两种分子分型技术在乳制品克诺罗杆菌污染溯源分析上的比较  

Application of whole genome sequencing (WGS) to Cronobacter sakazakii in dairy products,comparing two subtyping methods of MLST and SNP

作　　者：郭清艳 钮冰[1] 杨捷琳[2] GOU Qingyan;NIU Bing;YANG Jielin(College of Life Science,Shanghai University,Shanghai 200444,China;Shanghai Entry-Exit Inspection and Quarantine Bureau,Shanghai 200135,China)

机构地区：[1]上海大学生命科学学院,上海200444 [2]上海出入境检验检疫局,上海200135

出　　处：《中国乳品工业》2018年第8期13-17,20,共6页China Dairy Industry

基　　金：国家自然基金(31671936);上海市自然基金(16ZR1410900);上海市长三角科技联合攻关项目(16395810100)

摘　　要：对2005-2006年进口婴幼儿配方奶粉等乳制品的原料及产品中分离获得的49株阪崎肠杆菌(Enterobacter sakazakii),通过二代测序技术获得其全基因组序列,并比较两种分子分型技术的优缺点。通过二代测序技术获得49个菌株的全基因组序列,通过fusA确定菌株种属,根据多位点序列分型(Multi-locus Sequence Typing, MLST)确定序列型(ST, Sequence type)。再对32株ST13菌株进行单核苷酸多态性位点分析(single nucleotide polymorphism, SNP),并构建进化树。结果 49株阪崎肠杆菌均确认为阪崎克罗诺杆菌(C.sakazakii)。49株C.sakazakii由8个ST(Sequence type,序列型)组成。ST13的菌株占分离菌株的绝对优势(65.3%, 32/49)。ST13菌株的SNP结果显示32株菌被分成4个组和5个独立的菌株。表明随着高通量测序技术的不断完善,通过全基因组序列的MLST分型方法完成初步分型,而针对遗传相似性很高的菌株,应用SNP分析深入分型,能对被克罗诺杆菌属(Cronobacter spp.)污染的乳粉进行快速溯源,对全球疫情调查有重要意义。49 strains of Enterobacter sakazakii isolated from the raw materials and products of imported dairy products such as infant formula and milk powder during 2005-2006 were obtained. Their whole genome sequences were obtained by the second generation sequencing. Comparing MLST and SNP molecular typing techniques was done.Using the next-generation sequencing technology we obtained 49 gehomes which first were analyzed by.fusA, followed by using MLST （Multi-locus Sequence Typing） to identity ST（Sequence Type）. SNP （Single Nucleotide Polymorphism） analysis was performed on sequenced C. sakazakii strains belonging to CC13. Then the maximum hkeh- hood tree was constructed.MLST was used to unambiguously assign 49 strains to one species, namely, C. sakazakii. We identified 8 different sequence types （STs） for the 49 isolates, among which ST13 （65.3%, 32/49） was predominant. The 32 isolates belonged to CC13 were divided into 4 Group and 5 single isolates by SNP analysis.With the improvement of high-throughput sequencing technology, WGS not only can be used for MLST typing, but alsofor highly similar strains, like SNP analysis, which will make better accurate pathogen classification to provide helpness for the global epidemiological survey and faster traceability analysis for dairy contaminated by C.sakazakii.

关 键 词：阪崎克罗诺杆菌 全基因组测序 多位点序列分型 单核苷酸多态性位点 

分 类 号：Q93-331[生物学—微生物学] Q933