Metagenomic Population-Based Surveillance of Antimicrobial Resistance In South Africa

The proposed project aims to investigate the prevalence of AMR in the human population and will work from the hypothesis that metagenomic sequencing of human sewage can be used to detect, and in combination with epidemiological / ecological modeling, explain and predict emergence and trends of AMR. Sewage will be sampled from eight cities and sites across South Africa, deep metagenomic sequenced, the raw data shared into a common global secure cloud and thoroughly analyzed for abundances of AMR genes, taxonomic composition and other genes of relevance using a standardized bioinformatics pipeline for this purpose.