摘要
细菌分型与溯源对食品安全监管、流行病学调查具有重要意义。全基因组分型技术以全基因组多位点序列分型(whole genome multilocus sequence typing,wgMLST)、核心基因组多位点序列分型(core genome multilocus sequence typing,cgMLST)、全基因组单核苷酸多态性(whole genome single nucleotide polymorphism,wgSNP)等为代表,具有分辨率高、重复性好的优点,能够实现精准溯源,逐渐成为细菌分型和溯源的主流技术。然而,wgMLST、wgSNP消耗巨大的计算资源,而且wgSNP对测序的准确性要求极高,推广难度大;相比之下,cgMLST需要较少的计算能力,应用性更强。本文重点介绍了细菌核心基因组的筛选、等位基因的赋值、cgMLST分型原理及操作步骤和细菌基因组溯源评价,为细菌的cgMLST分型与溯源提供了技术指导,有助于保证cgMLST分型结果的客观性和可比性。
The typing and traceability of bacteria are very important for food safety monitoring and epidemiological investigation.The whole genome typing technology mainly includes whole genome multilocus sequence typing(wgMLST),core genome multilocus sequence typing(cgMLST),and whole genome single nucleotide polymorphism(wgSNP),with high resolution and good repeatability,which results in accurate traceability.However,the analysis of wgMLST and wgSNP consumes a huge quantity of computing resources,and wgSNP requires a very high accuracy of sequencing;both of which make the technology difficult to be popularized.Compared with wgMLST and wgSNP,cgMLST has the same resolution,but less computing power and stronger applicability.In this paper,the methods of core genome screening,allele coding,cgMLST operation steps,evaluation criteria and bacterial genome traceability are briefly introduced,which provides technical guidance for bacterial cgMLST typing and traceability,standardized bacterial cgMLST typing,and helps in making the typing results objective and comparable.
作者
朱丽萍
张文成
颜世敢
陈蕾蕾
崔生辉
ZHU Liping;ZHANG Wencheng;YAN Shigan;CHEN Leilei;CUI Shenghui(School of Bioengineering,Qilu University of Technology/Shandong Province Key Laboratory of Bioengineering,Jinan 250353,China;Institute of Agro-food Science and Technology,Shandong Academy of Agricultural Sciences,Jinan 250100,China;National Institute of Food and Drug Control,Beijing 100050)
出处
《畜牧与兽医》
北大核心
2021年第6期140-146,共7页
Animal Husbandry & Veterinary Medicine
基金
国家重点研发计划(2017YFC1601400)
山东省重点研发计划(2014GGB01661)。
关键词
细菌
核心基因组多位点序列分型
溯源
评价
bacteria
core genome multilocus sequence typing
traceability
evaluation
