Abstract
BackgroundDuring 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.ResultsIn 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/).ConclusionsWe 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.
Highlights
During outbreak of livestock diseases, contact tracing can be an important part of disease control
EpiContactTrace was tested during an FMD-outbreak contingency exercise in Sweden during 18-21st of October 2010
An EpiContactTrace-report was generated for each farm for which there was a suspicion or confirmed case according to the predefined exercise scenario
Summary
During outbreak of livestock diseases, contact tracing can be an important part of disease control. There are several reasons for preventing and controlling contagious diseases in livestock; securing food production, farmer economy, animal welfare and the zoonotic aspect. Both past and recent outbreaks have had large consequences both for the farming industry as well as other parts of the society [1,2]. For most diseases, moving animals is considered to be one of the major risks for spreading disease between herds [5] This is one of the main reasons for registering transport of livestock in national databases, i.e. to enable contact tracing in case of an outbreak [6]. The data are not always structured in such a way that information relevant for contact tracing or design of surveillance programmes can be accessed by the end user
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