<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p><jats:italic>Mycobacterium abscessus</jats:italic>is an extensively drug resistant pathogen that causes pulmonary disease particularly in cystic fibrosis (CF) patients. Identifying direct patient-to-patient transmission of<jats:italic>M. abscessus</jats:italic>is critically important in directing infection control policy for the management of risk in CF patients. A variety of clinical labs have used molecular epidemiology to investigate transmission. However there is still conflicting evidence as to how<jats:italic>M. abscessus</jats:italic>is acquired and whether cross-transmission occurs. Recently labs have applied whole-genome sequencing (WGS) to investigate this further and in this study we investigate whether WGS can reliably identify cross-transmission in<jats:italic>M. abscessus</jats:italic>.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We retrospectively sequenced the whole genomes of 145<jats:italic>M. abscessus</jats:italic>isolates from 62 patients seen at four hospitals in two countries over 16 years.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>We have shown that a comparison of a fixed number of core single nucleotide variants (SNVs) alone cannot be used to infer cross-transmission in<jats:italic>M. abscessus</jats:italic>but does provide enough information to replace multiple existing molecular assays. We detected one episode of possible direct patient-to-patient transmission in a sibling pair. We found that patients acquired unique<jats:italic>M. abscessus</jats:italic>strains even after spending considerable time on the same wards with other<jats:italic>M. abscessus</jats:italic>positive patients.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>This novel analysis has demonstrated that the majority of patients in this study have not acquired<jats:italic>M. abscessus</jats:italic>through direct patient-patient transmission or a common reservoir. Tracking transmission using WGS will only realise its full potential with proper environmental screening as well as patient sampling.</jats:p></jats:sec><jats:sec><jats:title>Key points</jats:title><jats:list list-type="bullet"><jats:list-item><jats:p>Whole genome sequencing should replace current molecular typing used routinely in clinical microbiology laboratories.</jats:p></jats:list-item><jats:list-item><jats:p>Patient-to-patient spread of<jats:italic>M. abscessus</jats:italic>is not common.</jats:p></jats:list-item><jats:list-item><jats:p>Environmental screening may provide a better understanding acquisition of<jats:italic>M. abscessus</jats:italic>infections.</jats:p></jats:list-item></jats:list></jats:sec>