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 strategies aimed at mitigating the disease’s substantial economic burden. 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 MLVA-16 and cgSNP genotyping. Epidemiological and molecular data were integrated to assess transmission links. Results A total of 26 related cases were identified in this outbreak. Epidemiological investigation revealed that the outbreak originated from a flock of infected lambs introduced by an index case in 2022, with subsequent spread through local livestock trading networks affecting multiple villages. Ten Brucella strains were isolated, including nine of B. melitensis bv. 3 and one of B. melitensis bv.1. cgSNP analysis showed that the nine bv. 3 strains formed a single clonal cluster (SNP difference = 0) 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 that incorporate shared human and animal data in key endemic regions to support coordinated brucellosis control.