| 尤元海,何利华,彭贤慧,孙路,张建中.中国幽门螺杆菌基因组多样性与种群结构分析[J].Chinese journal of Epidemiology,2016,37(10):1397-1403 |
| 中国幽门螺杆菌基因组多样性与种群结构分析 |
| Genomic diversity and population structure of Helicobacter pylori isolates in China |
| Received:May 12, 2016 |
| DOI：10.3760/cma.j.issn.0254-6450.2016.10.016 |
| KeyWord: 幽门螺杆菌 种群结构 基因组 |
| English Key Word: Helicobacter pylori Population structure Genome |
| FundProject:传染病预防控制国家重点实验室自主项目，病原菌质谱鉴定的标志物识别与分析（2014SKLID102） |
| Author Name | Affiliation | E-mail | | You Yuanhai | State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China | | | He Lihua | State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China | | | Peng Xianhui | State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China | | | Sun Lu | State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China | | | Zhang Jianzhong | State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China | zhangjianzhong@icdc.cn |
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| Abstract: |
| 目的 了解中国幽门螺杆菌（Helicobacter pylori，HP）基因组特征及种群结构。方法 利用中国不同地域不同疾病分离的10株HP的基因组序列，并整合公共数据库中其他地域的HP基因组数据，通过比较基因组和生物信息学方法分析中国HP的基因组与种群结构特征。结果 中国HP核心基因为1 203个。菌株特异基因为19～32个，这些基因可能与中国HP在不同地域、不同疾病宿主中的适应性进化有关。基因组变异较大区域主要集中在编码限制修饰系统的基因和编码四型分泌系统的基因。基于核心基因组单核苷酸多态性（SNP）的种群分析确定中国菌株均属于hpEastAsia群，hspEAsia亚群，且不同地域菌株具有地域聚集性特点。在3株中国HP基因组序列中发现了前噬菌体序列，携带噬菌体组装所需的必要元件。结论 基于核心基因组SNP分析中国菌株均属于hpEastAsia群，hspEAsia亚群，且具有地域聚集性。为深入挖掘中国不同地域不同疾病相关HP的遗传特征及研究噬菌体在HP进化与致病中的作用奠定了基础。 |
| English Abstract: |
| Objective To learn about the overall genomic characteristics and population structure of Helicobacter pylori isolated in China. Methods In this study, we used 10 public available genome sequences of H. pylori strains isolated in China, combined with other H. pylori sequences from GenBank, to analyzed the overall genomic characteristics of H. pylori isolated in China. Core genes and strain specific genes were determined for a further function definition. Results A total of 1 203 core genes were found among all sequenced China H. pylori isolates. The number of strain specific genes ranged from 19 to 32. These genes mainly encodes hypothetical proteins which might play an important role in adaption to different hosts. Genomic variation regions were mainly in genes encoding type four secretion systems and restriction modification systems. All the China isolates belong to hpEastAsia group, hspEAsia subgroup. Prophages sequences were found in three China H. pylori strains, carrying key elements required for phage assembly. Conclusion China H. pylori isolates belong to hpEastAsia group, hspEAsia subgroup, and some isolates contain prophages. |
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