Abstract
European Union legislation requires member states to keep national databases of all bovine animals. This allows for disease spread models that includes the time-varying contact network and population demographic. However, performing data-driven simulations with a high degree of detail are computationally challenging. We have developed an efficient and flexible discrete-event simulator SimInf for stochastic disease spread modelling that divides work among multiple processors to accelerate the computations. The model integrates disease dynamics as continuous-time Markov chains and livestock data as events. In this study, all Swedish livestock data (births, movements and slaughter) from July 1st 2005 to December 31st 2013 were included in the simulations. Verotoxigenic Escherichia coli O157:H7 (VTEC O157) are capable of causing serious illness in humans. Cattle are considered to be the main reservoir of the bacteria. A better understanding of the epidemiology in the cattle population is necessary to be able to design and deploy targeted measures to reduce the VTEC O157 prevalence and, subsequently, human exposure. To explore the spread of VTEC O157 in the entire Swedish cattle population during the period under study, a within- and between-herd disease spread model was used. Real livestock data was incorporated to model demographics of the population. Cattle were moved between herds according to real movement data. The results showed that the spatial pattern in prevalence may be due to regional differences in livestock movements. However, the movements, births and slaughter of cattle could not explain the temporal pattern of VTEC O157 prevalence in cattle, despite their inherently distinct seasonality.
Highlights
European Union legislation requires member states to keep a registry of all bovine animals in national databases [1, 2]
The use of real livestock data allows for disease spread models with data-driven introduction of population demographics and the time-varying contact network
Disease spread model The VTEC O157 infection dynamics was modelled in each holding with a stochastic within-holding model, coupled to other holdings through animal movements
Summary
European Union legislation requires member states to keep a registry of all bovine animals in national databases [1, 2]. The use of real livestock data allows for disease spread models with data-driven introduction of population demographics and the time-varying contact network. Performing detailed data-driven stochastic simulation is computationally challenging and requires efficient algorithms. Both model selection and parameter inference are challenging when exploiting rich livestock data in infectious diseases modelling [6]. Computational tools need improvements to allow network models to include epidemiologically relevant data [7]. We recently presented an efficient computational and flexible modelling framework for fast event-based epidemiological simulations of infectious diseases [8, 9]. The framework integrates within-herd infection dynamics as continuous-time Markov chains and livestock data as scheduled events
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