The threat of multidrug resistant pathogenic bacteria looms in hospitals and communities worldwide. Efforts to use DNA sequencing to track and characterise outbreaks have typically been limited by their use of lower-resolution multi-locus sequence typing schemes. In this study, we use the higher resolution method of high-throughput whole-genome sequencing combined with phylogenetic methods to investigate the emergence of carbapenem-resistant A. baumannii in a hospital ward in Ho Chi Minh City, Vietnam. The data indicate that carbapenem-susceptible infections on the ward were due to a diverse range of A. baumannii clones that were also carried asymptomatically on the skin and respiratory tract of patients in the ward, suggesting that they were caused by the patients’ own colonizing bacteria. In contrast, carbapenem resistant infections were attributable to a single sublineage of the globally disseminated clone known as GC2, indicative of hospital transmission.