木糖葡萄球菌与金黄色葡萄球菌、表面葡萄球菌的基因组比较(阐述毒力、侵染性,样本是健康人的鼻腔)副本

LETTER TO THE EDITOR

Genome of Staphylococcus xylosus and Comparison with S.aureus

and S.epidermidis

Staphylococci are Gram-positive,AT-rich cocci,and often stick together in grape-like clusters.The genus can be classi-fied into two groups based on their ability to produce coagu-lase,an enzyme that causes clotting of blood plasma (Otto,2004).Coagulase-positive Staphylococci include Staphylo-coccus aureus ,a common pathogen of community-acquired and nosocomial infections (Smith et al.,2009).Their inva-siveness is associated with the ability to adhere to host sur-faces (Vuong et al.,2003).Among coagulase-negative Staphylococci (CNS),S.epidermidis is the most frequently found pathogen in humans,and is also a common cause of nosocomial infections (Nostro et al.,2007;Wang et al.,2009).S.epidermidis is believed to account for most of the infections caused by CNS and is highly resistant to many antibiotics including penicillins and cephalosporins (Al-Shuneigat et al.,2005).S.xylosus is also a CNS.It is naturally present in raw meat and milk and is commonly used in starter culture for fermentation (Planchon et al.,2006,2007).This species is normally regarded as non-pathogenic,but a few strains are related to human opportunistic infections (Akhaddar et al.,2010).In addition,some S.xylosus strains have the ability to form biofilm (Planchon et al.,2006).

Bacterial virulence genes can be regulated by diffusible signal molecules termed autoinducers (AIs).Because the control of gene expression by AIs is cell-density dependent,this phenomenon has been called quorum sensing (Brelles-Marino and Bedmar,2001;Antunes et al.,2010).In Staphy-lococci,there are two quorum sensing systems,P2and P3.Their regulatory mechanism was described earlier by Liu et al.(2012).Other regulatory genes and virulence factors shared by S.epidermidis and S.aureus have also been reported (Frebourg et al.,2000;Gelosia et al.,2001).However,it is still not clear whether these virulence related genes are also present in non-pathogenic S.xylosus genome.

In this study,we isolated S.xylosus NJ from a nasal sample of a healthy person at Jiangsu People’s Hospital in China and determined its genome sequence using whole-genome shotgun sequencing strategy with a Hiseq2000(Illumina,CA,USA)sequencer.The project generated a total of w 2739Mb

sequences and w 927folds coverage of the genome.The draft genome data were assembled using the Velvet assembly pro-gram.The assembly generated 45contigs with a size of >200bp,22of which were longer than 500bp with the N 50length of 396,400bp.These 45contigs were deposited in GenBank and annotated using Rapid Annotation using Sub-system Technology (RAST)server.In addition,96tandem repeat sequences were found in these contigs.The draft genome contained a chromosome of 2,940,053bp with a 32.40%G þC content.The general features are listed in Table 1.There are 6predicted rRNA genes and 22tRNA genes,and 83.64%nucleotides are predicted to encode proteins.By a combination of coding potential prediction and homology search,2783coding DNA sequences (CDSs)with an average length of 884bp were identified on the draft genome (Table 1).The 2199CDSs annotated by specific Clusters of Orthologous Groups (COG)function groups can be classified into 21COG categories,and 2456CDSs can be annotated into 1221KEGG orthology by KAAS (Moriya et al.,2007).The organization of the genome of S.xylosus NJ was shown in a circular map in Fig.1A.In addition,phylogenetic dendrogram based on a comparison of 16S rRNA sequences for S.xylosus NJ with members of the Staphylococcus was shown in Fig.S1.There is another S.xylosus draft genome,S.xylosus DMB3-Bh1,in GenBank.Therefore,we compared S.xylosus NJ with S.xylosus DMB3-Bh1using BLAST (version 2.2.26).The result showed that there are 2319CDSs in S.xylosus DMB3-Bh1(89.30%)similar to S.xylosus NJ (Fig.S2).

The metabolic network of S.xylosus NJ was constructed using the RAST server with the 411subsystems identified in the genome.There are many carbohydrate subsystem features,including genes involved in organic acids,fermentation,sugar alcohols,di-and oligo-saccharides,central carbohydrates,monosaccharides,and one-carbon metabolisms.Many protein metabolism features are also present,including protein biosynthesis machinery such as the small subunit (SSU)and large subunit (LSU)of the bacterial ribosome.Moreover,we prepared the comparative analysis of this genome with other staphylococcal genomes (S.aureus subsp.aureus N315(

S.

Available online at

ScienceDirect

Journal of Genetics and Genomics 41(2014)413e 416

JGG

1673-8527/$-see front matter Copyright Ó2014,Institute of Genetics and Developmental Biology,Chinese Academy of Sciences,and Genetics Society of China.Published by Elsevier Limited and Science Press.All rights reserved./10.1016/j.jgg.2014.03.007