Department of Disease Control and Epidemiology, SVA, National Veterinary Institute, 751 89 Uppsala, Sweden.
BMC Vet Res. 2014 Mar 17;10:71. doi: 10.1186/1746-6148-10-71.
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.
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/).
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.
在牲畜疾病爆发期间，接触者追踪可能是疾病控制的重要组成部分。动物的活动也与基于风险的监测和抽样有关，即评估传入的后果或传入的可能性时都是如此。在许多国家，动物运动数据的收集主要目的之一是为接触者追踪提供便利。然而，通常需要进行分析步骤才能检索出用于接触追踪或监测的适当信息。
在这项研究中，开发了一种开源工具，以对牲畜运动数据进行结构化处理，以便在疾病爆发期间实时进行接触追踪，并为基于风险的监测和抽样提供输入。该工具称为 EpiContactTrace，是用 R 语言编写的，使用网络参数入度、出度、传入接触链和传出接触链（也称为感染链），它们分别与向前和向后追踪有关。可以独立指定向后和向前追踪的时间范围，并可以一次在一个农场或在数据集中的所有农场进行搜索。提供了不同的输出；带有网络度量的数据集、在地图中可视化的联系人以及为每个农场自动生成的报告，这些报告以 HTML 或 PDF 格式提供，旨在供最终用户（即兽医当局、区域疾病控制官员和现场兽医）使用。EpiContactTrace 可在 R 项目网站（http://cran.r-project.org/web/packages/EpiContactTrace/）上作为 R 包获得。
我们相信，该工具可以帮助控制疾病，因为它可以快速从大型数据集结构化出重要的联系信息。可重现的报告使该工具具有强大的功能且无需手动编译数据。开源使其易于访问且可以轻松适应不同的需求。
