Genomic and spatial heterogeneity of Brucella melitensis underscores latent brucellosis risks in non-endemic zones in Southwest China

Zoonotic pathogens are increasingly emerging in previously low-risk regions with the accelerating process of globalization. Understanding the genomic evolution and spatial dissemination of these pathogens is essential for the rapid response and targeted control of future outbreaks. Brucellosis, caused by Brucella melitensis, is one of the global neglected zoonotic diseases now expanding beyond its traditional endemic zones. Here, we present the comprehensive genomic analysis of B. melitensis isolates from an emerging hotspot of human brucellosis in Southwest China. A total of 103 isolates were collected from 10 cities across Yunnan in 2019-2022. Phylogenetic analyses of the 850 global genomes revealed the coexistence of a dominant lineage (Lineage 1.1) and a novel lineage (Lineage 1.3) in non-epidemic regions in Southwest China. Importantly, we identified lineage-specific patterns of genomic differentiation, indicating the great variability of evolutionary dynamics among the co-circulating lineages. Our results showed higher rates of gene gain and loss events for Lineage 1.1, and a decrease in gene similarity along the gradient of spatial distance for Lineage 1.3. Additionally, spatiotemporal phylogeographic inference indicated that Lineage 1.1 has undergone recent interprovincial spread within China, while Lineage 1.3 remains geographically restricted to Yunnan. Our findings highlight the distinct evolutionary and transmission dynamics of B. melitensis in a non-traditional epidemic region. We provide critical insights into the value of genome-informed lineage-specific surveillance and targeted control strategies in addressing the emerging threat of neglected zoonotic diseases in the context of rapid ecological and social change.