Integrating epidemiology with genomic tracing to uncover concealed transmission networks in a brucellosis outbreak, Shandong, China

Background: This study integrated epidemiological investigation with whole-genome sequencing to elucidate the transmission chain and pathogen characteristics of a 2023 brucellosis outbreak in Shandong Province, providing evidence for targeted prevention and control. Methods: Transmission chains were reconstructed through field epidemiological investigations, active case finding, and retrospective data review. Isolated strains were cultured and identified, followed by molecular tracing using multilocus variable-number tandem repeat analysis (MLVA) and core-genome single-nucleotide polymorphism (cgSNP) genotyping. Epidemiological and molecular data were integrated to assess transmission links. Results: bv. 1. cgSNP analysis showed that the nine bv. 3 strains formed a single clonal cluster (0 SNP difference) and grouped with historical Shandong strains, indicating sustained local transmission. The bv. 1 strain represented a separate infection event, genetically distinct from the main outbreak cluster. Integrated analysis confirmed a complete molecular-epidemiological concordance for 38.5% (10/26) of cases; the remaining 61.5% could not be definitively linked due to missing epidemiological data or lack of isolate recovery. Phylogenetic analysis further indicated co-circulation of multiple lineages in the region. Conclusion: This outbreak was primarily driven by the trade of locally infected sheep, facilitating regional spread. High-resolution molecular typing effectively complemented traditional epidemiology by uncovering concealed transmission chains and revealing the co-circulation of multiple lineages. These findings underscore the value of integrated molecular surveillance systems in key endemic regions to support human brucellosis control.