Complete genome sequencing and comparative analysis of the linezolid-resistant Enterococcus faecalis strain DENG1
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Original Paper
Complete genome sequencing and comparative analysis of the linezolid‑resistant Enterococcus faecalis strain DENG1 Zhijian Yu · Zhong Chen · Hang Cheng · Jinxin Zheng · Duoyun Li · Xiangbin Deng · Weiguang Pan · Weizhi Yang · Qiwen Deng
Received: 12 April 2014 / Accepted: 14 April 2014 © Springer-Verlag Berlin Heidelberg 2014
Abstract Genome level analysis of bacterial strains provides information on genetic composition and resistance mechanisms to clinically relevant antibiotics. To date, whole genome characterization of linezolid-resistant Enterococcus faecalis isolated in the clinic is lacking. In this study, we report the entire genome sequence, genomic characteristics and virulence factors of a pathogenic E. faecalis strain, DENG1. Our results showed considerable differences in genomic characteristics and virulence factors compared with other E. faecalis strains (V583 and OG1RF). The genome of this LZD-resistant E. faecalis strain can be used as a reference to study the mechanism of LZD resistance and the phylogenetic relationship of E. faecalis strains worldwide. Keywords Comparative genomics · Virulence factors · Antibiotic resistance Abbreviations LZD Linezolid MRSA Methicillin-resistant Staphylococcus aureus VRE Vancomycin-resistant Enterococci PAIs Pathogenicity islands Communicated by Erko Stackebrandt. Electronic supplementary material The online version of this article (doi:10.1007/s00203-014-0986-y) contains supplementary material, which is available to authorized users. Z. Yu · Z. Chen · H. Cheng · J. Zheng · D. Li · X. Deng · W. Pan · W. Yang · Q. Deng (*) Shenzhen Key Lab for Endogenous Infection, Department of Infectious Diseases, The Affiliated Shenzhen Nanshan Hospital, Guangdong Medical College, No 89, Taoyuan Road, Nanshan district, Shenzhen 518052, China e-mail: [email protected]
Introduction Enterococcus faecalis infections are among the most frequent causes of death in hospitals globally, and antibiotic resistance severely complicates the treatment of such infections (Arias and Murray 2012). Linezolid (LZD) is a member of a novel class of antibiotics and is highly effective against a number of clinically important gram-positive pathogens including methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococci and several others (Ager and Gould 2012). Recently, reports of LZD-resistant Enterococci have emerged in the clinic. LZD resistance arises from three mechanisms: mutations in the domain V region of 23S rRNA genes, acquisition of the ribosomal methyltransferase gene cfr and mutations in the rplD or rplC gene encoding the 50S ribosomal proteins (Ager and Gould 2012; Long and Vester 2012). Whole genome sequencing of laboratory-generated LZD-resistant Streptococcus pneumoniae recently revealed mutations in several new genes, including a chromosomally encoded methyltransferase and two ABC transporters, showing that genome level information facilitates the identification of genetic mutations involved in LZD resistance (Billal et al. 2011; Feng et
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