FOCAL - Foodborne Disease Epidemiology, Surveillance and Control in African LMIC
By Tine Hald 06 January 2021
Location/s:
Ethiopia,
Mozambique,
Nigeria,
Tanzania
FOCAL_Global_Sewage_Surveillance_Project_Diagram

Collaborating Institutions: 

  • Technical University of Denmark (DTU)
  • Eduardo Mondlane University (UEM)
  • Kilimanjaro Clinical Research Institute (KCRI)
  • University of Waterloo (WU)
  • Mountain Top University
  • University of Pretoria (UP)
  • Haramaya University (HU)

  • Otago University (OU) 

Project duration: 48 months (Nov 2018 to Oct 2022) 

Total budget (USD): $3,387,108

Principal Investigator: Prof. Tine Hald 

Project summary

Foodborne diseases (FBD) have a high public-health and economic impact worldwide, with developing countries, and particularly young children, bearing a disproportionately large part of the total burden. In FOCAL, we will estimate the burden of FBD in four African low-middle-income countries (LMIC) by combining different methodologies including population surveys, metagenomics analyses of sewage, literature review and analysis of available health-care surveillance data. In particular for children under 5 years of age, we focus on identifying the most important sources and risk factors for FBD by taking a One Health approach that links public-health surveillance data with pathogen occurrence data from food, animals and the environment (see Figure). We will compare samples from children with diarrhea with samples taken from their exposure environments using whole-genome sequencing (WGS), and we will investigate the role of contributing factors such as undernourishment, co-infections and living conditions. Overall, the results will provide the best evidence of the health impact of, and the relative contribution from different sources to foodborne infections in African LMIC.

Despite the evident importance of FBD in developing countries, few have prioritized implementation of surveillance and mitigation strategies. An important limitation is that the majority of these infections are transmitted not only through a variety of foods, but also through the environment (e.g. contaminated water), by zoonotic means (e.g. direct animal contact) and by person-to-person transmission. So in order for surveillance and control to be effective, both humans and their major infectious sources need to be covered, which typically requires the involvement of stakeholders from different administrative sectors. Ideally, surveillance of FBD should be integrated across sectors and provide real-time data on occurrences of all relevant pathogens. In FOCAL, we investigate whether metagenomics (MG) analyses of samples from humans, food and reservoirs is both an effective and efficient future approach for FBD surveillance in LMIC. MG is chosen because, it is a “one method takes all” approach, as it is based on detection of RNA/DNA, which are a “universal language“ common across pathogens, and the method can potentially be used to survey large populations for several pathogens at the same time. In addition, MG analysis is culture independent, allowing for almost real-time data generation, and data sharing in a standardized format. However, we also apply ‘traditional’ culturing methods followed by whole-genome sequencing of isolates for comparison. An important output of the project is a fully functioning surveillance platform, where public-health, animal health and food safety organizations can share and analyze cutting edge genomic pathogen data across sectors and countries.

Overall, we aspire to strengthen the cross-sectorial collaboration and capacity building within and between countries for prioritization and allocation of resources for FBD prevention, and to pave the way for a future approach for FBD surveillance in LMIC. Although, our research and developments are limited to four African countries, we envisage that the results and developed methodologies will be relevant and applicable to other LMIC on the African continent (and elsewhere).

Brief project status as of September 2020

The project has three subprojects:

  1. The population survey aims to estimate the incidence of diarrheal diseases and the burden of FBD in defined populations in the four countries under research. The approach is a mix of conducting face-to-face interviews with randomly selected participants and dissemination of the same questionnaire through a web application for self-enrolment. Interviews were delayed due to COVID-19, but are now up running in most countries again. At this point around 450 interviews in total have been recorded. The estimated diarrheal incidences per age and sex group will be used for estimating the burden of specific foodborne diseases (Salmonella, Campylobacter and pathogenic E. coli). For this, it is necessary to estimate how big a proportion of the diarrheal cases that are caused by these pathogens, i.e. the aetiology proportion. Here we apply different approaches including a systematic review of previous community studies, using data collected in subproject 2, and applying metagenomics sequencing to sewage samples (see subproject 3).

  2. The attribution study aims to investigate causes and sources of diarrheal diseases in children under 5 years in the four countries under research. Children with diarrhoea are sampled and their care givers asked about their possible exposure source and other potential risk and confounding factors using a structured questionnaire. During visits to the children’s households (when consent is given), samples are taken from exposure sources such as food, water and animals. We also sample nearby food/meat markets, grocery stores, and slaughter facilities, from where the children may have been exposed to food products. Kick-off of this subproject was delayed in all countries due to COVID-19, but is slowly starting up.

  3.  The sewage surveillance study aims at investigating the usefulness of applying metagenomics to sewage or waste water for monitoring infectious disease occurrence in a population. If we can reliably detect and quantify bacterial pathogens in sewage, this approach will also be used to estimate the aetiology proportion needed for estimating the burden of FBD as described under subproject 1. We collect samples of urban and rural sewage/waste water every 6 months in the four research countries and in the same populations as investigated in subproject 1 and 2. So far to rounds of samples have been collected in each country.

Project resources

The Technical University of Denmark is hosting the Center of Global Epidemiology (CGE) (http://www.genomicepidemiology.org/index.html), which develops and provide algorithms for rapid analyses of whole genome DNA-sequences and metagenomics samples, tools for analyses and extraction of information from sequence data and internet/web-interfaces for using the tools in the global scientific and medical community. FOCAL will apply the tools developed by CGE for data analyses.

The Technical University of Denmark is also leading the “Global Sewage Surveillance Project”, which will serve as proof‐of‐concept for applying metagenomic approaches for global surveillance of human infectious diseases with an initial focus on antimicrobial resistance from sewage collected in major cities around the world. In FOCAL, we will explore the usefulness of metagenomics for surveillance of foodborne disease by collecting samples from sewage, animal reservoirs and wastewater from food production facilities from four African countries. The research conducted in FOCAL is, therefore, highly relevant for the Global Sewage project and vice versa and the two projects will collaborate closely. More information on the metagenomics approach used in the Global Sewage project can be found on the project’s homepage: https://www.compare-europe.eu/Library/Global-Sewage-Surveillance-Project, and in this video: https://www.youtube.com/watch?v=Cp_B5ddbT40

Other useful information and links

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