Conserved intracellular virulence architecture and focal genomic diversification in sub-Saharan African Brucella melitensis

Abstract

ABSTRACT Brucella melitensis has a highly conserved genome, but the distribution of core-genome, gene-content, virulence-associated, mobile-element-associated, and antimicrobial-resistance-relevant variation among available sub-Saharan African genomes has not been examined in an integrated regional analysis. We analyzed 51 curated B. melitensis genomes from human and animal hosts using core-genome phylogenomics, pangenome reconstruction, virulence profiling, mobile genetic element (MGE) analysis, and mutation-based screening of antimicrobial resistance (AMR)-associated loci. A phylogeny reconstructed from 6,060 shared SNP sites resolved a dominant ST12-associated lineage, together with ST7, ST8, ST42, and novel sequence type branches. Individual genomes differed from the reference by 1,677–2,579 SNPs. The pangenome comprised 3,457 gene families, including 3,049 persistent families, indicating strong genome conservation, and limited accessory expansion. Virulence profiling identified 66 VFDB-associated genes; 48 genomes carried all 66, and the remaining three retained more than 98% of the virulence repertoire. Conserved determinants included the VirB type IV secretion system, lipopolysaccharide biosynthesis, intracellular survival pathways, and stress-response functions. MGE-associated variation was restricted to a small number of regions dominated by transposases and insertion-sequence-associated proteins. A GspF-domain-containing secretion-associated locus was detected only in BM2, although no complete type II secretion system gene cluster was identified. Recurrent substitutions occurred in AMR-relevant chromosomal loci, including rpoB, gyrA, gyrB, parC, parE, folA, folP, bepCDEFG, and mprF, but none corresponded to validated resistance-conferring alleles. The available regional genomes therefore comprise multiple phylogenetic lineages within a strongly conserved gene and intracellular virulence framework, with diversity concentrated in core-genome SNPs and localized genomic regions. IMPORTANCE Brucella melitensis is a major zoonotic pathogen at the livestock-human interface, but genome-resolved evidence from sub-Saharan Africa remains limited. This study curates available regional genomes and shows that the population is dominated by a conserved intracellular virulence backbone, strong core-genome conservation, and focal genomic diversification rather than by extensive accessory-genome expansion. By integrating phylogenomics, pangenome analysis, virulence profiling, mobile-element characterization, and mutation screening of antimicrobial-resistance-associated loci, the work provides a regional framework for One Health genomic surveillance and identifies candidate loci requiring phenotype-linked validation. Brucella melitensis is a major zoonotic pathogen at the livestock-human interface, but genome-resolved evidence from sub-Saharan Africa remains limited. This study curates available regional genomes and shows that the population is dominated by a conserved intracellular virulence backbone, strong core-genome conservation, and focal genomic diversification rather than by extensive accessory-genome expansion. By integrating phylogenomics, pangenome analysis, virulence profiling, mobile-element characterization, and mutation screening of antimicrobial-resistance-associated loci, the work provides a regional framework for One Health genomic surveillance and identifies candidate loci requiring phenotype-linked validation.