WGS of 1058 Enterococcus faecium from Copenhagen, Denmark, reveals rapid clonal expansion of vancomycin-resistant clone ST80 combined with widespread dissemination of a vanA-containing plasmid and acquisition of a heterogeneous accessory genome

Abstract

Objectives: From 2012-2015, a sudden huge increase of vancomycin-resistant (vanA) Enterococcus faecium (VREfm) was observed in the Capital Region of Denmark. Clonal relatedness of VREfm and vancomycin-susceptible E. faecium (VSEfm) was investigated, transmission events between hospitals were identified and the pan-genome and plasmids from the largest VREfm clonal group were characterized.Methods: WGS of 1058 E. faecium isolates was carried out on the Illumina platform to perform SNPanalysis and to identify the pan-genome. One isolate was also sequenced on the PacBio platform to close the genome. Epidemiological data were collected from laboratory information systems.Results: Phylogeny of 892 VREfm and 166 VSEfm revealed a polyclonal structure with a single clonal group (ST80) accounting for 40% of the VREfm isolates. VREfm and VSEfm co-occurred within many clonal groups; however, no VSEfm were related to the dominant VREfm group. A similar vanA plasmid was identified in ≥99% of isolates belonging to the dominant group and 69% of the remaining VREfm.Ten plasmids were identified in the completed genome and approximately 29% of this genome consisted of dispensable accessory genes. The size of the pan-genome among isolates in the dominant group was 5,905 genes. Conclusions:Most likely, VREfm emerged due to import of a successful VREfm clone which has rapidly transmitted to the majority of hospitals in the region whilst simultaneously disseminating a vanA plasmid to pre-existing VSEfm. Acquisition of a heterogeneous accessory genome may account for the success of this clone by facilitating adaption to new environmental challenges.

Trend of clinical vancomycin-resistant enterococci isolated in a regional Italian hospital from 2001 to 2018

“…As in Denmark [22], the increase in VRE infections in our hospital could be related to the influx of new successful VRE lineages such as ST80. The increasing tolerance of VRE to the biocides used in hospital settings [21] and the renewed widespread use of vancomycin to treat severe infections caused by multidrug-resistant enterococci and MRSA may also be contributing factors.…”

Increase of vancomycin-resistant Enterococcus faecium strain type ST117 CT71 at Charité - Universitätsmedizin Berlin, 2008 to 2018

“…Thus, an overall increase of VRE may not be the only explanation for the rise of ST117/CT71. An increase in ST117 was also observed in other European countries such as Denmark (19), Switzerland (20), Norway (21), the Netherlands (22,23), Spain (24), and Portugal (25).…”

“…Enterococcus strains (19,20,27,28). The same set of virulence factors as in CT71 strains was also found in 15 other ST117 non-CT71 strains, mainly CT36, a CT frequently identified in 2015 (33%).…”

“…Zhou et al have demonstrated that both cgMLST and transposon analysis for the detection of horizontal gene transfer is important in order to understand the complex transmission routes and outbreaks of VREfm (22). Pinholt et al have reported a clonal expansion of one specific VREfm clone based on a vanA-plasmid that was transferred via horizontal gene transfer to already existing hospital-adapted vancomycin-susceptible E.faecium and, thus, generated new VREfm(19). The exchange of genomic material between VRE and VSE may be responsible for the dissemination of vanB resistance in Germany(32).…”

Increase of vancomycin-resistant Enterococcus faecium strain type ST117 CT71 at Charité - Universitätsmedizin Berlin, 2008 to 2018

“…The detected resistance genes (msrC, efmA, erm(B), dfrG, and aac(6')-Ii) and virulence factors (acm, esp, hylEfm, ecbA and sgrA) of CT71 strains have already been reported in connection with high risk Enterococcus strains (24,25,31,32). The same set of virulence factors as in CT71 strains was also found in 15 other ST117 non-CT71 strains, mainly CT36, a CT frequently identified in 2015 (33%).…”