利用基因芯片技术分析空肠弯曲菌的遗传特征  

Genetic analysis with DNA microarray for Campylobacter jejuni isolated in China

作　　者：梁昊[1] 刘红莹[1] 尤元海[1] 顾一心[1] 张艾煜 王敏[1] 何利华[1] 孟凡亮[1] 张建中[1] 张茂俊[1] 

机构地区：[1]中国疾病预防控制中心传染病预防控制所传染病预防控制国家重点实验室,北京102206

出　　处：《疾病监测》2016年第2期159-165,共7页Disease Surveillance

基　　金：国家自然科学基金(No.81271789);国家重点基础研究发展计划(973计划)(No.2013CB127204)~~

摘　　要：目的为分析我国弯曲菌遗传特征,本研究根据已发表多株弯曲菌的全基因组测序特征及比对结果自行设计基因芯片,利用芯片对我国不同宿主来源菌株进行遗传特异性分析。方法根据前期基因组水平比对分析的结果,利用Combimatrix tiling Custom ArrayTM90K芯片,设计DNA芯片。芯片包含已测序菌株ICDCCJ07001、269.97、NCTC11168、81-176、81-116和RM1221共3384个CDS的探针序列,以及空肠弯曲菌耐药及致病性相关2个质粒共80个CDS的探针序列,与脂寡糖的合成相关基因簇16种共219个CDS的探针序列、荚膜多糖合成相关基因簇7种共160个CDS的所有序列。对我国不同宿主来源27株分离菌株提取DNA,利用芯片进行杂交,获得杂交信息并分析不同菌株CDS分布特征分析及聚类特点。结果中国菌株的主要变异区域主要存在于与脂寡糖、荚膜多糖合成相关的基因簇、鞭毛修饰相关的基因簇、DNA限制/修饰相关的基因簇以及空肠弯曲菌Mu样噬菌体基因簇。基因组水平不同来源菌株CDS分布的聚类结果没有发现显著的宿主归因特点,但GBS相关菌株脂寡糖合成相关基因组成具有共性特征。结论通过验证以及与过去研究的比较,本次研究中的基因芯片技术结果准确可信,本研究所用基因芯片在分析空肠弯曲菌基因多态性方面具有很好的优势,可用于弯曲菌遗传特征和重要毒力因子的分析和检测。Objective To understand the genetic diversity of the Campylobacter jejuni strains isolated in China,a high efficient DNA microarray for C. jejuni were designed based on the genome sequences. The increasing released numbers of the released genomes for C. jejuni in these days gave us more information to design the high efficient DNA microarray. Methods A Combimatrix tiling Custom ArrayTM（ 90 K chip） were designed according to our previous comparative genomic study. The chip included third sections of the DNA probes. The first section was the probes for the CDSs in the chromosome of the C.jejuni and the second section was the probes for the CDSs from the plasmid. The third section were the probes for the gene clusters related to lipooligosaccharides and polysaccharide capsule biosynthesis. In addition to the whole genome sequence of C. jejuni strain ICDCCJ07001,it included 1579 CDS on chromosome and 37 CDS on the plasmid and 1768 CDSs from other five sequenced strains： 269. 97,NCTC11168,81-176,81-116 and RM1221. The entire 1768 CDSs from five strains were all the strain specific CDSs. All these 3384 CDSs formed the first section probes of the chip. 53 CDSs from a antibiotic resistance plasmids and 37 CDSs from a pathogenicity associated plasmid in C. jejuni formed the second section of the chip. Sixteen and7 gene clusters related to lipooligosaccharides and polysaccharide capsule biosynthesis respectively were represented in the chip as the third section. The analysis on the distribution of CDSs in different strains and the hierarchical clustering were performed for 27 C. jejuni strains isolated from different sources in China. Results The results revealed that the main hypervariable regions were in the genes clusters related to lipooligosaccharides and polysaccharide capsule biosynthesis, flagellum modification,Campylobacter M u-like phage as well as DNA restriction and modification. None host attribution feature was obtained by hierarchical clustering analysis of ORF distribution among strains from different

关 键 词：空肠弯曲菌 基因芯片 遗传变异 

分 类 号：R378[医药卫生—病原生物学]