日前，上海交通大学生命学院微生物代谢教育部重点实验室欧竑宇副教授与英国莱斯特大学和马来西亚马来亚大学合作，在对沙门菌基因组比较分析的基础上，成功地利用多重PCR方法，快速和准确地鉴定了甲型副伤寒沙门菌——一种在东南亚地区广泛流行的重要病原菌。该项研究成果以封面论文发表在2007年11月出版的《分子诊断学杂志》（The Journal of Molecular Diagnostics）上。同期，编辑部还配发专评文章。文章称“这项精细的研究描述了一个在基因组时代如何通过挖掘DNA序列信息来设计多重PCR实验以鉴定病原菌的通用方法”。
《分子诊断学杂志》是由美国分子病理学会和美国研究病理学会联合出版，发表分子诊断医学领域最新进展及技术应用方面原始论文的专业刊物。
欧竑宇是生命学院邓子新团队去年才新引进的青年教师。在不到两年的时间里，他作为课题主持人，获得了国家863计划生物信息学专题探索类项目、国家自然科学基金面上项目(青年基金)和上海市青年科技启明星计划的资助，取得了一些可喜的研究成果。他通过与英国莱斯特大学的密切合作，结合生物信息学方法和分子生物学实验技术提出了一个发现细菌基因组岛的新策略，并建立了相关的生物信息学网站Mobilome FINDER。其策略和方法于今年七月全文发表在国际生物学权威刊物《核酸研究》上。上述的沙门菌分析工作也是利用该网站提供的生物信息学工具完成的。
此外，欧竑宇与本团队从事分子微生物学研究的贺新义老师合作，确定了变铅青链霉菌染色体上携带编码DNA磷硫酰化基因簇dnd的基因组岛。同时发现通过水平转移方式，基因簇dnd以基因组岛的形式广泛存在于分类地位和生态差异很大的细菌和古细菌中。合作论文于今年八月发表在国际生物学权威刊物《分子微生物学》上。近年来，以水平转移方式获得的基因组岛，如致病岛和耐药岛等，被认为在反映细菌生活史、致病发生机理和在特定生态环境中进化等方面都扮演着十分重要的角色，是微生物基因组学的研究热点之一。欧竑宇的研究成果提高了这个热点领域的研究水平。（上海交通大学）
原始出处:
Journal of Molecular Diagnostics 2007, Vol. 9, No. 5
DOI: 10.2353/jmoldx.2007.070064
Translational Genomics to Develop a Salmonella enterica Serovar Paratyphi A Multiplex Polymerase Chain Reaction Assay
Hong-Yu Ou*, Cindy Teh Shuan Ju, Kwai-Lin Thong, Norazah Ahmad, Zixin Deng*, Michael R. Barer¶ and Kumar Rajakumar¶
From the Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, * Shanghai Jiaotong University, Shanghai, China; the Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia; the Institute for Medical Research, Kuala Lumpur, Malaysia; the Department of Infection, Immunity, and Inflammation, Leicester Medical School, University of Leicester, Leicester, United Kingdom; and the Department of Clinical Microbiology, ¶ University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
The use of pathogen genome sequence data for the control and management of infections remains an ongoing challenge. We describe a broadly applicable, web-enabled approach that can be used to develop bacteria-specific polymerase chain reaction (PCR) assays. Salmonella enterica Paratyphi A has emerged as a major cause of enteric fever in Asia. Culture-based diagnosis is slow and frequently negative in patients with suspected typhoid and paratyphoid fever, potentially compromising patient management and public health. We used the MobilomeFINDER web-server to perform in silico subtractive hybridization, thus identifying 43 protein-coding sequences (CDSs) that were present in two Paratyphi A strains but not in other sequenced Salmonella genomes. After exclusion of 29 CDSs found to be variably present in Paratyphi A strains by microarray hybridization and grouping of remaining CDSs by genomic location, four dispersed targets (stkF, spa2473, spa2539, hsdM) were used to develop a highly discriminatory multiplex PCR assay. All 52 Paratyphi A strains within the diverse panel investigated produced one of two pathognomonic four-band signatures. Given rapid and ongoing expansion of DNA and comparative genomics databases, our universally accessible web-server-supported do-it-yourself approach offers the potential to contribute significantly to the rapid development of species-, serovar-, or pathotype-specific PCR assays targeting pre-existing and emerging bacterial pathogens.
