Genomic and Evolutionary Insights into Host-Specific Adaptation in Brucella melitensis Across Human and Animal Hosts

Background. Brucella melitensis is a major cause of brucellosis in humans and livestock worldwide, yet the genomic basis by which this largely conserved pathogen persists across distinct host environments remains incompletely understood. We aimed to characterize global population structure, the directionality of host transitions within the sampled host system, and whether host-type-associated genomic differentiation converges on specific functional pathways.Methods. We assembled and curated 754 publicly available B. melitensis genomes, generating staged datasets to balance breadth and metadata completeness. A recombination-filtered core SNP alignment from 543 genomes was used to reconstruct maximum-likelihood phylogeny and genotype structure. A subset of 192 genomes with complete host, location, and sampling year metadata was analyzed using strict-clock Bayesian phylodynamics to infer time-scaled history, demographic change, and host-transition dynamics under a BSSVS framework. Host-type-associated selection signals were assessed by integrating multiple statistics (F_ST, nucleotide diversity π and π-ratio, ΔAF, and gene-wise pN/pS; XP-EHH reported as exploratory), followed by functional annotation and KEGG pathway enrichment.Results. Global phylogenomic analyses resolved five well-supported genotypes with extensive lineage sharing between humans and livestock hosts. Time-calibrated inference supported predominantly twentieth-century diversification and a recent expansion signal, while discrete-trait analyses indicated a livestock-dominated transmission network with strong connectivity among small ruminants and cattle; putative rodent-linked transitions were detected but remain tentative due to sparse wildlife sampling. Despite similar genome-wide SNP burdens and broadly conserved mutation spectra across hosts, multi-method selection scans identified a restricted set of genomic regions showing consistent human–animal differentiation. Candidate genes were enriched in pathways related to membrane remodeling and CAMP resistance, base excision repair and stress tolerance, central carbon metabolism, and sulfur-dependent redox homeostasis.Conclusion. These results support a model in which cross-host persistence of B. melitensis is underpinned not by genome-wide divergence, but by pathway-level fine-tuning at a limited set of loci against a conserved genomic background, while emphasizing that inferences about wildlife-mediated routes require more systematic sampling.