Using whole genome sequencing to develop Antimicrobial Resistance Reference Facility for One Health in South Africa

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Antimicrobial resistance (AMR) in human pathogens is reaching a crisis point with many pathogens becoming multidrug resistant and thereby untreatable. Although much work has been done to improve surveillance for AMR in nosocomial pathogens and sexually transmitted infections, surveillance for resistance in food and waterborne pathogens, with the exception of typhoid fever, remains problematic in the developing world. This is further complicated in that AMR may not be related purely to antimicrobial use in humans, but may also be affected by antimicrobial use in food and domestic animals and the persistence of antimicrobial in the environment.
Whole genome sequencing (WGS) is proving to be a powerful tool in the identification of microbial evolution, including monitoring for the development of antimicrobial resistance. WGS is additionally the most exacting method to compare to bacterial isolates to confirm epidemiological linkage and has been invaluable in investigating food and waterborne outbreaks globally. International experience has shown WGS may be used as an alternative to conventional methods to characterise, serotype and define AMR in enteric pathogens.
This project proposes to develop WGS techniques in South Africa to characterise enteric bacteria from South Africa human, animal and environmental sources to promote the rapid investigation of food and waterborne disease outbreaks in the country, which remain a significant public health burden. Experience gained from this work will be shared across the subcontinent and possibly the greater sub-Saharan Africa region.
This project falls within: New technology innovations to improve surveillance. How can technology be used to improve and scale surveillance?