Evolutionary origins of the emergent ST796 clone of vancomycin resistantEnterococcus faecium

Abstract

From early 2012, a novel clone of vancomycin resistant Enterococcus faecium (assigned the multi locus sequence type ST796) was simultaneously isolated from geographically separate hospitals in south eastern Australia and New Zealand. Here we describe the complete genome sequence of Ef_aus0233, a representative ST796 E. faecium isolate. We used PacBio single molecule real-time sequencing to establish a high quality, fully assembled genome comprising a circular chromosome of 2,888,087 bp and five plasmids. Comparison of Ef_aus0233 to other E. faecium genomes shows Ef_aus0233 is a member of the epidemic hospital-adapted lineage and has evolved from an ST555-like ancestral progenitor by the accumulation or modification of five mosaic plasmids and five putative prophage, acquisition of two cryptic genomic islands, accrued chromosomal single nucleotide polymorphisms and a 80 kb region of recombination, also gaining Tn1549 and Tn916, transposons conferring resistance to vancomycin and tetracycline respectively. The genomic dissection of this new clone presented here underscores the propensity of the hospital E. faecium lineage to change, presumably in response to the specific conditions of hospital and healthcare environments.

Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium

“…3). This finding is in line with previous reports which showed that isolates from clade A1 are enriched for mobile genetic elements (6,17).…”

State-Wide Genomic and Epidemiological Analyses of Vancomycin-Resistant Enterococcus faecium in Tasmania’s Public Hospitals

“…The origins of ST796 can be traced back to Australia, where it was first discovered in 2012, and subsequently identified as the source of a notable increase in VREfm colonization at a Melbourne neonatal intensive care unit in 2013 (Lister et al, 2015). By 2015, ST796 had become the dominant vanB sequence type among patient episodes of E. faecium bacteremia in Melbourne hospitals (Buultjens et al, 2017) displacing the previously endemic vanB sequence type ST203 (Coombs et al, 2014b). The ability of ST796 to establish relatively quickly in new geographical locations and out-compete existing strains of VREfm suggests the potential existence of inherent advantageous properties in this sequence type.…”

“…The ability of ST796 to establish relatively quickly in new geographical locations and out-compete existing strains of VREfm suggests the potential existence of inherent advantageous properties in this sequence type. Indeed, generation of a complete genome sequence for an ST796 isolate revealed that it likely evolved from an ST555-like ancestral progenitor through the acquisition of transposons Tn1549 and Tn916 conferring resistance to vancomycin and tetracycline, respectively, along with plasmids, prophages, cryptic genome islands, and chromosomal SNPs (Buultjens et al, 2017). Similarly, the recently described ST1421 VREfm strain has been identified as a variant of the ST17 strain due to a mutation in the housekeeping gene, pstS, that is used for MLST (Andersson et al, 2019).…”

Vancomycin-Resistant Enterococcus: Issues in Human Health, Animal Health, Resistant Mechanisms and the Malaysian Paradox

“…These tools have successfully categorized E. faecium into clades A and B (Lebreton et al, 2013;Hullahalli et al, 2015). Clade A usually involve hospital infection related to humans and subdivided into two; that which is a species in a hospital during an epidemic referred to as A1 and that which occurs in livestock and humans in an unpredictable manner and clade B which are mostly found within the community and are not hospital-based (Mikalsen et al, 2015;Buultjens et al, 2017).…”