AntiMicrobial Resistance (AMR)
Since 2018, members of the AoS Health Initiative have been working to develop, pilot and implement an AMR One Health surveillance system, in support of the Foundation for Innovative New Diagnostics (FIND). The effort began under a Global AMR Innovation Fund (GAMRIF, UK Government) grant, during which a pilot system was developed and implemented in Zambia and Senegal. In 2021 the capabilities of the AoS Health AMR Surveillance System were expanded and the platform implemented in Nepal and Kenya, under the Fleming Fund regional grant programme. The objective of this work has been to establish a platform to rapidly build AMR surveillance capacity in low- and middle-income countries, enable better decision-making for AMR policy through automated data collection and reporting, and to use best practices for digital system implementation to better ensure adoption.
Software and tools within the AMR Surveillance System
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DHIS2 AMR Metadata Package: A metadata configuration package for DHIS2 that enables data collection, representation, and analysis of One Health AMR data. The system has been configured with a standard sample-based AMR data model that can be expanded depending on surveillance needs. It serves as the data endpoint for human, animal, environmental, food, and feed data. Indicators have been created for priority pathogen-antimicrobial combinations, and a standard set of AMR dashboards and reports have been created to visualize resistance trends. Users can leverage DHIS2 functionalities for creating and sharing their own dashboards, visualizations, and reports.
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Open Interop: An open-source interoperability tool that transforms and transmits data from any source into the DHIS2 system.
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ODC: A desktop-based data loading tool that sends data from spreadsheets or WHONET files to Open Interop for transmission to DHIS2.
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ODX: A desktop-based automated data cleaning tool for AMR AST data, enabling automated spelling and error correction, and facilitating AMR data standardisation. Cleaned spreadsheets can then be loaded into DHIS2. This application is designed to significantly reduce manual data management burden.
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GLASS Reporting Module: A reporting module that enables the automatic creation of GLASS reports (both RIS and Sample files) from the DHIS2 system that are ready for submission to GLASS.
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Supporting Software: The platform also includes software tools that support AMR surveillance and data management workflows, such as document management.
Innovation Spotlight: Data Management in Nepal
ODX is a bespoke desktop client. It was developed as part of the installation of an AMR One Health Surveillance System in Nepal as a means to significantly reduce the manual effort required to cleanse and standardise spreadsheet data from different laboratories. ODX can correct for common variations found within the data, such as spelling mistakes or date formats. Where this is not possible, ODX calls out errors that require a manual fix to allow the user to rapidly identify where data will not transmit. To enable country self-sufficiency, ODX has a ‘spell mappings’ component where users can add additional correction variations. The standardised data output that is produced by ODX ensures that data can consistently and cleanly be transmitted into a data end-point for further analysis.
Prior to the development of ODX, data from the 21 AMR labs in Nepal was manually cleansed by two data managers. Since each lab uses different software systems with varied data entry practices and spreadsheet outputs, the manual cleansing was a significant time burden and caused substantial analysis delay.