Modeling and simulation of the spread of VTEC

Escherichia coli O157:H7 is a toxin-producing type of E. coli that may cause serious and even deadly disease conditions in humans. Bovine cattle act as the main reservoir of the bacteria, carrying the bacteria for a limited amount of time during which the bacteria is shed to the free environment. Importantly, the animals show no sign of the disease and computational modeling is an important means by which to understand the actual spread of the bacteria. The simulation above shows the dynamics of the infectious pressure, essentially the amount of bacteria in the free environment. This simulation is very strongly data-driven as all actual animal transports are included, thus accurately taking the time-varying contact network into account. Also, the effect of the varying weather conditions is incorporated by using weather data as illustrated in the animation below.


  • SimInf is an R-package with the ability to simulate arbitrary models of epidemics using temporal contact data. The package can be found here, see also SimInf at CRAN. The SimInf manual is available via arXiv.
  • The modeling and the simulation method is described in P. Bauer, S. Engblom, S. Widgren: Fast event-based epidemiological simulations on national scales in Int. J. High Perf. Comput. Appl., 2016: (doi).
  • The epidemiological details and the veterinary investigations that went into this is found in: S. Widgren, S. Engblom, P. Bauer, J. Frössling, U. Emanuelson, and A. Lindberg: Data-driven network modelling of disease transmission using complete population movement data: spread of VTEC O157 in Swedish cattle in Veterinary Res. 47:81(1):1--17, (2016). (doi).
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    Stefan Engblom
    Last modified: Fri Nov 11 11:04:19 MEST 2016