant phyla, and at genus level, Campylobacter and Kingella showed highest relative abundance, at 15.5 and 7.8%, respectively. Diversity analyses revealed a significant increase of diversity after the 1-wk adaptation but a decrease of diversity and species richness after the 4-wk SARA feeding challenge, although without distinction between responders and nonresponders. At the level of the operational taxonomic unit, we detected diet-specific shifts in epimural community structure, but in the overall epimural bacterial community structure, we found no differences between responders and nonresponders. Correlation analysis revealed significant associations between grain intake and operational taxonomic unit abundance. The study revealed major shifts in the 3 dominating phyla and, most importantly, a loss of diversity in the epimural bacterial communities during a long-term SARA diet challenge, in which 60% concentrate supply for 4 wk was instrumental rather than the magnitude of the drop of ruminal pH below 5.8.

Infection with bovine viral diarrhea virus (BVDV) results in major economic losses either directly through decreased productive performance in cattle herds or indirectly, such as through expenses for control programs. The aim of this systematic review was to review financial and/or economic assessment studies of prevention and/or mitigation activities of BVDV at national, regional and farm level worldwide. Once all predefined criteria had been met, 35 articles were included for this systematic review. Studies were analyzed with particular focus on the type of financially and/or economically-assessed prevention and/or mitigation activities. Due to the wide range of possible prevention and/or mitigation activities, these activities were grouped into five categories: i) control and/or eradication programs, ii) monitoring or surveillance, iii) prevention, iv) vaccination and v) individual culling, control and testing strategies. Additionally, the studies were analyzed according to economically-related variables such as efficiency, costs or benefits of prevention and/or mitigation activities, the applied financial and/or economic and statistical methods, the payers of prevention and/or mitigation activities, the assessed production systems, and the countries for which such evaluations are available. Financial and/or economic assessments performed in Europe were dominated by those from the United Kingdom, which assessed mostly vaccination strategies, and Norway which primarily carried out assessments in the area of control and eradication programs; whereas among non-European countries the United States carried out the majority of financial and/or economic assessments in the area of individual culling, control and testing. More than half of all studies provided an efficiency calculation of prevention and/or mitigation activities and demonstrated whether the inherent costs of implemented activities were or were not justified. The dairy sector was three times more likely to be assessed by the countries than beef production systems. In addition, the dairy sector was approximately eight times more likely to be assessed economically with respect to prevention and/or mitigation activities than calf and youngstock production systems. Furthermore, the private sector was identified as the primary payer of prevention and/or mitigation activities. This systematic review demonstrated a lack of studies relating to efficiency calculations, in particular at national and regional level, and the specific production systems. Thus, we confirmed the need for more well-designed studies in animal health economics in order to demonstrate that the implementation and inherent costs of BVDV prevention and/or mitigation activities are justified.

Bovine viral diarrhoea (BVD) leads to substantial economic losses in beef and dairy herds worldwide. Two case-control studies were carried out using production data from 1996 to 2012 to analyse the impact of BVD virus (BVDV) on fertility in dairy herds in the province of Styria during an eradication programme. In study 1, herds in which at least one persistently BVDV-infected (PI) animal was detected (case herds) were compared to a group of control herds proven free from BVDV infection (contro herds). In study 2, within BVD infected herds the period during which P animals were present (exposed period) was compared to the period after successful BVD eradication (unexposed period). Calving interval (CAl) and the probability of a first service conception (FSC) were used as indicators in a mixed regression model to investigate the impact of BVD on reproductive performance. The model results indicated that BVD had a significant influence on CAl and FSC. Cows from control herds were 1.1 times more likely to conceive at first service compared to cows from case herds and cows served during the BVDV unexposed period were 1.3 times more likely to conceive at first service than those inseminated during the exposed period. In BVD-infected herds the CAI averaged seven days shorter in unexposed periods than in exposed periods. Besides BVD the animal breed and the parity substantially impact the analysed fertility indicators.

The aim of this paper is to analyze the structure of the trade network between milk producers, dairies and milk collection companies in Germany through a network analysis using suitable centrality measures. The study shows that structures exist among the relevant enterprises which are critical for the spread of a contamination in the German milk trade network. The results may be used to improve food security

The exploration of microbiomes in lymphatic organs is relevant for basic and applied research into explaining microbial translocation processes and understanding cross-contamination during slaughter. This study aimed to investigate whether metabolically active bacteria (MAB) could be detected within tonsils and mandibular lymph nodes (MLNs) of pigs. The hypervariable V1-V2 region of the bacterial 16S rRNA genes was amplified from cDNA from tonsils and MLNs of eight clinically healthy slaughter pigs. Pyrosequencing yielded 82,857 quality-controlled sequences, clustering into 576 operational taxonomic units (OTUs), which were assigned to 230 genera and 16 phyla. The actual number of detected OTUs per sample varied highly (23-171 OTUs). Prevotella zoogleoformans and Serratia proteamaculans (best type strain hits) were most abundant (10.6% and 41.8% respectively) in tonsils and MLNs, respectively. To explore bacterial correlation patterns between samples of each tissue, pairwise Spearman correlations (rs) were calculated. In total, 194 strong positive and negative correlations |rs| ≥ 0.6 were found. We conclude that (i) lymphatic organs harbor a high diversity of metabolically active bacteria, (ii) the occurrence of viable bacteria in lymph nodes is not restricted to pathological processes and (iii) lymphatic tissues may serve as a contamination source in pig slaughterhouses. This study confirms the necessity of the EFSA regulation with regard to a meat inspection based on visual examinations to foster a minimization of microbial contamination.

With the bluetongue virus serotype 8 (BTV-8) outbreak in 2006, vector monitoring programmes (according to EU regulation 1266/2007) were implemented by European countries to obtain information on the spatial distribution of vectors and the vector-free period. This study investigates the vector monitoring programmes in Austria and Switzerland by performing a retrospective cost analysis for the period 2006–2010. Two types of costs were distinguished: costs financed directly via the national bluetongue programmes and costs contributed in-kind by the responsible institutions and agricultural holdings. The total net costs of the monitoring programme in Austria amounted to €1,415,000, whereby in Switzerland the costs were valued at €94,000. Both countries followed the legislation complying with requirements, but differed in regard to sampling frequency, number of trap sites and sampling strategy. Furthermore, the surface area of Austria is twice the area of Switzerland although the number of ruminants is almost the same in both countries. Thus, for comparison, the costs were normalised with regard to the sampling frequency and the number of trap sites. Resulting costs per trap sample comprised €164 for Austria and €48 for Switzerland. In both countries, around 50 per cent of the total costs can be attributed to payments in-kind. The benefit of this study is twofold: first, veterinary authorities may use the results to improve the economic efficiency of future vector monitoring programmes. Second, the analysis of the payment in-kind contribution is of great importance to public authorities as it makes the available resources visible and demonstrates how they have been used.

In case of an outbreak of a foodborne disease, administrative decisions in the context of crisis management are only efficient if they follow standard practices and are specifically adapted to the outbreak situation in a timely manner. These goals are hard to achieve. The complexity of national and global trade structures obscures a clear view of trade flows and, consequently, it is often impossible to unravel complex trade links quickly. Furthermore, increasing public concerns about possible health hazards caused by global trade put additional pressure on decision makers. The aim of this paper was to unveil the specific trade structures of the German milk supply chain, to highlight how these structures could affect the spatial spread of a hypothetical contaminant, and to quantify the risk of the contaminant reaching the consumer. To achieve this goal, the vertical and horizontal trade links between milk producers, dairies, and consumers were taken into account. The horizontal flow of milk between dairies (inter-dairy trade), which is intended to compensate a temporary over- or undersupply of milk, is of special importance in this respect. We hypothesized that the extent of inter-dairy trade would significantly influence the spatial spread of contaminated milk and the contamination risk. This hypothesis was tested using a computer simulation model that predicts the hypothetical spread of a contaminant via trade of milk. The model parameters were estimated using trade data collected in 2004 and 2010. The results of our study indicate that inter-dairy trade significantly influenced the contamination risk. Compared with a scenario with no inter-dairy trade, the risk that contaminated milk will reach the consumer was up to 4 times higher, even with moderate inter-dairy trade. The contamination risk depended on the extent of inter-dairy trade in a nonlinear way and reached its maximum asymptotically when inter-dairy trade increased. The contamination risk exhibited considerable spatial variation, which could be utilized to implement more accurate food control interventions in times of crisis caused by a foodborne disease.

To minimize financial losses in times of crisis, it is necessary to prove methods of maintaining trade in a case of disease. This work shows that the identification of modules and clusters could be of high relevance if these clusters impede disease spread or if so-called Ad hoc-connector-points serving as routes of transmission between clusters could be identified. Furthermore the advantages of a risk-based selection of critical control points for surveillance or monitoring can be shown. This work provides new approaches to review and possibly optimize existing disease prevention and control strategies.