ODIN Protocol for Environmental Pathogen Surveillance in Sub-Saharan Countries
In the ODIN project, setting-up environmental surveillance system for multiple human pathogens is on-going in three sub-Saharan countries: Tanzania, Burkina Faso and the Democratic Republic of Congo (DRC). The goal is to develop a harmonized wastewater and environmental surveillance (WES) system to serve these regions, with the potential for expansion across other countries in sub-Saharan Africa. ODIN project has published a deliverable 2.2 that summarizes the planning and developing the environmental surveillance strategy, including the piloting phase of the wastewater and environmental surveillance for the selected priority pathogens. The deliverable was produced in the ODIN consortium Work Package 2 under the task 2.2 “Developing a proposal for a cost-efficient environmental surveillance strategy” which is done in close cooperation with the task 2.1 “Gathering information on the existing clinical and environmental surveillance systems”, task 2.3 “Preparing guidance and a handbook for microbiological investigations”, and task 2.4 “Collecting the environmental surveillance data”. The report also provides information on how the performance of laboratory methods were checked and metagenome sequence library production tested with environmental samples during the pilot sampling in Tanzania, Burkina Faso and the DRC.
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ODIN Laboratory Handbook – Standard Operating Procedures for Pre-treatment of Environmental Samples, Pathogen Analytics and Whole Genome Sequencing
ODIN project has published a handbook of the analytical workflow for processing environmental samples, generating whole genome sequence libraries and gathering the wastewater and environmental surveillance data generated for further use among the local health authorities and other stakeholders. The laboratory handbook contains detailed protocol for generating microbiological and genomic information from the collected environmental samples and bacterial isolates. The handbook will be used at the ODIN research laboratories to analyze the wastewater and environmental samples collected from the study sites during the monthly sampling campaign. The handbook was prepared in collaboration with clinical microbiology and water laboratories in Tanzania, Burkina Faso and the Democratic Republic of Congo to produce a common operation procedure for conducting ODIN environmental surveillance scheme. The procedure entails guidance for collecting the environmental samples, sample pretreatment protocols for each sample matrix, detailed laboratory methods for microbiological and molecular investigations and protocols for whole genome sequencing of environmental isolates. During the handbook preparation, we first identified the exact capacities at the microbiological expert laboratories in regards of conducting the desired investigations from wastewater and environmental samples and agreed on the list of microbial targets to be analyzed in each study location where the ODIN environmental surveillance system will be tested. Based on the methods described in the handbook, the establishment of integrated environmental multi-pathogen and AMR surveillance system for sub-Saharan countries is possible.
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