Vancomycin-resistant Enterococcus faecium (VREfm) ST78 is a major subtype within the E. faecium clonal-complex 17 (CC17), a clinically significant group associated with nosocomial infections and outbreaks. During the period of active genomic surveillance, we observed an increasing trend of VREfm ST78 in a Brisbane hospital. To investigate the changing dynamics on the epidemiology of this strain, we performed analysis based on whole-genome sequencing (WGS) and epidemiological data.
Genomic DNA of 63 VREfm ST78 isolates derived from 60 patients and 1 environmental sample collected from routine surveillance of VRE were sequenced with Illumina. The sequence data were used to identify antimicrobial resistance and virulence genes, and to reconstruct the phylogenetic relationships. Complete genomes from international collections were used to contextualize isolates within global population. Single nucleotide polymorphism (SNPs) and patient ward sharing information were collectively analyzed to characterize closely related clusters and transmissions.
In silico genotyping confirmed all study isolates are multi-drug resistant VanB-type VREfm with virulence characteristics of the hospital-adapted strain. Phylogenetic analysis based on isolate’s recombination-adjusted core-genome SNPs identified two major phylogenetic clades (clade 1 and 2) separated by 253 SNPs. Comparison with publicly available ST78 and closely related genomes showed that the two clades were closely related with two different Australian regions, suggesting at least two separate introductions of ST78 into the hospital. Of which, clade 2 that consists of the majority of isolates had minimal genetic differences with a median of pair-wise SNP distances of 3 SNPs (IQR 2 - 12 SNPs) and so indicates an active cluster. Further investigation based on network clustering on pair-wise SNP distances revealed at least four closely related clusters were present, showing several recent transmissions. Inference on transmission trees suggested complex transmission routes with unsampled ST78 reservoirs within the setting.
In summary, we have performed a local genomic epidemiology of VREfm ST78 in a Brisbane hospital and highlighted the use of WGS and epidemiological information for better target future control measures.