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.