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1.  EpiContactTrace: an R-package for contact tracing during livestock disease outbreaks and for risk-based surveillance 
Background
During outbreak of livestock diseases, contact tracing can be an important part of disease control. Animal movements can also be of relevance for risk-based surveillance and sampling, i.e. both when assessing consequences of introduction or likelihood of introduction. In many countries, animal movement data are collected with one of the major objectives to enable contact tracing. However, often an analytical step is needed to retrieve appropriate information for contact tracing or surveillance.
Results
In this study, an open source tool was developed to structure livestock movement data to facilitate contact-tracing in real time during disease outbreaks and for input in risk-based surveillance and sampling. The tool, EpiContactTrace, was written in the R-language and uses the network parameters in-degree, out-degree, ingoing contact chain and outgoing contact chain (also called infection chain), which are relevant for forward and backward tracing respectively. The time-frames for backward and forward tracing can be specified independently and search can be done on one farm at a time or for all farms within the dataset. Different outputs are available; datasets with network measures, contacts visualised in a map and automatically generated reports for each farm either in HTML or PDF-format intended for the end-users, i.e. the veterinary authorities, regional disease control officers and field-veterinarians. EpiContactTrace is available as an R-package at the R-project website (http://cran.r-project.org/web/packages/EpiContactTrace/).
Conclusions
We believe this tool can help in disease control since it rapidly can structure essential contact information from large datasets. The reproducible reports make this tool robust and independent of manual compilation of data. The open source makes it accessible and easily adaptable for different needs.
doi:10.1186/1746-6148-10-71
PMCID: PMC3974595  PMID: 24636731
Cattle-transport; Control strategies; Decision support systems; Epidemics; Eradication programs; Network analysis; GIS
2.  A survey of visitors on Swedish livestock farms with reference to the spread of animal diseases 
Background
In addition to livestock movements, other between-farm contacts such as visitors may contribute to the spread of contagious animal diseases. Knowledge about such contacts is essential for contingency planning. Preventive measures, risk-based surveillance and contact tracing may be facilitated if the frequency and type of between-farm contacts can be assessed for different types of farms. The aim of this study was to investigate the frequency and types of visitors on farms with cloven-hoofed animals in Sweden and to analyse whether there were differences in the number of visitors attributable to region, season, and type of herd. Data were collected from Swedish farmers through contact-logs covering two-week periods during four different seasons.
Results
In total, 482 (32%) farmers filled in the contact log for at least one period and the data represent 18,416 days. The average number of professional and non-professional visitors per day was 0.3 and 0.8, respectively. Whereas the number of professional visitors seemed to increase with increasing herd size, this relation was not seen for non-professional visits. The mean numbers of visitors per day were highest in the summer and in the farm category ‘small mixed farm’. Reports of the visitors’ degree of contact with the animals showed that veterinarians, AI-technicians, animal transporters and neighbours were often in direct contact with the animals or entered the stables and 8.8% of the repairmen were also in direct contact with animals, which was unexpected. In a multivariable analysis, species, herd size and season were significantly associated with the number of professional visitors as well as the number of visitors in direct contact with the animals.
Conclusion
In conclusion there was a large variation between farms in the number and type of contacts. The number of visitors that may be more likely to spread diseases between farms was associated with animal species and herd size.
doi:10.1186/1746-6148-9-184
PMCID: PMC3848732  PMID: 24040830
3.  The prevalence of atypical scrapie in sheep from positive flocks is not higher than in the general sheep population in 11 European countries 
Background
During the last decade, active surveillance for transmissible spongiform encephalopathies in small ruminants has been intensive in Europe. In many countries this has led to the detection of cases of atypical scrapie which, unlike classical scrapie, might not be contagious. EU legislation requires, that following detection of a scrapie case, control measures including further testing take place in affected flocks, including the culling of genotype susceptible to classical scrapie. This might result in the detection of additional cases. The aim of this study was to investigate the occurrence of additional cases in flocks affected by atypical scrapie using surveillance data collected in Europe in order to ascertain whether atypical scrapie, is contagious.
Results
Questionnaires were used to collect, at national level, the results of active surveillance and testing associated with flock outbreaks in 12 European countries. The mean prevalence of atypical scrapie was 5.5 (5.0-6.0) cases per ten thousand in abattoir surveillance and 8.1 (7.3-9.0) cases per ten thousand in fallen stock. By using meta-analysis, on 11 out of the 12 countries, we found that the probability of detecting additional cases of atypical scrapie in positive flocks was similar to the probability observed in animals slaughtered for human consumption (odds ratio, OR = 1.07, CI95%: 0.70-1.63) or among fallen stock (OR = 0.78, CI95%: 0.51-1.2). In contrast, when comparing the two scrapie types, the probability of detecting additional cases in classical scrapie positive flocks was significantly higher than the probability of detecting additional cases in atypical scrapie positive flocks (OR = 32.4, CI95%: 20.7-50.7).
Conclusions
These results suggest that atypical scrapie is not contagious or has a very low transmissibility under natural conditions compared with classical scrapie. Furthermore this study stressed the importance of standardised data collection to make good use of the analyses undertaken by European countries in their efforts to control atypical and classical scrapie.
doi:10.1186/1746-6148-6-9
PMCID: PMC2832631  PMID: 20137097
4.  A descriptive study of the prevalence of atypical and classical scrapie in sheep in 20 European countries 
Background
The development of active surveillance programmes for transmissible spongiform encephalopathies of small ruminants across Europe has led to the recent identification of a previously undetected form of ovine prion disease, 'atypical' scrapie. Knowledge of the epidemiology of this disease is still limited, as is whether it represents a risk for animal and/or public health.
The detection of atypical scrapie has been related to the use of only some of the EU agreed rapid tests. Information about the rapid tests used is not, as yet, available from public reports on the surveillance of transmissible spongiform encephalopathies in small ruminants. We collected detailed results of active surveillance from European countries to estimate and to compare the prevalence of atypical scrapie and classical scrapie in sheep for each country stratified by each surveillance stream; healthy slaughtered and found dead adult sheep.
Results
From the 20 participating countries, it appeared that atypical scrapie was detected in Europe wherever the conditions necessary for its diagnosis were present. In most countries, atypical scrapie and classical scrapie occurred at low prevalence level. The classical scrapie prevalence estimates were more variable than those for atypical scrapie, which appeared remarkably homogeneous across countries, surveillance streams and calendar years of surveillance. Differences were observed in the age and genotype of atypical scrapie and classical scrapie cases that are consistent with previous published findings.
Conclusion
This work suggests that atypical scrapie is not rare compared to classical scrapie. The homogeneity of its prevalence, whatever the country, stream of surveillance or year of detection, contrasts with the epidemiological pattern of classical scrapie. This suggests that the aetiology of atypical scrapie differs from that of classical scrapie.
doi:10.1186/1746-6148-4-19
PMCID: PMC2442063  PMID: 18544152

Results 1-4 (4)