Genomic analysis of 495 vancomycin-resistant Enterococcus faecium reveals broad dissemination of a vanA plasmid in more than 19 clones from Copenhagen, Denmark.
From 2012 to 2014, there has been a huge increase in vancomycin-resistant (vanA) Enterococcus faecium (VREfm) in Copenhagen, Denmark, with 602 patients infected or colonized with VREfm in 2014 compared with just 22 in 2012. The objective of this study was to describe the genetic epidemiology of VREfm to assess the contribution of clonal spread and horizontal transfer of the vanA transposon (Tn1546) and plasmid in the dissemination of VREfm in hospitals.



VREfm from Copenhagen, Denmark (2012-14) were whole-genome sequenced. The clonal structure was determined and the structure of Tn1546-like transposons was characterized. One VREfm isolate belonging to the largest clonal group was sequenced using long-read technology to close a 37 kb vanA plasmid.



Phylogeny revealed a polyclonal structure where 495 VREfm isolates were divided into 13 main groups and 7 small groups. The majority of the isolates were located in three groups (n = 44, 100 and 218) and clonal spread of VREfm between wards and hospitals was identified. Five Tn1546-like transposon types were identified. A dominant truncated transposon (type 4, 92%) was spread across all but one VREfm group. The closed vanA plasmid was highly covered by reads from isolates containing the type 4 transposon.



This study suggests that it was the dissemination of the type 4 Tn1546-like transposon and plasmid via horizontal transfer to multiple populations of E. faecium, followed by clonal spread of new VREfm clones, that contributed to the increase in and diversity of VREfm in Danish hospitals.
Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark mette.pinholt@regionh.dk.|Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
Mette
M
Pinholt
Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.
Heidi
H
Gumpert
Department of Biology and Biochemistry, University of Bath, Bath, UK.
Sion
S
Bayliss
Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.
Jesper B
JB
Nielsen
Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.
Veronika
V
Vorobieva
Department of Clinical Microbiology, Herlev University Hospital, Herlev, Denmark.
Michael
M
Pedersen
Department of Biology and Biochemistry, University of Bath, Bath, UK.
Edward
E
Feil
Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.
Peder
P
Worning
Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.|Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
Henrik
H
Westh
D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001426:Bacterial Proteins / Q000235:genetics*; D019729:Carbon-Oxygen Ligases / Q000235:genetics*; D002648:Child; D002675:Child, Preschool; D004251:DNA Transposable Elements; D003718:Denmark / Q000453:epidemiology; D016984:Enterococcus faecium / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D005260:Female; D022761:Gene Transfer, Horizontal; D014644:Genetic Variation; D005838:Genotype; D016908:Gram-Positive Bacterial Infections / Q000453:epidemiology / Q000382:microbiology*; D006801:Humans; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D058889:Molecular Typing; D010802:Phylogeny; D010957:Plasmids / Q000032:analysis*; D017422:Sequence Analysis, DNA; D065507:Vancomycin-Resistant Enterococci / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D055815:Young Adult
D001426:Bacterial Proteins; D004251:DNA Transposable Elements; C071437:VanA ligase, Bacteria; D019729:Carbon-Oxygen Ligases