SILAB for Africa: laboratory information management system for African countries

Transcription

1 SILAB for Africa: laboratory information management system for African countries Patrizia Colangeli, Ercole Del Negro, Massimo Scacchia Istituto Zooprofilattico Sperimentale dell Abruzzo e del Molise G. Caporale, Campo Boario, ITALY p.colangeli@izs.it, e.delnegro@izs.it, m.scacchia@izs.it corresponding author: p.colangeli@izs.it ABSTRACT SILAB for Africa (SILABFA) consists of a web application employed as a supporting information system to the Laboratory diagnostic activity and developed by IT personnel of the Istituto Zooprofilattico Sperimentale dell Abruzzo e del Molise, G. Caporale (IZSAM), Italy, for the Veterinary Laboratories of the African Countries. The system is hosted on a local server accessible via any computer connected to LAN and, where facilities exist, from any computer with an Internet connection and traces out the whole procedure from the arrival of the sample to the Final Test Report. SILABFA system ensures the traceability of the diagnostic phase. This tool led to a considerable quality improvement of analysis results, made more efficient the management of diagnostic activity and allowed to collect data useful for management of diseases and allows to standardize and track all the diagnostic phases (it is compliant with ISO/IEC rules) and at the same time increases the efficiency of technical scientific services and quality of reporting (test reports). SILABFA can be connected to the Livestock traceability systems in use in the national veterinary services (e.g. LITS, NAMILITS). Until now, SILABFA is installed and used in Namibia's CVL, Botswana's BNVL, Zambia's CVRI, Zimbabwe's CVL and Tanzania's TVLA. Keywords: Diagnostic activity, Information System, Web application, Laboratory Information Management System (LIMS), Software open source, Animal Health, Food Safety. INTRODUCTION The SILAB for Africa application has been developed from the basic structure of Italian Laboratory Information Management System (SILAB) by the Istituto Zooprofilattico Sperimentale dell Abruzzo e del Molise, G. Caporale (IZSAM) during a cooperation program based on a bilateral agreement between Italy and Republic of Namibia for information exchange and scientific collaboration in the fields of interest (exotic diseases, food safety and risk analysis). SILAB for Africa (SILABFA) is based on a completely free software and runs on any operative system (not only Windows, but also Linux or Unix like). Furthermore, SILABFA is easily accessible, supports any language, is easy to administer, safe and highly customizable. SILABFA is a Laboratory Information Managements Systems (LIMS) automated electronic record-keeping function, ranging from paper systems to highly complex computer systems, and details the process through which a laboratory goes while processing a sample, testing it and then reporting the results to the submitter in a secure manner and charging appropriate fees for the testing, if necessary. Until now, SILABFA has been implemented into national veterinary laboratories of many countries. In fact SILABFA is now installed in Namibia's CVL, Botswana's BNVL, Zambia's CVRI, Zimbabwe's CVL and Tanzania's TVLA (figure 1). In Ethiopia and Uganda the pre-audit visit was performed to assess the feasibility and needs for implementation of SILABFA in the AU-PANVAC in Debre-Zeit and in the NADDEC in Entebbe. The FAO is the main SILABFA supporter and the request for LIMS has been expressed to FAO by other African countries. A software supporting diagnostic activity would be important to standardize the diagnostic process thus facilitating the accreditation process, to carry out epidemiological surveillance activities and rapidly notifying outbreaks. SILABFA led to a considerable improvement of diagnosis and alert capacities of Laboratories and will help it making the diagnostic activity more efficient and strengthening Laboratory capacities of epidemiological surveillance and alert. A better management of sampling and analysis activities will help to improve animal Health and Food Safety and consequently the socio-economic situation of the population. In fact, the reduction of disease and in particular zoonosis as well as greater safety of the food have a direct effect on human health. In addition, the increased efficiency of a laboratory, and in particular the accreditation according to UNI / ISO rule, is a pre-requisite for the country to access international trades. MATERIALS AND METHODS Technical Architecture SILABFA is a web application, hosted on a local server, accessible via any computer connected to LAN and, where facilities exist, from any computer with an Internet connection. Access is subject to user authentication by username and 97

2 password. It was developed using open source software and freeware only. The server Operating System can be Unix, Linux or Windows. It runs on Apache Tomcat web server using Java 2 Enterprise Edition (J2EE) technology platform. The Relational Database Management System (RDBMS) used is Oracle 10g Express. This free source product requires a server with a CPU, 1 Gb of RAM and 4 Gb hard disk. Reports are generated with Jasper Report, an open source reporting tool enabling writing, display, and printing to a printer and to PDF, HTML, Microsoft Excel, RTF, ODT, Comma-separated values and XML files. The application is code-oriented; internal codifications used are linked to descriptions. All codes and relevant descriptions are entered into domain tables; for example, all species of interest are codified so that in the data tables only codes are reported, while in domain tables codes are linked to the relevant description and additional information. The management of domain tables is run by the application: same tables can be accessed by everyone (clients, users..), some others (tests, assays, ) only by administrator role. Main General Features Able to support any language: both the user interface and the database support different languages simultaneously. Users can choose which language they prefer on every access. Easy to administer: every lab is independent of others, has its own administrator (not IT person). Every database table can be modified by administrator role (e.g.: adding a new test or method, or species). Administrator can create a new user or delete an old one or change user's role (figure 2). Secure accesses: highly customizable users and roles. All SILABFA s functionalities are accessible only for authenticated users with username and password. Users can change their password at any moment. Any user has a role assigned by administrator. The role limits access to functionalities and content (e.g.: a technician of Food Hygiene Section can only insert results of his section and not validate them). SILABFA can be supported by remote using an Internet connection. Daily automatic Backup available: disaster planning is also a critical function that involves all LIMS. A disaster can be as large as a facility fire or as small as the unexpected departure of a critical employee. Help desk service: In order to ensure the sustainability of the project, an English help desk service is daily available in Italy via Remote Control (figure 3). Main Functional Features (figure 4) Sample reception and acceptance: during samples acceptance, all requests and samples information are recorded. Data concerning the reason for testing, the area of competence (animal health, feed, food safety, etc.,), the person requesting the test and the sample s origin, beside its species, number and type of material are entered into the system. Other information (number of authorities report, number of aliquots, condition of sample, type of container ), necessary for sample management, can be provided. Additional information can be collect for epidemiological needs (e.g. in case of outbreak how many animals have died or been slaughtered, if any humans infected) and local administrator is able to add these new fields autonomously (figure 5). Distribution: after univocal identification, samples are properly prepared and distributed to the various departments to undergo requested tests. In order to reduce working time, samples distribution by groups is automatically performed: by selecting a distribution group (previously properly created), samples are distributed to all tests and laboratories included in the group. Entered data and distributions are reported on printed forms, which can be used both as data verification and as working sheets by the laboratories operators. Distributions can also be deleted. Results Entry: Laboratories operators, after receiving accepted matrixes, perform required tests according to assigned distributions and enter results into the information system. In some cases, data acquisition is done directly by connecting testing equipment with the system. Results Validation: after results are entered, the head Section validates them, in order to comply with general and specific requirements and satisfy customer needs. Until data are not validated, results cannot be communicated to the customer. Test Report: at the end of the diagnostic route of the sample, the test report is issued and sent to the customer requesting the test. The test report varies according to the test performed. The report is dispatched by or by mail after the head of the department has signed it. SILABFA implements automatic signature as well. Test Report Rectification: if it is necessary to rectify a test report already dispatched to customer, the report must be re-opened, the previous version is collected and the rectifications made. It is possible to have progress reports on registered samples by enquiring at any time about data entered so far (number of samples accepted, distributed, validated, etc ). Costs: SILAB For Africa doesn't require any license fee, it's free. Only the mission costs and a share of the cost of IT dedicated person have to be paid by a new country. Workplan: Due to past experiences, the possible steps to introduce a LIMS in a new laboratory (beneficiary) have to be as following: First step: pre-audit visit of Italian experts to know laboratory organization and pre-requisites (server-lan-pc'squality system) (2 days) Second step: 1-2 beneficiary s people (future SILABFA administrators) should come to the Italian Institute to see SILABFA in use and to fill the domain tables (2-3 weeks) 98

3 Third step: Italian experts go back to beneficiary's lab to install SILABFA and train the personnel of Reception and other 2-3 pilot sections. In general, this step lasts 3-4 weeks. Fourth step: Autonomously, with remote support, the trained people will be able to extend SILABFA use to entire LAB Fifth step: Italian team returns for annual audit visit (examinations with certificate for all roles) are foreseen. During all times, an Italian support service works via and remote support. DISCUSSION A successfully implemented LIMS will increase laboratory productivity, improve data accuracy, and increase the laboratory s overall effectiveness. This software can organize all the information that is pertinent to the laboratory and allows for rapid data retrieval and reporting. It also allows data to be accessible to others, promoting collaboration among different departments (figures 6 and 7). A LIMS like SILABFA can be a powerful tool that gives laboratory a competitive advantage over other laboratories, saving time and money. Benefits of SILABFA implementation include faster turnaround times, automation, increased productivity, higher quality of data, electronic reporting, and integration with other enterprise databases. A software supporting diagnostic activity has proved to be very important because it standardizes the diagnostic process, facilitating the accreditation process and the linkage between diagnostic results and response in the field. SILABFA is compliant to the ISO and is an important tool to help, maintain and simplify compliance with requirements of this ISO standard. In fact, the use of a LIMS is an integral part of the overall quality system, to streamline data management and reporting processes. Any LIMS would enable to monitor, on a continued basis and in real time, the dynamics of the health status of animal population and Food Safety and, in case of outbreaks, rapidly notify animal diseases. Without a system like SILAB For Africa, it's difficult for a Laboratory to carry out epidemiological surveillance, intended as an application of epidemiology for planning, management and assessment of veterinary activity. The possibility for SILABFA to be connected to other systems, such as the Livestock Identification and Traceability System (e.g. LITS in Botswana, NAMLITS in Namibia), will allow to insert data only once and make them immediately available for all that may be needed, enhancing the exchange of information and promoting a better communication among operators, even across the borders. SILABFA will increase the efficiency of each Laboratories involved, helping it to improve animal health level and Food Safety system inside the country and to respect animal health international standards. If several countries use the same (or similar) LIMS, the advantages and positive effects will be evident. Communication and cooperation among laboratories will be eased, epidemiological studies on a large scale could be facilitated and this will support the prevention and management of outbreaks. The use of SILABFA in different countries will facilitate the exchange of information and the creation of a regional network of laboratories. The SILABFA's implementation can help strategies adopted by different Governments that aim to control nationally and economically important animal diseases, prevent disease outbreak, Food Safety control, as well as improving sustainable livestock production and management practices. Furthermore, the initiative follows guidelines of World Organization for Animal Health (OIE), World Health Organization (WHO) and Food and Agriculture Organization (FAO), that promote multisectorial cooperation and the constitution of strong partnerships focused on One Health approach. CONCLUSIONS The control of trans-boundary disease depends mainly on rapid, accurate and reliable diagnostic tools supporting early detection, surveillance and response to disease outbreaks. A software supporting diagnostic activity is very important because it standardizes the diagnostic process, increasing the number of accredited tests and facilitating the linkage between diagnostic results and response in the field. An informative system for management of Lab enables to monitor, on a continued basis and in real time, the dynamics of the health status of population, carry out epidemiological surveillance activities and, in case of outbreaks, rapidly notify animal diseases. In few words, it would increase the efficiency of veterinary services, helping countries to respect Food Safety international standards and fulfill the export requirements, essential conditions to maintain the much needed EU market access. A more efficient management of veterinary services is also essential to improve food safety level in a country where surveillance activities are inadequate and only few cases of food borne disease outbreak are reported due to late reporting, lack of resources and improper sampling. Without a system like SILABFA it cannot monitor, on a continued basis, the dynamics of the health status of population and carry out epidemiological surveillance, intended as an application of epidemiology for planning, management and assessment of veterinary activity. SILAB for Africa is a tool used to enhance diagnosis and alert capacities of their central laboratory and therefore improve food safety in the countries and the access exports to international markets. Indirect beneficiary of the health status of the entire population that will benefit of a more efficient management of veterinary services with the consequent improvement of food safety and animal health in the country. Furthermore, the project will bring undeniable improvements at economic and social level. 99

4 A successfully implemented LIMS increases laboratory productivity, improves data accuracy, and increases the laboratory s overall effectiveness. It also allows data to be accessible to others, promoting collaboration among different departments and laboratories. The need to create greater networking of veterinary laboratories to enable rapid and fluid data transfer as well as collaboration is leading to the development of LIMS networks. Many African Countries have established an Animal Disease Surveillance System whose purpose is to provide information on animal diseases and other livestock production parameters and avail inferences for planning, implementing, monitoring, evaluating and re-planning disease control programs. A LIMS would enable the Laboratories monitor, on a continued basis and in real time, the dynamics of the health status of animal population and, in case of outbreaks, rapidly notify animal diseases. With a common dedicated LIMS, it is possible to build a Laboratory network for information sharing and it is easy to collect information from different African Regional Support Laboratories. For example BNVL is OIE Reference Laboratory for Contagious bovine PleuroPneumonia (CBPP) and Testing Centre for the export of livestock products. SILABFA system helps these Laboratories to standardize the diagnostic process, from submission of sample to reporting, and to carry out epidemiological surveillance activities and rapidly notify outbreaks. The implementation of a LIMS in each of these laboratories would largely benefit the quality of the information as well as the overall management of the laboratory. It is not a short-term investment and it will have a long-term effect on the vitality of the laboratory for many years following installation. The perspective of having the same system installed in a majority of African Countries is a unique opportunity as it will improve the laboratories diagnostic activities and will strengthen laboratory capacity for epidemiological surveillance, food safety and nationally and regionally alert. REFERENCES Colangeli P., Ferrilli M., Quaranta F., Malizia E., Mbulu R.S., Mukete E., Iipumbu L., Kamhulu A., Tjipura-Zaire G., Di Francesco C., Lelli R., Scacchia M. Laboratory information management system: an example of international cooperation in Namibia 2012 Veterinaria Italiana, 48 (3), Colangeli P., S. Iannetti, A. Cerella, C. Ippoliti, A. Di Lorenzo, U. Santucci, P. Simonetti, P. Calistri& R. Lelli, 2011: The national information system for the notification of animal diseases in Italy. Vet Ital Jul-Sep;47(3):303-12, Colangeli P., Ruggieri E., Mercante M.T., Ricci L : Once Upon a Time the Book of Technical: a Dematerialisation Experience EMMIT 2012 Nannini D., Giovannini A., Fiore G.L., Marabelli R. & Caporale V Quality assurance of veterinary services at the international level: a proposed approach. Rev Sci Tech, 18 (3), FIGURES Figure 1: Countries involved in SILABFA project up to 10 April

5 Figure 2: SILABFA users roles defined Figure 3: Helpdesk activities- years 2012 and The Network issues not solved include interventions on charge of local management. 101

6 Figure 4: Main functionalities (inside circle line) Figure 5: Additional information for disease report form 102

7 Figure 6: SILABFA Namibian CVL activities Figure 7: SILABFA Botswana's BNVL activities 103