Denote by S wjt , C wjt , and A wjt the number of patients on ward w on day t who are, respectively, susceptible to MRSA type j, known to be colonized or infected with type j, and found to be colonized or infected with type j for the first time on day t (having had a prior negative admission screening swab). Here we take C wjt to be the number of patients on ward w on day t who have had at least one previous positive swab with MRSA type j on or before day t. We take A wjt to be the number of patients on ward w who have their first positive swab with MRSA of type j on day t. In our default method 2 analysis we take S wjt as the number of remaining patients (i.e. those with no prior MRSA positive swabs during the current episode) excluding those patients who are discharged on day t since we assume that acquisitions on the day of discharge would be not be detected. The tree reconstruction approach (method 1), in contrast, does not require knowledge of S wjt to estimate reproduction numbers.