Web-GIS and livestock trace tools for epidemiological surveillance, control and management
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1
Experimental Zooprophylactic Institute of Abruzzo and Molise G. Caporale, Italy
In epidemic emergencies, an efficient management of outbreaks of animal diseases can be obtained only if the competent authority has access to updated and reliable information. In such situations, a quick generation and processing of information is required for a timely and efficient delivery of control and eradication activities. The impact of emerging diseases can be minimized through a well-prepared and strong surveillance system (1).
The main challenge faced by surveillance systems is the ability to expedite the process of collection and analysis of data. Following the confirmation of an outbreak of a contagious animal disease, a pressing question is the identification of the most likely sources of infection and
of the animals that might have further spread the disease. The efficiency of surveillance systems can be increased by using specific software for data collection and analysis to provide the competent authorities with tools for better focusing the surveillance activities and the disease control measures. Information systems are the crucial tool for making information available for risk analysis.
Several information systems have been developed at international and national levels, with the aim of helping the veterinary services in the prevention and management of epidemic emergencies.
At the international level, the World Animal Health Information System (WAHIS) of the World Organisation for Animal Health (OIE) is the reference for all national or regional systems. Through its web interface and e-alert system, WAHIS collects and disseminates a large quantity of information on animal disease outbreaks occurring worldwide (2).
In the European Union, the Animal Disease Notification System (ADNS), instituted by the Council Directive 82/894/EEC (subsequently amended by Commission Decision 2008/650/EC), provides the rapid exchange of information on outbreaks of contagious animal diseases between the authorities competent for animal health.
At the national level, in Italy the veterinary services have at their disposal a variety of disease specific and non-disease specific information systems. This paper is focused on the second case and, in particular, on the System for the notification of animal diseases (SIMAN) with its innovative aside system for tracing animal movements, called Trace GIS, and on the Wildlife Information System Web-GIS.
SIMAN collects data on outbreaks and has been in place since 2008. It is available on the website of the veterinary information systems of the Italian Ministry of Health (https://www.vetinfo.sanita.it), together with BDN and other National Information Systems. SIMAN is accessed by veterinary services of the local and regional levels, National Reference Laboratories, Italian Ministry of Health and Public Health Institutes. This system was developed to collect and make data available to the national veterinary services, and to dispatch data on outbreaks to the international Authorities (European Commission and OIE). Data and information collected by SIMAN were formatted according to the requirements of both ADNS and WAHIS (3). The SIMAN Web-GIS application provides users with tools to query the outbreaks database and produce interactive thematic maps, statistics and tables (figure 1). In addition to the query and map navigation tools, it also offers spatial analysis functions to perform proximity analysis like, for example, finding farms in a certain distance from one or more outbreaks using buffer or a custom drawing (figure 2). All search and analysis results can be exported in Excel format for further offline investigations and maps can be printed in PDF format.
Trace GIS has been developed to facilitate an approach that integrates techniques of Temporal Network Analysis and accounts the dynamic nature of animal trade to perform a quickly and efficiently trace-back and trace-forward activities from a specified seed and timeframe (4). The movement of animals along the edges of the network represents a major source of contact between populations of animals in the holdings of origin and destination and can be considered as a path for the diffusion of a disease, in particular when infectious diseases transmissible by direct contact are considered (5). In this way, the veterinary service can plan the inspections of farm in contact with the outbreak according to its level of risk, so expediting the process of disease control and eradication (3, 6). The Web-GIS application (figure 3) passes a series of input parameters to an R-based network model: date range, seed (structure id), species, direction of the trace (forward or backward). The result is displayed both as a thematic map and an interactive table full of useful information like the number of moved animals, the date of the movement and all the details of the moving and receiving holding (like the holding type: farm, market, staging point, etc. and its production type: milk, meat, wool, etc.).
The Wildlife Web-GIS (figure 4) aims to collect information useful for monitoring the health status of wild animal populations, to investigate domestic-wild interaction and possibly to plan ad hoc investigative actions to monitor wildlife. The application, now available as a prototype, is still under active development and it will include two sections. The first one will be the Early Warning section, with the purpose to provide the competent authority with a rapid alert system capable of highlighting the suspected cases given in the context of the general surveillance plan for diagnostic investigations. The system will allow searches selecting the reference period, the species of interest and the suspected cause of death. The second section will focus on the Epidemiological analysis aspects and its purpose is to provide a tool for the visualization, search and analysis of the georeferenced data on the health status of domestic livestock and wildlife. This section will allow viewing on the Web-GIS application negative and positive wild animals for a given disease, the grazing areas where at least one farm with at least one animal positive to the disease under examination is present, the outbreaks of the given disease that were notified in SIMAN.
SIMAN and Wildlife Web-GIS applications share the same architecture (figure 5). On the server-side, ArcGIS for Server spreads the spatial data stored in an Oracle RDBMS as protected ReST webservices. On the client-side, the open source OpenLayers JavaScript library has been used to build all the GIS functionalities, while the widget of the user interface has been developed using the Twitter Bootstrap CSS Framework to give a modern style to the application. The client application includes a Java part that is responsible to send to ArcGIS server the credential used to unlock the webservices and to retrieve (and transmit to the JavaScript part) the authorization token required to successfully perform Ajax requests asking for the webservices.
In the case of Trace GIS the server-side architecture is completely different and the full software stack is open source (figure 6). The network model was implemented using R and then spread as a webservice through the rApache open source software, providing the Apache module named mod_R that embeds the R interpreter inside the web server. The client Web-GIS application, instead, is very similar to the SIMAN and Wildlife ones and it has been developed using OpenLayers and Twitter Bootstrap. The client application sends an Ajax request with all the required parameters to the R-based webservice. The server-side R-model evaluate the request and produces a response that is sent back to the client application as a json object containing information about animal movements (edges) and the involved structures (nodes).
Any tool helping for better focusing the surveillance actions is fundamental, and the identification of points at major risk for the introduction and spread of infectious diseases has become a priority. Nowadays, Web-GIS application and geospatial web services are often used as decision support systems in public and animal health. Web-GIS applications represent the best way to show and share georeferenced information about disease distribution and outbreaks on the Internet. Basic and analytical applications of GIS in epidemiology can help in visualizing and analyzing geographic distribution of diseases through time, thus revealing space-temporal trends, patterns, and relationships that would be more difficult or obscure to discover in tabular or other visualization formats. The integration between network models based layers and Web-GIS applications adds the ability to show and identify the possible path of infections spread.
References
1. Merianos, A., 2007. Surveillance and response to disease emergence. Curr. Top. Microbiol. Immunol. 315, 477L 509.
2. Ben Jebara, K., 2007. WAHIS and the role of the OIE’s reference laboratories and collaborating centres. DevBiol (Basel) 128, 69–72.
3. Colangeli, P., Iannetti, S., Cerella, A., Ippoliti, C., Di Lorenzo, A., Santucci, U., Simonetti, P., Calistri, P., Lelli, R., 2011. The national information system for the notification of animal diseases in Italy. Vet. Ital. 47 (3), 303–312.
4. Bender-deMoll, S.and Morris, M., 2016. R Package “tsna” [Internet]. https://CRAN.R-project.org/package=tsna. Available: https://CRAN.R-project.org/package=tsna
5. Konschake, M., Lentz, H.H.K., Conraths, F.J., Hovel, P., Selhorst, T., 2013. On the robustness of in- and out-components in a temporal network. PLOS ONE 8 (2), e55223.
6. Iotti, B., Valdano, E., Savini, L., Candeloro, L., Giovannini, A., Rosati, S., Colizza, V., Giacobini, M., 2019. Farm productive contexts and the dynamics of bovine viral diarrhea (BVD)
Keywords:
Animal Health,
animal disease outbreaks,
Epidemiological surveilance,
Epidemiological management,
Early detection,
Social Network Analsysis,
Information System,
WebGIS,
ESRI ArcGIS,
r,
OpenLayers
Conference:
GeoVet 2019. Novel spatio-temporal approaches in the era of Big Data, Davis, United States, 8 Oct - 10 Oct, 2019.
Presentation Type:
Poster-session
Topic:
Operational GIS tools for policy-makers, planners, researchers
Citation:
Di Lorenzo
A,
Savini
L,
Candeloro
L,
Tora
S,
Cerella
A,
Di Sabatino
D,
Conte
A and
D'Alterio
N
(2019). Web-GIS and livestock trace tools for epidemiological surveillance, control and management.
Front. Vet. Sci.
Conference Abstract:
GeoVet 2019. Novel spatio-temporal approaches in the era of Big Data.
doi: 10.3389/conf.fvets.2019.05.00041
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Received:
10 Jun 2019;
Published Online:
27 Sep 2019.
*
Correspondence:
Mx. Alessio Di Lorenzo, Experimental Zooprophylactic Institute of Abruzzo and Molise G. Caporale, Teramo, Abruzzo, Italy, a.dilorenzo@izs.it