28 Isolates in this study are most closely related to strains from a variety of settings. The majority of isolates (52%) belong to Clade E (figure 1B), whose nearest sequenced relative is the Liverpool Epidemic Strain, a clone often isolated from patients in the UK and Canada with cystic fibrosis. 36 37 Isolates from Clade E were found in the buy 3-Methyladenine burns unit’s water and the ward environment, as well as from two patient’s wounds. However

it was never detected in the critical care unit. Clade E was detected throughout the study in a total of 10 different rooms (figure 2). Figure 1 An overview of all samples collected during the study in global phylogenetic context with other sequenced strains of Pseudomonas aeruginosa from the set of Stewart et al.28 Samples collected in this study are widely dispersed in the tree, which contains … Figure 2 A schematic view of the 300-day study of Pseudomonas aeruginosa in a burns centre and critical care unit. Time in days is shown along the x axis with bed numbers in the critical care unit and burns unit along the y axis. Each circular icon indicates a … Inferring potential transmission

events by WGS Microevolutionary changes occurring over rapid time-scales (ie, days to months) have been used to detect potential chains of transmission in hospital and community outbreaks.19–21 38 39 The number of distinct mutations between given isolates has been used to infer whether transmission events are likely to have occurred. Such inferences are aided by prior knowledge of mutation rates in similar populations. Two patients (1 and

4) in our study both had P. aeruginosa from Clade E isolated from their wounds. These isolates had an indistinguishable genotype from those present in water and the environment of the room they were nursed within (figures 1C and 3). This genotype was detected in the patient’s shower water after initial patient screening, during screening of the second patient admission, twice during the second patient’s stay and then 127 days later (days 27, 65, 89 and 216, respectively). When water isolates were positive, the genotype was also detected in wet environment sites (shower drain, shower rosette and patient’s trolley) on the same days. Patient 5 was nursed on the critical care unit due to concomitant medical problems. P. aeruginosa belonging to Clade Cilengitide G was isolated from sputum during this time. Identical genotypes were detected contemporaneously in the water from the associated sink and sink tap handle (see online supplementary appendix 4). Two further patients (patients 2 and 3) were positive for P. aeruginosa. Isolates from these patients belonged to Clade C and D, respectively. Neither clade was ever isolated from hospital water. In both cases, identical genotypes were detectable in the environment associated with the patient but these were not detected before or after the patients’ stay, indicating that the environment was not persistently contaminated.