Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin resistant Enterococcus faecium

Whole genome sequencing is increasingly applied to healthcare-associated vancomycin resistant Enterococcus faecium (VREfm) outbreak investigations using single bacterial colonies from individual patients. However, within-patient diversity could complicate transmission resolution. We sequenced 14 colonies from VREfm positive rectal swabs over a 1-month period on a haematology unit. In total, 224 isolates from 11 patients were sequenced. Carriage of 2-3 sequence types was detected in 27% of patients. Presence of antimicrobial resistance genes and plasmids was variable within isolates from the same patient and sequence type. We identified two dominant sequence types (ST80 and ST1424), with two putative transmission clusters of two patients within ST80, and a single cluster of six patients within ST1424. We found transmission resolution was impaired using fewer than 14 colonies, and therefore there is a need to capture and consider VREfm within-patient diversity to ensure accurate resolution of transmission networks.