Draft Genome Sequence of Multidrug-Resistant Enterococcus faecium Clinical Isolate VRE3, with a Sequence Type 16 Pattern and Novel Structural Arrangement of Tn1546.

Multidrug-resistant Enterococcus faecium has emerged as a nosocomial pathogen that may infect the body at various sites, including the gastrointestinal tract, and has serious implications in human health and disease. Here, we present the draft genome sequence of clinical strain VRE3, which exhibited a sequence type 16 (ST16) pattern and carried truncated Tn1546, a mobile genetic element encoding a high level of vancomycin resistance.

GENOME ANNOUNCEMENT

Enterococcus faecium is a Gram-positive nonmotile bacterium that constitutes part of the normal microbiota in both animal and human gastrointestinal tracts (1) and causes severe to life-threatening infections (2, 3). E. faecium VRE3 is a vancomycin-resistant clinical isolate obtained from Brooks Air Force Base, San Antonio, TX, USA. It lacks the vanR, vanS, orf1, and orf2 elements of Tn1546 (4). The vanR and vanS were replaced by orf29, orf30, and orf31 of pRUM-like plasmid (4) and were observed in contig 31. More recently, VRE isolates have been found to possess an altered left end of Tn1546, partially deleted orf1, and insertions between the vanS-vanH and the orf2-vanS genes (5, 6). A comparative data analysis indicated that VRE3 has novel features in Tn1546 that make it an interesting candidate strain to study the alternative regulatory mechanism for vancomycin resistance.

The genomic DNA of E. faecium VRE3 was extracted by using a Master Pure Gram-positive DNA purification kit (Epicentre Biotechnologies). TruSeq DNA library preparation and paired-end cluster kits (Illumina) were used for the DNA preparation and cluster generation. The Illumina HiSeq2500 system was used for sequencing. De novo assembly of a total of 25,585,258 high-quality paired-end reads, 100 bp in length, was conducted using the CLC Genomics Workbench version 6.5.1 (CLC Bio), and further genome annotation was performed using the GeneMarkS+ method in the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok). The draft genome sequence of E. faecium VRE3 was 2,820,231 bp in length with a G+C content of 37.8%, which is distributed in 142 contigs (N50 length, 60,432; average coverage, 40.0×) with 2,689 coding sequences (CDS) and 52 RNAs.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JSET00000000. The version described in this paper is the first version, JSET01000000.