Results from method 2 showed broad agreement with these findings, but in contrast to method 1 made a priori assumptions about the timing of the changes in transmissibility (tables 2-3, figure S1 ). On both wards, averaging over all phases, there was about a 1 in 400 chance of a given susceptible patient acquiring MRSA from a particular MRSA-positive patient on a particular day (table 2) . When estimates of daily transmission probabilities from a single MRSA positive patient were constrained to take the same values for the TW and non-TW clones but were allowed to vary by ward and study phase, we found clinically significant variation between the four study phases in both ICUs (table 2). In particular, while estimates were similar in phases 1 to 3, there was a marked reduction in phase 4. There was no strong evidence that these joint estimates (for all MRSA clones) varied by ICU in any of the study phases (table 2) . These findings were robust to the assumptions made about acquisition events and times (supplementary table S3).