Both methods 1 and 2 assume that MRSA acquisition events occur as a result of patient-to-patient transmission from known carriers and exclude observations where there are no potential source patients. An additional sensitivity analysis therefore extended method 2 by allowing for both patient-to-patient transmission and background transmission (for example, from colonized staff or persistent environmental contamination). If the daily probability of a susceptible patient on ward i at time t acquiring strain j from such background sources is q' ijt , then the P i1t term above is replaced by (1{q' i2t )(1{q i2t ) C i2(t{1) 1{(1{q' i1t )(1{q i1t ) C i1(t{1) À Á in the new model, with similar changes for other terms. When applying this model, q' i1t was assumed to vary by ward, MRSA type and study phase, but to remain constant within in a phase. Figure S1 Single admission reproduction numbers (R a ) estimated using method 2. Estimates (95% CIs) of the wardlevel reproduction number, R a , according to study phase, MRSA type and ward obtained using method 2 and assuming complete bacterial interference and no interaction between ICU 1 and ICU 2. (PDF) Protocol S1 Protocol for defining MRSA importation and acquisition events.