Evolutionary dynamics of Enterococcus faecium reveals complex genomic relationships between isolates with independent emergence of vancomycin resistance

• Published in: Microbial genomics Vol. 2; no. 1
• Main Authors: van Hal, Sebastiaan J., Ip, Camilla L. C., Ansari, M. Azim, Wilson, Daniel J., Espedido, Bjorn A., Jensen, Slade O., Bowden, Rory
• Format: Journal Article
• Language: English
• Published: England Microbiology Society 19.01.2016
• Subjects: Bacterial Typing Techniques; Enterococcus faecium - genetics; Enterococcus faecium - isolation & purification; Evolution, Molecular; Genome, Bacterial - genetics; Multilocus Sequence Typing; Phylogeny; Species Specificity; Vancomycin Resistance - genetics; transposon; Enterococcus faecium; multi-locus sequence typing; infection control; recombination; vancomycin resistance
• DOI: 10.1099/mgen.0.000048
• ISSN: 2057-5858

, a major cause of hospital-acquired infections, remains problematic because of its propensity to acquire resistance to vancomycin, which currently is considered first-line therapy. Here, we assess the evolution and resistance acquisition dynamics of in a clinical context using a series of 132 bloodstream infection isolates from a single hospital. All isolates, of which 49 (37 %) were vancomycin-resistant, underwent whole-genome sequencing. was found to be subject to high rates of recombination with little evidence of sequence importation from outside the local population. Apart from disrupting phylogenetic reconstruction, recombination was frequent enough to invalidate MLST typing in the identification of clonal expansion and transmission events, suggesting that, where available, whole-genome sequencing should be used in tracing the epidemiology of nosocomial infections and establishing routes of transmission. Several forms of the Tn -like element- gene cluster, which was exclusively responsible for vancomycin resistance, appeared and spread within the hospital during the study period. Several transposon gains and losses and instances of evolution were inferred and, although usually chromosomal, the resistance element was also observed on a plasmid background. There was qualitative evidence for clonal expansions of both vancomycin-resistant and vancomycin-susceptible with evidence of hospital-specific subclonal expansion. Our data are consistent with continuing evolution of this established hospital pathogen and confirm hospital vancomycin-susceptible and vancomycin-resistant patient transmission events, underlining the need for careful consideration before modifying current infection control strategies.