Draft Genome Sequences of Six Enterococcus faecalis Strains Isolated from Malaysian Clinical and Environmental Origins

ABSTRACT Enterococcus faecalis is known to cause a variety of nosocomial infections, including urinary tract infections. Antibiotic resistance and virulence properties in this species are of public concern. The draft genome sequences of six E. faecalis strains isolated from clinical and environmental sources in Malaysia are presented here.

E nterococcus faecalis is an opportunistic pathogen that is often recovered from urinary tract infections (UTIs). E. faecalis is known to cause infections mainly due to the expression of virulence factors associated with adherence of mucosal and abiotic surfaces (1). The number of complete or draft genome sequences available for E. faecalis as of April 2017 is 503, comprising the bulk of enterococcal genome sequences available. However, there is a poor representation of genomic sequences for enterococci from Malaysia with only approximately seven assemblies reported (2). In this study, six E. faecalis strains, designated S12, S13, S14, S15, S16, and S17, were sequenced. These six strains were previously isolated from water sources, farm animal feces, and UTI patients in Malaysia and selected on the basis of different pulsed-field gel electrophoresis pulsotypes reported in a previously published experiment (3), and different biofilm and attachment properties (our unpublished data).
Genomic DNA was extracted using a GF-1 bacterial DNA extraction kit (Vivantis, Malaysia), tagmented with Nextera XT (Illumina, USA) according to the manufacturer's instructions and sequenced on the MiSeq desktop sequencer located at the Monash University Malaysia Genomics Facility (2 ϫ 250-bp run configuration). The raw reads generated were trimmed (quality score limit of 0.05) and assembled de novo using CLC Genomics Workbench version 7.0 (CLC bio, Denmark). Genome annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline and the Rapid Annotations using Subsystems Technology server (4,5). The identification of acquired antibiotic resistance and virulence genes was performed with the web tools ResFinder and VirulenceFinder, respectively (6, 7). Contigs coding for each antibiotic resistance and virulence gene (represented by contig accession number) were filtered based on 90% identity to the reference sequence and are presented in Table 1.
Genomic statistics-mean coverage, N 50 contig length, number of contigs, assembly size, number of coding sequences, and number of tRNAs and rRNAs for the six assembled genomes are provided in Table 1. An orthologous average nucleotide identity tool based on OrthoANI values revealed a Ͼ98% similarity of all six strains to the whole genome of E. faecalis ATCC 19433 (PRJNA157741) (8).
Strain S14 harbors the complete gene cassette for vancomycin resistance, corroborating a previous wet lab report that recorded a MIC value of 64 g/mL (3), whereas strain S12 was found to have a tetracycline resistance gene (tetM) with a MIC value of 32 g/mL (3). In addition, all six strains harbor genes coding for virulence factorsgelatinase production (gelE), endocarditis antigen (efaA), collagen adhesion (ace), and biofilm-associated pili (eep)-that are associated with adherence and invasion of the host tissue among enterococcal strains (9). Genes ebpC and ebpR, which are also biofilm-associated virulence factors, were identified in all strains except S16 and S15, respectively.
Accession number(s). The whole genome shotgun project of E. faecalis strains S12, S13, S14, S15, S16, and S17 have been deposited in DDBJ/ENA/GenBank under the accession numbers listed in Table 1.

ACKNOWLEDGMENTS
The project was supported by the School of Science, Monash University Malaysia. We are grateful to Yin Peng Lee from the Monash University Malaysia Tropical Medicine and Biology Multidisciplinary Platform for her assistance in next-generation sequencing.