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目的研究利奈唑胺耐药粪肠球菌的全基因组序列,并探讨与其它肠球菌序列的差异。方法从1例男性急性白血病患者的气管分泌物中分离到粪肠球菌株Deng1(E.fecalis Deng1)。通过Illumina Hiseq2000和Roche454 FLX+进行高通量全基因组鸟枪法测序(high-throughput whole-genome shotgun sequencing)。基因组Contigs和scaffolds通过Newbler汇编软件分析。基因组gap closures通过Sanger测序法确定。通过Phred/Phrap/Consed软件构建圆环型的基因组图,并通过软件Prokaryote Genomes Automatic Annotation Pipeline(PGAAP)进行基因组注释。参考序列和粪肠球菌Deng1基因组之间的系统发育分析(phylogenice analysis)通过muscle软件分析。结果 E.fecalis Deng1圆环形基因组包含2,961,043碱基对,GC含量37.5%。基因组含有2 854个编码序列(CDS),62个tRNA的编码基因,以及4个完整的rRNA基因编码的操纵子。E.fecalis Deng1基因组共有443个毒力因子。E.fecalis Deng1基因组致病岛(PAI)约170kb,含有编码溶细胞毒素、肠球菌表面蛋白Esp和Gls-24-样蛋白等的毒力因子,E.fecalis Deng1含有对链霉素高水平耐药的氨基糖苷类6-腺苷酰转移酶基因(aadK),以及与抗生素耐药相关的emea,lsa和tetM基因。结论完成了一株粪肠球菌完整基因组的测序分析,加深了对LZD耐药流行菌株的认识。
Objective To study the genomic sequence of linezolid resistant Enterococcus faecalis and to explore the differences with other enterococci sequences. Methods E. facalis Deng1 was isolated from the tracheal secretions of 1 male acute leukemia. High-throughput whole-genome shotgun sequencing was performed by Illumina Hiseq 2000 and Roche 454 FLX +. Genome Contigs and scaffolds were analyzed by Newbler assembly software. Genomic gap closures were determined by Sanger sequencing. Torus genomic maps were constructed using Phred / Phrap / Consed software and genomic annotated using the software Prokaryote Genomes Automatic Annotation Pipeline (PGAAP). Phylogenice analysis between the reference sequence and E. faecalis Deng 1 genome was analyzed by muscle software. Results The E. fecalis Deng1 circular genome contained 2,961,043 base pairs with a GC content of 37.5%. The genome contains 2 854 coding sequences (CDS), 62 tRNA coding genes, and 4 complete rRNA genes encoding the operon. There are 443 virulence factors in E.fecalis Deng1 genome. The E.fecalis Deng1 genome causative island (PAI) is about 170 kb containing virulence factors encoding cytolytic cytotoxins, enterococcal surface protein Esp and Gls-24-like proteins, etc. E. facalis Deng1 contains a high level of resistance to streptomycin Aminoglycoside 6-adenylyltransferase gene (aadK), and emea, lsa and tetM genes associated with antibiotic resistance. Conclusion The sequencing analysis of a complete genome of Enterococcus faecalis completes the understanding of the epidemic strains resistant to LZD.