日前,，上海交通大學(xué)生命學(xué)院微生物代謝教育部重點(diǎn)實(shí)驗(yàn)室歐竑宇副教授與英國(guó)萊斯特大學(xué)和馬來西亞馬來亞大學(xué)合作,，在對(duì)沙門菌基因組比較分析的基礎(chǔ)上，成功地利用多重PCR方法,，快速和準(zhǔn)確地鑒定了甲型副傷寒沙門菌——一種在東南亞地區(qū)廣泛流行的重要病原菌,。該項(xiàng)研究成果以封面論文發(fā)表在2007年11月出版的《分子診斷學(xué)雜志》（The Journal of Molecular Diagnostics）上。同期,，編輯部還配發(fā)專評(píng)文章,。文章稱“這項(xiàng)精細(xì)的研究描述了一個(gè)在基因組時(shí)代如何通過挖掘DNA序列信息來設(shè)計(jì)多重PCR實(shí)驗(yàn)以鑒定病原菌的通用方法”,。
《分子診斷學(xué)雜志》是由美國(guó)分子病理學(xué)會(huì)和美國(guó)研究病理學(xué)會(huì)聯(lián)合出版，發(fā)表分子診斷醫(yī)學(xué)領(lǐng)域最新進(jìn)展及技術(shù)應(yīng)用方面原始論文的專業(yè)刊物,。
歐竑宇是生命學(xué)院鄧子新團(tuán)隊(duì)去年才新引進(jìn)的青年教師,。在不到兩年的時(shí)間里，他作為課題主持人,，獲得了國(guó)家863計(jì)劃生物信息學(xué)專題探索類項(xiàng)目,、國(guó)家自然科學(xué)基金面上項(xiàng)目(青年基金)和上海市青年科技啟明星計(jì)劃的資助，取得了一些可喜的研究成果,。他通過與英國(guó)萊斯特大學(xué)的密切合作,，結(jié)合生物信息學(xué)方法和分子生物學(xué)實(shí)驗(yàn)技術(shù)提出了一個(gè)發(fā)現(xiàn)細(xì)菌基因組島的新策略，并建立了相關(guān)的生物信息學(xué)網(wǎng)站Mobilome FINDER,。其策略和方法于今年七月全文發(fā)表在國(guó)際生物學(xué)權(quán)威刊物《核酸研究》上,。上述的沙門菌分析工作也是利用該網(wǎng)站提供的生物信息學(xué)工具完成的。
此外,，歐竑宇與本團(tuán)隊(duì)從事分子微生物學(xué)研究的賀新義老師合作,，確定了變鉛青鏈霉菌染色體上攜帶編碼DNA磷硫酰化基因簇dnd的基因組島,。同時(shí)發(fā)現(xiàn)通過水平轉(zhuǎn)移方式,，基因簇dnd以基因組島的形式廣泛存在于分類地位和生態(tài)差異很大的細(xì)菌和古細(xì)菌中。合作論文于今年八月發(fā)表在國(guó)際生物學(xué)權(quán)威刊物《分子微生物學(xué)》上,。近年來,，以水平轉(zhuǎn)移方式獲得的基因組島，如致病島和耐藥島等,，被認(rèn)為在反映細(xì)菌生活史,、致病發(fā)生機(jī)理和在特定生態(tài)環(huán)境中進(jìn)化等方面都扮演著十分重要的角色，是微生物基因組學(xué)的研究熱點(diǎn)之一,。歐竑宇的研究成果提高了這個(gè)熱點(diǎn)領(lǐng)域的研究水平,。（上海交通大學(xué)）
原始出處:
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.
