Comparative analysis of the first complete Enterococcus faecium genome

Abstract

Vancomycin-resistant enterococci (VRE) are one of the leading causes of nosocomial infections in health care facilities around the globe. In particular, infections caused by vancomycin-resistant Enterococcus faecium are becoming increasingly common. Comparative and functional genomic studies of E. faecium isolates have so far been limited owing to the lack of a fully assembled E. faecium genome sequence. Here we address this issue and report the complete 3.0-Mb genome sequence of the multilocus sequence type 17 vancomycin-resistant Enterococcus faecium strain Aus0004, isolated from the bloodstream of a patient in Melbourne, Australia, in 1998. The genome comprises a 2.9-Mb circular chromosome and three circular plasmids. The chromosome harbors putative E. faecium virulence factors such as enterococcal surface protein, hemolysin, and collagen-binding adhesin. Aus0004 has a very large accessory genome (38%) that includes three prophage and two genomic islands absent among 22 other E. faecium genomes. One of the prophage was present as inverted 50-kb repeats that appear to have facilitated a 683-kb chromosomal inversion across the replication terminus, resulting in a striking replichore imbalance. Other distinctive features include 76 insertion sequence elements and a single chromosomal copy of Tn1549 containing the vanB vancomycin resistance element. A complete E. faecium genome will be a useful resource to assist our understanding of this emerging nosocomial pathogen.

Fig 1

Analysis of the Enterococcus faecium AUS0004 complete genome. (A) Circular map of AUS0004 by comparative BLASTN analysis against the contigs from the partially assembled genomes of 11 E. faecium strains, showing the locations of a large chromosomal inversion and Aus0004 accessory genome elements. Track identification, moving outwards, is as follows: G+C content, GC skew (G-C/G+C), IS elements, E. faecium isolates (next 11 tracks, as listed here and in Table 1), followed by regions (red arcs) potentially acquired by HGT revealed by AlienHunter, location of prophage, Aus004 unique regions revealed by read mapping against 23 E. faecium genomes (blue arcs), and finally the location of the eight MLST genes. Dotted lines indicate likely replication origin (dnaA) and terminus (dif) and highlight a replichore imbalance, caused by a phiEnfa001-mediated chromosomal inversion. (B) NcoI optical map of E. faecium AUS0004 compared with in silico-derived NcoI map demonstrating correct chromosome assembly. (C) Artemis linear view of Aus0004 chromosome and plasmids (appended), with vertical blue bars identifying the positions of accessory genome elements as determined by read mapping against 23 publicly available partially assembled genome sequences. Increasing height of vertical blue lines on this map indicates increasing specificity for Aus0004.

Fig 2

(A) Neighbor-joining tree showing relationship of AUS0004 compared to 22 other publicly available E. faecium genome sequences. Phylogeny was inferred by alignment of the 54,250 variable nucleotide positions (gaps removed) among all 23 E. faecium strains. Strains belonging to ST17 are highlighted. Red dot indicates Aus0004. E. faecium 1_231_408 was used as an outgroup to root the tree. (B) Network structure revealed among the same strains by split decomposition analysis of the same data set. All nodes in both trees had greater than 90% bootstrap support (1,000 replicates).