Common bacterial nosocomial pathogens have distinct dynamics from typical community pathogens and call for different analytical approaches. Important features of hospital epidemics with such organisms include: i) a host population that changes rapidly over time in comparison with the timescale of epidemic dynamics; ii) a high proportion of infected (or colonized) hosts who are already infected when they enter the population (the hospital or ward); iii) a dominant role for asymptomatic infection so infected hosts can usually only be identified using screening swabs, leading to large uncertainty in the timing of transmission events; iv) a lack of a well-defined serial interval or generation time (since asymptomatic carriage can persist for months or years, but transmission is only intermittently observed during hospital admissions). The probabilistic tree reconstruction approach described above (method 1) overcame these limitations by using a hazards-based approach applied to patient screening data to assign probabilities to potential source patients for observed Phase-specific estimates for the daily probability of a susceptible patient acquiring MRSA from an MRSA positive patient in the same ward, for ICU 1 and ICU 2 (without distinguishing between TW and non-TW strains). In the Combined row, the estimates are constrained to be the same in both wards, and the All phases column constrains the estimates to be the same in the four phases. acquisition events. Using hazards in this way to reconstruct epidemic trees and estimate reproduction numbers appears to have first been suggested by Kenah et al [36] . Results using this method were supplemented with a maximum likelihood approach (method 2) where the timing of cross-infection events was assumed to be known but which allowed estimation of the daily transmission probability, enabling us to study effects related to study phase and MRSA type while controlling for differences in length of stay. These methods were applied to data from two adjacent general ICUs in which admission and weekly MRSA screens and culture results from clinical samples identified patients admitted with and acquiring MRSA over a four year period. During that time there was sustained transmission with endemic MRSA and a newly introduced TW variant.