ODIN

The challenge

Conventional surveillance relies on analysis of clinical samples. An alternative strategy, increasingly used, is monitoring wastewater or environmental samples. This approach does not provide information about specific clinical cases, but it is a convenient way to identify which pathogen strains are present in a community and how their numbers change over time. 

Genomic sequencing enables the identification of multiple pathogens and strains in the same sample. Different pathogen strains can also be distinguished, and information can be gathered on the presence of antimicrobial resistance (AMR) genes. 

Wastewater surveillance has been widely used to monitor SARS-CoV-2 and is increasingly being applied to a wider range of pathogens. Key challenges include interpreting large volumes of raw sequence data, presenting analyses so policymakers can act on them, and managing sequence data and associated metadata (e.g., sampling time and location). 

The project

The ODIN project is introducing infrastructure and processes to pilot wastewater and environmental surveillance in Burkina Faso, the Democratic Republic of the Congo (DRC), and Tanzania. Sampling sites will be established at two cities of differing sizes in each of the three countries, targeting a variety of wastewater outlets and environmental water sources. The focus pathogens in each country will be agreed with local policymakers.

The project will also create a mobile surveillance laboratory – a converted bus that will be equipped with portable Nanopore sequencing technology and other molecular tools. When wastewater sampling detects an increase in a particular pathogen, the mobile surveillance laboratory will be deployed to conduct more detailed analyses to identify potential sources of infection and routes of transmission within the community.  

Other aspects of the project include an extensive training programme and the development of a framework for data sharing, within and between countries. It will work closely with national public health institutes and laboratories to build capacity within national systems. Team members will collaborate with policymakers to design semi-automated bioinformatics tools and dashboard visualisations, ensuring sequencing activities inform programme planning as quickly as possible.

The project will also address emerging scientific questions, such as the abundance of different strains and species of Vibrio, the bacteria that cause cholera. Data from environmental monitoring will be integrated with local health data to determine how the two might best be used together to detect and track outbreaks. The environmental sampling data will also be used to develop water and sanitation safety plans in study areas. 

Impact

The ODIN project will establish pilot capabilities for wastewater and environmental surveillance in three countries. It will:

• Provide public health officials with experience in setting up and managing environmental genomic surveillance systems.
• Create new tools to guide public health responses to water-borne pathogens.
• Offer additional opportunities to detect and respond rapidly to new outbreaks.

With waterborne diseases responsible for the bulk of infectious diseases in Africa, genomic environmental surveillance could provide an essential early-warning system and a means to monitor the effectiveness of public health interventions.