Evolutionary origins of the emergent ST796 clone of vancomycin resistant Enterococcus 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.

Keywords: Accessory genome; Antibiotic resistance; Comparative genomics; Enterococcus faecium; Evolution; Genome sequence; Hospital adapted; PacBio; Recombination; Vancomycin resistant.

Figure 1. Ef_aus0233 chromosomal optical map and BRIG plot.

(A) Optical map of the Ef_aus0233 chromosome. (B) Referenced based alignment of blast hits of Ef_aus0085, Ef_aus0004 and DO genomes against the aus0233 chromosome. Prophage elements and the Tn1549 VanB containing transposon are annotated as arcs in the outermost ring.

Figure 2. Comparisons of chromosomal architecture, genomic islands and recombining segments associated with the ST555-796 and ST796 clades.

(A) Alignment of fully assembled chromosomes of Ef_aus0233, Ef_aus0085, Ef_aus0004 and DO. (B) Conservation of recombining segments in the ST555-796 and ST796 MRCAs. (C) Core genome phylogeny aligned with gene content blocks for identified genomic islands. Colours indicate the MLST designations.

Figure 3. Nested core genome SNP phylogeny of the greater E. faecium population.

(A) E. faecium population tree containing the major division between the community and hospital associated clades (B and A). (B) Nested tree focusing on the A1 clade containing the hospital associated isolates. (C) Nested tree focusing on the ST555-796 containing clade. Nodes with less than 70% bootstrap support have been collapsed. The VSE ST796 isolate is located within the ST796 clade. (D) Pairwise core SNP comparisons of within and between group diversity for the ST555 and ST796 clades (ST555: 13 SNPs, ST796: 68 SNPs, ST555-796: 330 SNPs). Y-axis depicts the number of SNP differences, error bars indicate one standard deviation above and below the mean and points represent the minimum and maximum values.

Figure 4. Prophage gene content comparisons: the presence and absence of orthologs within each of the five phages that were identified in the Ef_aus0233 genome.

The phylogeny depicts the evolutionary relationships among the genomes. Colours indicate the MLST designations.

Figure 5. Plasmid gene content comparisons: the presence and absence of orthologs within each of the five plasmids that were identified in the Ef_aus0233 genome.

The phylogeny depicts the evolutionary relationships among the genomes. Colours indicate the MLST designations.