LAUSR

Research aimed at understanding transmission networks, representing a network of "who infected whom" for an infectious disease outbreak, have been actively conducted in recent years. Transmission network models incorporating epidemiological and genetic data are valuable for elucidating disease transmission pathways. In this study, we reconstructed the transmission network of the foot-and-mouth disease (FMD) epidemic in Japan in 2010, and explored farm-level risk factors associated with increased risk of secondary transmission. A published, systematic Bayesian transmission network model was applied to epidemiological data of 292 infected farms and whole genome sequence data of 104 of the infected farms. This model can make inferences for known infected farms even lacking genetic data. After estimating the consensus network, the accuracy of the network was examined by comparison with epidemiological data. Then, risk factors inferred to have been sources of secondary transmission were explored using zero-inflated Poisson regression model. As far as we are aware, this study represents the largest FMD outbreak transmission network to be published by such means combining epidemiological and genetic data. The consensus network reasonably generated the epidemiological links, which were estimated from the actual epidemiological investigation. Among 292 farms, 101 farms (35%) were inferred to have been the sources of secondary transmission, and amongst these farms, the median number of secondary cases was 2 (min:1-max:18) farms. The farm-type (small and large -sized pig farms), the number of days from onset to notification, and the number of susceptible farms within a 1-km radius were significantly associated with secondary transmission. Transmission network modelling enabled inference of the connections between infected farms during the FMD epidemic and identified important factors for controlling the risk of secondary transmission. This study demonstrated that the predominant susceptible species held on a farm, farm size, and animal density were associated with increased onwards transmission.