Phylogeography and Resistome Epidemiology of Gram-Negative Bacteria in Africa: A Systematic Review and Genomic Meta-Analysis from a One-Health Perspective

Objectives/Backgrounds: Antibiotic resistance (ABR) remains a major threat to public health and infectious disease management globally. However, ABR ramifications in developing countries is worsened by limited molecular diagnostics, expensive therapeutics, inadequate skilled clinicians and scientists, and unsanitary environments. Methods: Data on specimens, species, clones, resistance genes, mobile genetic elements, and diagnostics were extracted and analysed from English articles published between 2015 and December 2019. The genomes and resistomes of the various species, obtained from PATRIC and NCBI, were analysed phylogenetically using RAxML and annotated with Figtree. The phylogeography of resistant clones/clades was mapped manually. Results & conclusion: Thirty species from 31 countries and 24 genera from 41 countries were respectively analysed from 146 articles and 3028 genomes. Genes mediating resistance to {beta}-lactams (including blaTEM-1, blaCTX-M, blaNDM, blaIMP, blaVIM, blaOXA-48/181), fluoroquinolones (oqxAB, qnrA/B/D/S, gyrA/B and parCE mutations etc.), aminoglycosides (including armA, rmtC/F), sulphonamides (sul-1/2/3), trimethoprim (dfrA), tetracycline (tet(A/B/C/D/G/O/M/39)), colistin (mcr-1), phenicols (catA/B, cmlA), and fosfomycin (fosA) were mostly found in Enterobacter spp. and K. pneumoniae, and also in Serratia marcescens, Escherichia coli, Salmonella enterica, Pseudomonas, Acinetobacter baumannii, etc. on mostly IncF-type, IncX3/4, ColRNAI, and IncR plasmids, within IntI1 gene cassettes, insertion sequences and transposons. Clonal and multiclonal outbreaks and dissemination of resistance genes across species, countries and between humans, animals, plants and the environment were observed; E. coli ST103, K. pneumoniae ST101, S. enterica ST1/2 and V. cholerae ST69/515 were common strains. Most pathogens were of human origin and zoonotic transmissions were relatively limited. One Health studies in Africa are needed.