Standard Operating Procedures for Pre-treatment of Environmental Samples, Pathogen Analytics and Whole Genome Sequencing
Authors: Haider Al-Hello, Outi Nyholm, Tarja Pitkänen, Elisa Salmivirta, Anni Vainio, Kristiina Valkama,Vito Baraka, Eric Lyimo, Steven Mnyawonga, Edward Msoma, Hillary Sebukoto, Modest Chuwa, Jackson Claver, Ibrahim Mauki, Nyambura Moremi, Zakaria Garba, Palpouguini Lompo, Yougbaré Sibidou, Marc Tahita, Melissa Kabena Kabengele, Vivi Maketa, Evodie Ngelesi, Mays Kisala, Brigitte Modadra Madakpa, Tavia Bodisa Matamu, Marie-Anne Kavira Muhindo, Michel Ngimba, Pascal Kabuyaya Nzoloka, Esperance Tsiwedi Tsilabia
DOI: https://doi.org/10.48060/tghn.154
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.
CLICK HERE TO DOWNLOAD THE HANDBOOK.