AMR Surveillance in Africa: Are We There Yet?

Delineating the burden of antimicrobial resistance (AMR), detecting outbreaks due to multidrug resistant-bacteria and monitoring AMR trends for the early warning of emerging/escalating AMR in humans, animals, plants and the environment requires high-quality AMR surveillance systems that generate representative, quality-assured data. AMR surveillance in Africa is largely laboratory-based and generates phenotypic data on causative bacterial pathogens and their susceptibility to a panel of antibiotics. Data reliability and validity, fidelity of laboratory methods and quality assurance are frequently cited limitations raising concerns on the utility of phenotypic AMR surveillance data for policy and practice action.Genomic AMR surveillance in Africa is limited to discrete research projects at Universities and research institutions that describe the resistome, mobilome, virulome and phylogeny using whole genomic sequencing and open-source bioinformatics tools in the main and genomic surveillance capacity is steadily increasing on the content. Genomic surveillance has showcased the mobility and fluidity of drug-resistant bacterial strains, antimicrobial resistance genes and their associated mobile genetic elements within and between humans, animals and the environment although regional phylogenomics is limited by the number of countries and the number and quality of whole genomes uploaded on open source databases. The concerns related to phenotypic and genomic data correlations, high costs, unstable supply chains and competing health priorities in resource-constrained settings precludes genomic surveillance becoming part of national AMR surveillance systems in Africa at this time. Countries should optimize the quality and representativeness of phenotypic surveillance and leverage the expansion in genomic capacity as a result of the COVID-19 pandemic to advance genomic AMR surveillance in Africa.