In contrast to method 1, which excludes susceptible patients from the analysis and enables estimates only of the net (or effective) reproduction number, this method accounts for susceptibles in the model and therefore allows us to estimate the single-admission reproduction number (the transmission potential of an MRSA positive patient in an otherwise fully susceptibility ward). This will be greater than or equal to the net single-admission reproduction number, and determines the threshold epidemic behaviour [25] . A further difference is that this method allows the transmission potential of an MRSA positive patient to change over time, according to the current study phase. In contrast, method 1 makes no explicit assumptions about the timing of changes in the transmission potential, and net reproduction numbers for a particular time period relate to the transmission potential of patients admitted to the ward during that time period even though the actual transmission events may occur at a later time.