A systematic review of whole genome sequencing evidence on zoonotic Brucella melitensis in Africa revealing lineage structure phylogenomic clusters antimicrobial resistance and genomic determinants

Abstract Brucella melitensis is a major zoonotic pathogen in Africa, yet its population structure and transmission dynamics remain poorly characterized due to the limited use of whole-genome sequencing (WGS). This systematic review synthesized all published WGS studies of B. melitensis from African settings to assess lineage distributions, phylogenomic patterns, antimicrobial resistance (AMR) determinants, and virulence repertoires. The review followed PRISMA 2020 guidelines and was prospectively registered in PROSPERO. PubMed, Scopus, and Embase were searched without date limits for studies generating or analyzing WGS data from B. melitensis isolates originating in Africa. Eligible studies reported primary genomic analyses, including lineage assignment, phylogenomics, AMR, or virulence profiling. Two reviewers independently screened records extracted data using a calibrated form and assessed methodological quality using the Joanna Briggs Institute (JBI) tools. Owing to methodological heterogeneity, findings were synthesized narratively. Of 96 records identified, nine studies met the inclusion criteria, representing six countries (Tunisia, Algeria, Egypt, Ethiopia, Tanzania, and South Africa) and 139 genomes. North African datasets were dominated by biovar 3 and sequence type (ST) 11 within West Mediterranean lineages, whereas East and Southern African studies showed ST12-dominated African-lineage clusters with several novel sequence types. Phylogenomic analyses consistently revealed tight within-country clusters (0–6 alleles or 0–2 SNPs) and substantially larger between-country and between-lineage distances. AMR determinants were limited to intrinsic loci such as mprF and bepC–G , with no classical acquired resistance genes detected. Virulence repertoires were highly conserved across regions, with intact LPS and type IV secretion system genes universally present. African B. melitensis populations form regionally distinct lineages with strong local clustering and conserved virulence and intrinsic AMR architectures. Major evidence gaps, particularly in West and Central Africa, highlight the need for coordinated, continent-wide genomic surveillance to inform One Health brucellosis control.