Project Objectives
1. To explore the social determinants, including sanitation-related service delivery failure related to
Campylobacteriosis risk
2. To integrate metagenomics and MLA to develop predictive models of risks to human health occasioned by
Campylobacter species contamination of source waters
3. To investigate ecological drivers of the persistence of Campylobacter species in contaminated source
water, and relate these to risk and poverty mapping in the selected study areas
4. To integrate the outcomes of objectives 1-3 into a comprehensive risk assessment framework that draws
on microbial ecology, risk and poverty mapping, NGS, and MLA and social drivers of exposure to
Campylobacter spp.
Study Design
(i) explore the link between incidences of Campylobacteriosis and social determinants, including sanitation-related service delivery failure (ii)explore ecological and social determinants of human health risk associated with exposure to Campylobacter-contaminated source water
iii) understand whether microplastics drive the persistence of antibiotic-resistant Campylobacter spp and their genes in source water and thus potential risk ;
(iv) integrate of Shotgun metagenomics and machine learning algorithm into comprehensive microbial risk assessment and development of predictive models for risk of Campylobacteriosis in the source water
Project Summary
South Africa remains one of the countries in the world with the widest disparities in wealth and access to resources. The majority of the population is overburdened with poverty-related diseases (PRD) such as HIV-AIDs, tuberculosis,
and diarrhoea. Despite the incidences of diarrhoea being as high as 10 per 1000 of children admitted to a tertiary
hospital in South Africa, the disease has not received much research attention compared to other PRD such as HIV/AIDs and tuberculosis. Campylobacteriosis, a disease caused by Campylobacter spp. is the main cause of
diarrhoea globally and in South Africa. Another critical dimension of Campylobacter infection of urgent relevance in
South Africa is Guillain-Barré syndrome (GBS), a neurological condition whereby the body's immune system incorrectly attacks part of its peripheral nervous system. Ingestion of faecal contaminated water is a principal risk factor for Campylobacteriosis. In South African urban centres, wastewater treatment works are overloaded, resulting in the discharges of poorly treated effluents into the receiving rivers. The urban poor, children and mothers as well as the adolescents who largely depend on rivers for recreational activities, spiritual activities such
as baptism, harvesting of medicinal plants from the riverside, and fishing, are at the most risk of
Campylobacteriosis. Given the link between diarrhoea, poverty, and environmental quality/sanitation, a more
integrated, systemic approach that pays attention to the multiple risk dimension associated with
Campylobacteriosis is crucial. Mapping the incidences of urban poverty, service delivery failure, as well as Campylobacteriosis, can provide policymaker- needed insights for comprehensive strategies for reducing the occurrence and potential risk associated with the disease in South Africa. Furthermore, microbial risk assessment is
useful to estimate microbial risks associated with contaminated surface water. The difficulty of culturing of Campylobacter spp. for risk assessment studies can be circumvented by using next generation sequencing (NGS).
By applying shotgun metagenomics, it is possible to sequence all the microorganisms within an environment to identify infectious etiologies and then by applying machine learning algorithms (MLA) to predict the risk from shotgun metagenomic sequences of an environmental sample. Therefore, this project will combine multiple approaches: NGS, MLA, microbial ecology, and risk mapping to attempt an integrated study of Campylobacteriosis-a key PRD in South African urban environments. The Swartkops River in the Nelson Mandela Bay Municipality (NMBM) and the Kowie River of Makana Local Municipality, of the Eastern Cape province in South Africa, are to be investigated in this study.
