Pujolar J.M.,University of Aarhus |
Jacobsen M.W.,University of Aarhus |
Frydenberg J.,University of Aarhus |
Als T.D.,Technical University of Denmark |
And 7 more authors.
Molecular Ecology Resources | Year: 2013
Reduced representation genome sequencing such as restriction-site-associated DNA (RAD) sequencing is finding increased use to identify and genotype large numbers of single-nucleotide polymorphisms (SNPs) in model and nonmodel species. We generated a unique resource of novel SNP markers for the European eel using the RAD sequencing approach that was simultaneously identified and scored in a genome-wide scan of 30 individuals. Whereas genomic resources are increasingly becoming available for this species, including the recent release of a draft genome, no genome-wide set of SNP markers was available until now. The generated SNPs were widely distributed across the eel genome, aligning to 4779 different contigs and 19 703 different scaffolds. Significant variation was identified, with an average nucleotide diversity of 0.00529 across individuals. Results varied widely across the genome, ranging from 0.00048 to 0.00737 per locus. Based on the average nucleotide diversity across all loci, long-term effective population size was estimated to range between 132 000 and 1 320 000, which is much higher than previous estimates based on microsatellite loci. The generated SNP resource consisting of 82 425 loci and 376 918 associated SNPs provides a valuable tool for future population genetics and genomics studies and allows for targeting specific genes and particularly interesting regions of the eel genome. © 2013 John Wiley & Sons Ltd.
Themudo G.E.,Copenhagen University |
Ostergaard J.,Kopenhagen Fur |
Ersboll A.K.,University of Southern Denmark
Preventive Veterinary Medicine | Year: 2011
Aleutian disease (Plasmacytosis) is caused by the Aleutian mink disease virus (AMDV), an autonomous parvovirus and affects many mustelid species, including the American mink (Neovisonvison). In Denmark, an eradication program reduced the prevalence of test-positive farms from 100% in 1976 to 15% in 1996. Nevertheless, the disease persists in the Vendsyssel district of Northern Jutland, despite the eradication efforts.In this study, we used spatial epidemiological analysis to test for spatial autocorrelation of the distribution of farms positive for the disease. We investigated 2375 farms in Denmark (342 of which were located in the Vendsyssel district), during the period 2000-2008. For the purpose of our study, a farm was considered positive when, on any test conducted in a year, at least three animals were tested positive. To detect spatial clusters, we performed a retrospective analysis with spatial scan statistics. We performed one analysis for each of the nine years (2000-2008). A separate analysis was conducted with only the farms in Vendsyssel included. The spatial cluster analysis revealed a significant cluster throughout the time period studied in Northern Jutland. The only exception was 2002 when an outbreak was detected in the southern part of Jutland, and not in the north. The farm-level prevalence of the disease in Denmark was highest in this year, suggesting that the outbreak in the south could have masked the persistent signal from the north; the northern cluster was still significant when analysing only the Vendsyssel populations. These results confirm that Northern Jutland continues to have a significantly higher number of cases than expected if the disease was randomly distributed. © 2011 Elsevier B.V.
Jensen V.F.,Technical University of Denmark |
Sommer H.M.,Technical University of Denmark |
Struve T.,Kopenhagen Fur |
Clausen J.,Kopenhagen Fur |
Chriel M.,Technical University of Denmark
Preventive Veterinary Medicine | Year: 2016
The American mink (Neovison vison) is used for commercial fur production in Denmark. In recent years, antimicrobial prescription for Danish mink has been increasing. In this study, the patterns and trends in antimicrobial use in mink were described and a multi-variable variance analysis was carried out with the objective of identifying risk factors for antimicrobial use on herd level. The study was based on register data for 2007-2012. Information on antimicrobial use was obtained from the national database VetStat, monitoring all medicinal products used for animals on prescription level. Data on microbiological feed quality was obtained from the Voluntary Feed Control under the Mink producers Organization, and data on herd size and the relation between farm and feed producer was obtained from the registers at Kopenhagen Fur, based on yearly reporting from the mink producers. Descriptive analysis showed a clear significant effect of season on antimicrobial use, with a peak in "treatment proportions", TP (defined daily doses per kg biomass-days) in May, around the time of whelping, and a high level in the following months. In autumn, a minor peak in antimicrobial use occurred throughout the study period. From 2007 to 2011, a 102% increase in annual antimicrobial TP was noted; on herd level, the increase was associated with an increasing frequency of prescription, and a decrease in the amounts prescribed in months with prescription. A binomial model showed that on herd level, the annual number of months with antimicrobial prescription was significantly (p < 0.01) affected by feed producer, veterinarian, disease (specific laboratory diagnosis) infection, herd size and year, with an interaction between feed producer and year. A log-normal model showed that in months with antimicrobial use, the TP on herd level was significantly (p < 0.001) affected by year, month (season), feed producer, feed quality score, veterinarian, herd size and laboratory confirmed diagnosis of specific infections; additionally the interaction terms year × feed producer and herd size × month were significant (p < 0.001).In conclusion, antimicrobial use on herd level was significantly associated with the microbiological food quality, the feed producer, and the veterinarian. The prescription patterns varied significantly between veterinarians, and some veterinarians were associated with both larger and more frequent prescriptions of antimicrobials at herd level. Herd size is associated with different prescription patterns. Finally, infection with Pseudomonas aeruginosa, astrovirus, influenza virus and Salmonella spp. was associated with an increase in antimicrobial use. © 2016 The Authors.
Espregueira Themudo G.,University of Southern Denmark |
Houe H.,Copenhagen University |
Agger J.F.,Copenhagen University |
Ostergaard J.,Kopenhagen Fur |
Ersboll A.K.,University of Southern Denmark
Preventive Veterinary Medicine | Year: 2012
Eradication of Aleutian disease was initiated in Denmark in 1976. The prevalence of positive farms has since then been reduced from 100% to only being continuously present in the region of Vendsyssel, Northern Denmark since 2004. In this study, we attempted to identify risk factors for the infection in this region based on logistic regression of spatial (environmental, neighbourhood) variables and biosecurity measures. Information on potential biosecurity (management) risk factors in the region was obtained from interviews in 342 registered farms in the region using a structured questionnaire. A total of 279 questionnaires were completed (response rate 82%). Additional spatial variables were included in the analysis. The study shows that farm size (the number of animals in the farm) and proportion of infected neighbouring farms were significant risk factors for infection with Aleutian Mink Disease Virus. These factors account for 35% of the variation of the infection status of mink farms located in Vendsyssel during 2009. These results indicate that only a coordinated effort from the farmers in the area will succeed in eradicating the disease from Denmark, because individual farms that have eradicated the disease will be at risk of re-infection from test-positive neighbours. © 2012 Elsevier B.V.