ODIN Laboratory Handbook Standard Operating Procedures for Pre-treatment of Environmental Samples, Pathogen Analytics and Whole Genome Sequencing
Authors: Al-Hello Haider ,   Finnish Institute for Health and Welfare (THL), Finland, Nyholm Outi ,   Finnish Institute for Health and Welfare (THL), Finland, Pitkänen Tarja ,   Finnish Institute for Health and Welfare (THL), Finland, Salmivirta Elisa ,   Finnish Institute for Health and Welfare (THL), Finland, Vainio Anni ,   Finnish Institute for Health and Welfare (THL), Finland, Valkama Kristiina ,   Finnish Institute for Health and Welfare (THL), Finland, Baraka Vito ,   The National Institute for Medical Research (NIMR), Tanzania, Lyimo Eric ,   The National Institute for Medical Research (NIMR), Tanzania, Mnyawonga Steven ,   The National Institute for Medical Research (NIMR), Tanzania, Msoma Edward ,   The National Institute for Medical Research (NIMR), Tanzania, Sebukoto Hillary ,   The National Institute for Medical Research (NIMR), Tanzania, Chuwa Modest ,   National Public Health Laboratory (NPHL), Tanzania, Claver Jackson ,   National Public Health Laboratory (NPHL), Tanzania, Mauki Ibrahim ,   National Public Health Laboratory (NPHL), Tanzania, Moremi Nyambura ,   National Public Health Laboratory (NPHL), Tanzania, Garba Zakaria ,   Clinical Research Unit of Nanoro/ IRSS-DRCO, Burkina Faso, Lompo Palpouguini ,   Clinical Research Unit of Nanoro/ IRSS-DRCO, Burkina Faso, Sibidou Yougbaré ,   Clinical Research Unit of Nanoro/ IRSS-DRCO, Burkina Faso, Tahita Marc ,   Clinical Research Unit of Nanoro/ IRSS-DRCO, Burkina Faso, Kabena Kabengele Melissa ,   University of Kinshasa, DRC, Maketa Vivi ,   University of Kinshasa, DRC, Ngelesi Evodie ,   University of Kinshasa, DRC, Kisala Mays ,   National Institute of Biomedical Research (INRB) Goma, DRC, Modadra Madakpa Brigitte ,   National Institute of Biomedical Research (INRB) Goma, DRC, Bodisa Matamu Tavia ,   National Institute of Biomedical Research (INRB) Goma, DRC, Kavira Muhindo Marie-Anne ,   National Institute of Biomedical Research (INRB) Goma, DRC, Ngimba Michel ,   National Institute of Biomedical Research (INRB) Goma, DRC, Kabuyaya Nzoloka Pascal ,   National Institute of Biomedical Research (INRB) Goma, DRC, Tsiwedi Tsilabia Esperance ,   National Institute of Biomedical Research (INRB) Goma, DRC
Published: February 2025

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.