肠道细菌基因间重复共有序列-聚合酶链式反应指纹图谱技术用于细菌分型的研究进展
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摘要
肠道细菌基因间重复共有序列-聚合酶链式反应(enterobacterial repetitive intergenic consensus-polymerase chain reaction,ERIC-PCR)指纹图谱技术利用普遍存在于生物体内的ERIC进行引物设计,通过基因扩增,获得能够表征其基因组结构的产物,该方法简单易行、重复性好、用时短,被广泛应用于细菌基因分型及同源性判别。本文简述细菌分型的研究背景和ERIC-PCR指纹图谱技术的原理及特点,归纳该技术在细菌基因分型方面的优缺点及其在常见食源性致病菌基因分型中的应用现状,并对ERIC-PCR指纹图谱技术应用于乳品企业污染菌溯源的研究进行展望。
Enterobacterial repetitive intergenic consensus-polymerase chain reaction(ERIC-PCR) allows gene amplification using primers designed based on ERIC, which are widely present in living organisms, yielding products that are useful to characterize the genomic structure. This method has been widely used in bacterial classification and research on the genetic relationship of strains because of its merits such as simplicity, ease of implementation, good repeatability and time saving. This paper reviews the background to bacterial classification research and the principle and characteristics of ERIC-PCR technique, and summarizes the advantages and disadvantages of ERIC-PCR technique in bacterial genotyping and recent progress in its application to genotype common food-borne pathogenic bacteria. At the same time, future prospects for the application of ERIC-PCR in traceability analysis of microbial contaminants in dairy enterprises.
Enterobacterial repetitive intergenic consensus-polymerase chain reaction(ERIC-PCR) allows gene amplification using primers designed based on ERIC, which are widely present in living organisms, yielding products that are useful to characterize the genomic structure. This method has been widely used in bacterial classification and research on the genetic relationship of strains because of its merits such as simplicity, ease of implementation, good repeatability and time saving. This paper reviews the background to bacterial classification research and the principle and characteristics of ERIC-PCR technique, and summarizes the advantages and disadvantages of ERIC-PCR technique in bacterial genotyping and recent progress in its application to genotype common food-borne pathogenic bacteria. At the same time, future prospects for the application of ERIC-PCR in traceability analysis of microbial contaminants in dairy enterprises.
引文
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[2]马俊英,刘健华,陈杖榴,等.细菌分型的分子生物学技术研究进展[J].中国兽医科学,2007,37(10):914-917.DOI:10.3969/j.issn.1673-4696.2007.10.021.
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[4] VAN BELKUM A, KLUYTMANS J, VAN LEEUWEN W, et al. Multicenter evaluation of arbitarily primed PCR for typing of Staphylococcus aureus strains[J]. Journal of Clinical Microbiology, 1995,33(6):1537-1547.DOI:10.1002/jctb.280630215.
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[6]乌日娜,郭邦成,刘翔,等.银川市食源性单增李斯特菌分子流行病学特征研究[J].医学美学美容旬刊,2014(5):89-90.
[7]NATH G,MAURYA P,GULATI A K.ERIC PCR and RAPD based fingerprinting of Salmonella typhi strains isolated over a period of two decades[J].Infection Genetics and Evolution,2010,10(4):530-536.DOI:10.1016/j.meegid.2010.02.004.
[8]MAITI B, RAGHUNATH P, KARNASAGAR I, et al. Typing of clinical and environmental strains of Aeromonas spp. using two PCR based methods and whole cell protein analysis[J]. Journal of Microbiological Methods,2009,78(3):312-318.DOI:10.1016/j.mimet.2009.07.009.
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[10] BRIAN M J, VAN R, TOWNSEND I, et al. Evaluation of the molecular epidemiology of an outbreak of multiply resistant Shigella sonnei in a day-care center by using pulsed-field gel electrophoresis and plasmid DNA analysis[J]. Journal of Clinical Microbiology, 1993, 31(8):2152-2156.
[11]卢强,任瑞文,胡岩,等.嗜水气单胞菌的随机扩增多态DNA分型[J].中国兽医学报,2002,22(1):34-36.DOI:10.3969/j.issn.1005-4545.2002.01.011.
[12] SHAPPLES G J, LLOYD R G. A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes[J]. Nucleic Acids Research,1990,18(22):6503-6508.DOI:10.1093/nar/18.22.6503.
[13]陈迎春,曹又方,赵立平.大肠杆菌MG1655菌株ERIC-PCR图谱主带序列组成分析[J].微生物学通报,2002,29(6):28-32.DOI:10.3969/j.issn.0253-2654.2002.06.008.
[14]GILLINGS M, HOLLEY M. Repetitive element PCR fingerprinting (REP-PCR) using enterobacterial repetitive intergenic consensus(ERIC) primers is not necessarily directed at ERIC elements[J]. Letters In Applied Microbiology,1997,25(1):17-21.DOI:10.1046/j.1472-765X.1997.00162.x.
[15] VERSALOVIC J, KOEUTH T, LUPSKI J R. Distribution of repetitive DNA sequences in eubacteria and application fingerprinting of bacterial genomes[J]. Nucleic Acids Research, 1991, 19(24): 6823-6831.DOI:10.1093/nar/19.24.6823.
[16]金莉莉,王秋雨,侯潇.E R I C-P C R技术在李斯特氏菌种、菌株鉴定中的应用[J].遗传,2003,25(2):195-197.DOI:10.3321/j.issn:0253-9772.2003.02.018.
[17]贾宁,林茂虎,陈世平,等.变形杆菌基因分型方法的评价[J].中华医院感染学杂志,2002,12(9):652-654.DOI:10.3321/j.issn:1005-4529.2002.09.005.
[18]庄孝飞,周秀娟,史贤明,等.2008-2012年上海市肠炎沙门氏菌分离株毒力基因筛查与ERIC-PCR分型[J].食品科学,2015,36(14):165-169.DOI:10.7506/spkx1002-6630-201514032.
[19]宋启发,徐景野,朱国良,等.肠道细菌基因间重复序列基因分型方法研究副溶血性弧菌的基因多态性[J].中华微生物学和免疫学杂志,2012,32(1):12-15.DOI:10.3760/cma.j.issn.0254-5101.2012.01.003.
[20]马月姣,孙晓红,赵勇,等.REP-PCR及ERIC-PCR法对分离白海产品副溶血性弧菌分型分析[J].食品科学,2013,34(10):263-266.DOI:10.7506/spkx1002-6630-201310058.
[21]王君,吴清平,吴克刚,等.蜡样芽孢杆菌ERIC-PCR分子分型方法的建立[J].现代食品科技,2013,29(7):1696-1700.DOI:10.13982/j.mfst.1673-9078.2013.07.059.
[22]刘丹,王培昌,赵霞,等.RAPD、ERIC-PCR联合REP-PCR对多重耐药鲍曼不动杆菌基因型的鉴定[J].山东医药,2010,50(40):99-100.DOI:10.3969/j.issn.1002-266X.2010.40.060.
[23]HUNTER P R,GASTON M A.Numerical index of the discriminatory ability of typing systems:an application of Simpson’s index of diversity[J].Journal of Clinical Microbiology,1988,26(11):2465-2466.
[24]NEMOY L L,KOTETISHVILI M,TIGNO J,et al.Multilocus sequence typing versus pulsed-fieldgel electrophoresis for characterization of extended-spectrum beta-lactamase-producing Escherichia coli isolates[J].Journal of Clinical Microbiology,2005,43(4):1776-1781.DOI:10.1128/JCM.43.4.1776-1781.
[25]伍晓锋,黎毅敏,卓超,等.18株铜绿假单胞菌的耐药谱和ERIC-PCR分型[J].中国抗生素杂志,2007,32(9):560-563.DOI:10.13461/j.cnki.cja.004023.
[26]丁翊君,王亚娟,姚开虎,等.住院新生儿大肠埃希菌分离株的肠杆菌基因间重复共有序列聚合酶链反应分型[J].中华实用儿科临床杂志,2013,28(22):1702-1705.DOI:10.3760/cma.j.issn.2095-428X.2013.22.007.
[27]D A L L A-C O S T A L M,I T I N O K,R O D R I G U E S J,e t a l.Characterisation of Diarrhoeagenic escherichia coil clones by ribotyping and ERIC-PCR[J].Journal of Medical Microbiology,1998,47(3):227-234.DOI:10.1099/00222615-47-3-227.
[28]HOUF K,DE ZUTTER L,VAN HOOF J,et al.Assessment of the genetic diversity among arcobacters isolated from poultry products by using two PCR-based typing methods[J].Applied Environment Microbiology,2002,68(5):2172-2178.DOI:10.1128/AEM.68.5.2172-2178.2002.
[29]李艳琴,孙永艳,崔丽方,等.ERIC-PCR在人工混合菌体系中的检出灵敏度[J].微生物学通报,2004,31(4):61-64.DOI:10.13344/j.microbiol.china.2004.04.016.
[30]KOSEK M,YORI P P,GILMAN R H,et a1.Facilitated molecular typing of Shigella isolates using ERIC-PCR[J].The American Journal of Tropical Medicine and Hygiene,2012,86(6):1018-1025.
[31]张美玲,周志华,赵立平.粪便样品中大肠杆菌多态性分子研究[J].微生物学通报,2005,32(2):5-9.DOI:10.3969/j.issn.0253-2654.2005.02.002.
[32]何力,傅玲琳,冯立芳,等.大肠埃希氏菌ERIC-PCR指纹图谱构建及贝类污染微生物源示踪[J].中国食品学报,2012,12(8):163-169.DOI:10.3969/j.issn.1009-7848.2012.08.024.
[33]钟召兵,侯磊,王宁,等.生鲜乳中大肠杆菌的分离及其ERIC-PCR指纹分析[J].中国奶牛,2017(3):36-39.DOI:10.19305/j.cnki.11-3009/s.2017.03.011.
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