Extended Data Fig. 4: Exemplars of E. faecium transmission clusters.

Each row represents the hospital admission period(s) of patients with the exception of the top four rows, which show different environmental sources. Ward of admission is denoted as A or B, and the room numbered and color-coded. Visits to other hospital wards or areas are colored in grey. Positivity results for stool and environmental samples are shown as circles and squares, respectively. Blunt lines and arrowed lines are drawn to point to the putative sources of index and acquired subtypes respectively, the numbers adjacent to these lines indicating the minimum genetic distance observed between connected samples, which ranged from 0 to 6 SNPs. Solid and dotted lines denote strong and weak epidemiological links, respectively. (a) Exemplar of transmission cluster in the same ward (subtype 49A – ST1454). Strong genetic and epidemiological links point to transmission of this subtype in different rooms of ward B among patients D040, D037, D036, D044 and D041. Strong links to the hospital environment, including communal bathrooms and medical devices, suggest their involvement as reservoirs for onward transmission to patients. (b) Exemplar of transmission cluster spanning both hematology wards and involving 7 patients (subtype 26B – ST80). Strong genetic and epidemiological links point to transmission of this subtype in room A3 among patients C015, C023, C009 and D021, followed by spread in different rooms of ward B among patients D021, D022, D010 and D045.