《中国药典》中标准菌种质控新方法的研究
|
摘要
目的研究《中华人民共和国药典》(简称《中国药典》)纳入的标准菌种质控新方法,并评价不同批号标准菌种的质量稳定性。方法对脉冲场凝胶电泳(PFGE)技术进行比较研究,同时整合16S rRNA基因序列分析、多位点序列分型和基质辅助激光解吸电离飞行时间质谱等质控新方法,进行标准菌种质控新方法的建立,并对标准菌种的质量进行评价。结果形成了适用于《中国药典》中标准菌种的方法,并通过整合的质控新方法对不同批号的标准菌种进行评价,结果显示,菌种质量稳定,遗传信息无改变。同时,建立了标准菌种16S rRNA基因标准序列、PFGE标准指纹图谱和标准基因型。结论标准菌种质控新方法的研究,为更加全面、深入地评价标准菌种的质量提供了依据;建立的标准菌种质量控制体系及标准菌种质控鉴定信息,为标准菌种持续的质量控制奠定了重要的参比信息基础。
Objective To carry out research on new methods for quality control of standard strains published in《Chinese Pharmacopoeia》, and to evaluate the quality stability for different batches of standard strains. Methods A new method for quality control of standard strains was integrated, including comparison of pulsed field gel electrophoresis(PFGE), 16S rRNA gene sequence analysis, multilocus sequence typing and matrix-assisted laser desorption/ionization time of flight mass spectrometry. The quality of the standard strain was evaluated. Results The suitable PFGE method was set up for the standard strains published in 《Chinese Pharmacopoeia》, and the standard strains of different batches were evaluated by the integrated quality control method. The tested quality was in stable and the genetic information was unchanged compared with the original strains. At the same time, the 16S rRNA gene standard sequences, the PFGE standard fingerprints and the standard genotypes were developed. Conclusion The developed new methods for quality control of standard strains can evaluate the quality of standard strains more comprehensively and deeply. It provided an important reference basis that the development of a set of standard strain quality control system and standard strain quality control identity information was applied in the continuous quality control of standard strains.
Objective To carry out research on new methods for quality control of standard strains published in《Chinese Pharmacopoeia》, and to evaluate the quality stability for different batches of standard strains. Methods A new method for quality control of standard strains was integrated, including comparison of pulsed field gel electrophoresis(PFGE), 16S rRNA gene sequence analysis, multilocus sequence typing and matrix-assisted laser desorption/ionization time of flight mass spectrometry. The quality of the standard strain was evaluated. Results The suitable PFGE method was set up for the standard strains published in 《Chinese Pharmacopoeia》, and the standard strains of different batches were evaluated by the integrated quality control method. The tested quality was in stable and the genetic information was unchanged compared with the original strains. At the same time, the 16S rRNA gene standard sequences, the PFGE standard fingerprints and the standard genotypes were developed. Conclusion The developed new methods for quality control of standard strains can evaluate the quality of standard strains more comprehensively and deeply. It provided an important reference basis that the development of a set of standard strain quality control system and standard strain quality control identity information was applied in the continuous quality control of standard strains.
引文
[1] 杨霞,陈陆,王川庆.16S rRNA基因序列分析技术在细菌分类中应用的研究进展[J].西北农林科技大学学报(自然科学版),2008,36(2):55-60.
[2] 彭海,周健武,牟晓明,等.MALDI-TOF MS技术在多重耐药大肠埃希菌同源性分析及自建库中的应用研究[J].中华医院感染学杂志,2018,28(24):3689-3694.
[3] 徐潇,石继春,王春娥,等.食品检验用标准菌株分子水平质控方法的建立与应用[J].疾病监测,2018,33(9):744-752.
[4] DELGADO S,SUAREZ A,MAYO B.Identification of dominant bacteria in feces and colonic mucosa from healthy Spanish adults by culturing and by 16S rDNA sequence analysis[J].Dig Dis Sci,2006,51(4):744-751.
[5] LANE D J.16S/23S rRNA sequencing[M].New York:John Wiley and Sons,1991.
[6] NIU L,LU S,LAI X H,et al.Streptococcus himalayensis sp.nov.,isolated from the respiratory tract of Marmota himalayana[J].Int J Syst Evol Microbiol,2017,67(2):256-261.
[7] RIBOT E M,FAIR M A,GAUTOM R,et al.Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7,Salmonella,and Shigella for PulseNet[J].Foodborne Pathog Dis,2006,3(1):59-67.
[8] CIGANA C,MELOTTI P,BALDAN R,et al.Genotypic and phenotypic relatedness of Pseudomonas aeruginosa isolates among the major cystic fibrosis patient cohort in Italy[J].BMC Microbiol,2016,16(1):142.
[9] TENOVER F C,ARBEIT R D,GOERING R V,et al.Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis:criteria for bacterial strain typing[J].J Clin Microbiol,1995,33(9):2233-2239.
[10] GRUNDMANN H,SCHNEIDER C,HARTUNG D,et al.Discriminatory power of three DNA-based typing techniques for Pseudomonas aeruginosa[J].J Clin Microbiol,1995,33(3):528-534.
[11] MERKIER A K,RODRIGUEZ M C,TOGNERI A,et al.Outbreak of a cluster with epidemic behavior due to Serratia marcescens after colistin administration in a hospital setting[J].J Clin Microbiol,2013,51(7):2295-2302.
[12] KRAWCZYK B,NAUMIUK L,LEWANDOWSKI K,et al.Evaluation and comparison of random amplification of polymorphic DNA,pulsed-field gel electrophoresis and ADSRRS-fingerprinting for typing Serratia marcescens outbreaks[J].FEMS Immunol Med Microbiol,2003,38(3):241-248.
[13] LIGOZZI M,FONTANA R,ALDEGHERI M,et al.Comparative evaluation of an automated repetitive-sequence-based PCR instrument versus pulsed-field gel electrophoresis in the setting of a Serratia marcescens nosocomial infection outbreak[J].J Clin Microbiol,2010,48(5):1690-1695.
[14] BANNERMAN T L,HANCOCK G A,TENOVER F C,et al.Pulsed-field gel electrophoresis as a replacement for bacteriophage typing of Staphylococcus aureus[J].J Clin Microbiol,1995,33(3):551-555.
[15] DE BAETS L,VAN IWAARDEN P,MEEUS N,et al.First certified reference materials for molecular fingerprinting of two approved probiotic Bacillus strains[J].Int J Food Microbiol,2009,129(1):16-20.
[16] MARTEN P,SMALLA K,BERG G.Genotypic and phenotypic differentiation of an antifungal biocontrol strain belonging to Bacillus subtilis[J].J Appl Microbiol,2000,89(3):463-471.
[17] OUOBA L I,DIAWARA B,AMOA-AWUA W,et al.Genotyping of starter cultures of Bacillus subtilis and Bacillus pumilus for fermentation of African locust bean (Parkia biglobosa) to produce Soumbala[J].Int J Food Microbiol,2004,90(2):197-205.
[18] GATSON J W,BENZ B F,CHANDRASEKARAN C,et al.Bacillus tequilensis sp.nov.,isolated from a 2000-year-old Mexican shaft-tomb,is closely related to Bacillus subtilis[J].Int J Syst Evol Microbiol,2006,56(Pt 7):1475-1484.
[19] LIU P Y,KE S C,CHEN S L.Use of pulsed-field gel electrophoresis to investigate a pseudo-outbreak of Bacillus cereus in a pediatric unit[J].J Clin Microbiol,1997,35(6):1533-1535.
[20] HELGASON E,CAUGANT D A,OLSEN I,et al.Genetic structure of population of Bacillus cereus and B.thuringiensis isolates associated with periodontitis and other human infections[J].J Clin Microbiol,2000,38(4):1615-1622.
[21] GARDE S,GAYA P,ARIAS R,et al.Enhanced PFGE protocol to study the genomic diversity of Clostridium spp.isolated from Manchego cheeses with late blowing defect[J].Food Control,2012,28(2):392-399.
[22] REDDY N R,MARSHALL K M,MORRISSEY T R,et al.Combined high pressure and thermal processing on inactivation of type A and proteolytic type B spores of Clostridium botulinum[J].J Food Prot,2013,76(8):1384-1392.
[23] SCHILL K M,WANG Y,BUTLER R R,et al.Geneticdiversity of Clostridium sporogenes PA 3679 isolates obtained from different sources as resolved by pulsed-field gel electrophoresis and high-throughput sequencing[J].Appl Environ Microbiol,2016,82(1):384-393.
[24] PARK J H,SONG J C,KIM M H,et al.Determination of genome size and a preliminary physical map of an extreme alkaliphile,Micrococcus sp.Y-1,by pulsed-field gel electrophoresis[J].Microbiology,1994,140 ( Pt 9):2247-2250.
[25] O'FARRELL B,HAASE J K,VELAYUDHAN V,et al.Transforming microbial genotyping:a robotic pipeline for genotyping bacterial strains[J].PLoS One,2012,7(10):e48022.
[26] CURRAN B,JONAS D,GRUNDMANN H,et al.Development of a multilocus sequence typing scheme for the opportunistic pathogen Pseudomonas aeruginosa[J].J Clin Microbiol,2004,42(12):5644-5649.
[27] WIRTH T,FALUSH D,LAN R,et al.Sex and virulence in Escherichia coli:an evolutionary perspective[J].Mol Microbiol,2006,60(5):1136-1151.
[28] SHARMA P,DAHIYA S,BALAJI V,et al.Typhoidal salmonellae:Use of Multi-locus sequence typing to determine population structure[J].PLoS One,2016,11(9):e0162530.
[29] ENRIGHT M C,DAY N P,DAVIES C E,et al.Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus[J].J Clin Microbiol,2000,38(3):1008-1015.
[30] KABORE D,GAGNON M,ROY D,et al.Rapid screening of starter cultures for maari based on antifungal properties[J].Microbiol Res,2018,207:66-74.
[31] DENG S P,HUANG D S.An integrated strategy for functional analysis of microbial communities based on gene ontology and 16S rRNA gene[J].Int J Data Min Bioinform,2015,13(1):63-74.
[32] XIA L P,BIAN L Y,XU M,et al.16S rRNA gene sequencing is a non-culture method of defining the specific bacterial etiology of ventilator-associated pneumonia[J].Int J Clin Exp Med,2015,8(10):18560-18570.
[33] 张国林,苏远科,沈海英,等.16S rRNA/ITS基因序列分析与微生物分类鉴定及其在药品微生物质量控制中的应用[J].中国现代应用药学,2017,34(10):1489-1495.
[34] 韩辉.伤寒和甲型副伤寒沙门菌遗传稳定性的试验室微进化研究[D].北京:中国疾病预防控制中心,2010.
[35] 王中强,邱少富,王勇,等.多位点序列分型技术及其研究进展[J].军事医学科学院院刊,2010(1):76-79.
[36] 上海市医学会检验分会临床微生物学组,上海市微生物学会临床微生物专委会,上海市微生物学会微生物耐药防控专委会.MALDI-TOF MS病原体鉴定质量保证专家共识[J].中华检验医学杂志,2018,41(8):567-570.
[37] 张仁峰,张炳昌,邵春红,等.MALDI-TOF MS用于碳青霉烯耐药肺炎克雷伯菌同源性分析的初步研究[J].中华检验医学杂志,2018,41(8):589-595.
[2] 彭海,周健武,牟晓明,等.MALDI-TOF MS技术在多重耐药大肠埃希菌同源性分析及自建库中的应用研究[J].中华医院感染学杂志,2018,28(24):3689-3694.
[3] 徐潇,石继春,王春娥,等.食品检验用标准菌株分子水平质控方法的建立与应用[J].疾病监测,2018,33(9):744-752.
[4] DELGADO S,SUAREZ A,MAYO B.Identification of dominant bacteria in feces and colonic mucosa from healthy Spanish adults by culturing and by 16S rDNA sequence analysis[J].Dig Dis Sci,2006,51(4):744-751.
[5] LANE D J.16S/23S rRNA sequencing[M].New York:John Wiley and Sons,1991.
[6] NIU L,LU S,LAI X H,et al.Streptococcus himalayensis sp.nov.,isolated from the respiratory tract of Marmota himalayana[J].Int J Syst Evol Microbiol,2017,67(2):256-261.
[7] RIBOT E M,FAIR M A,GAUTOM R,et al.Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7,Salmonella,and Shigella for PulseNet[J].Foodborne Pathog Dis,2006,3(1):59-67.
[8] CIGANA C,MELOTTI P,BALDAN R,et al.Genotypic and phenotypic relatedness of Pseudomonas aeruginosa isolates among the major cystic fibrosis patient cohort in Italy[J].BMC Microbiol,2016,16(1):142.
[9] TENOVER F C,ARBEIT R D,GOERING R V,et al.Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis:criteria for bacterial strain typing[J].J Clin Microbiol,1995,33(9):2233-2239.
[10] GRUNDMANN H,SCHNEIDER C,HARTUNG D,et al.Discriminatory power of three DNA-based typing techniques for Pseudomonas aeruginosa[J].J Clin Microbiol,1995,33(3):528-534.
[11] MERKIER A K,RODRIGUEZ M C,TOGNERI A,et al.Outbreak of a cluster with epidemic behavior due to Serratia marcescens after colistin administration in a hospital setting[J].J Clin Microbiol,2013,51(7):2295-2302.
[12] KRAWCZYK B,NAUMIUK L,LEWANDOWSKI K,et al.Evaluation and comparison of random amplification of polymorphic DNA,pulsed-field gel electrophoresis and ADSRRS-fingerprinting for typing Serratia marcescens outbreaks[J].FEMS Immunol Med Microbiol,2003,38(3):241-248.
[13] LIGOZZI M,FONTANA R,ALDEGHERI M,et al.Comparative evaluation of an automated repetitive-sequence-based PCR instrument versus pulsed-field gel electrophoresis in the setting of a Serratia marcescens nosocomial infection outbreak[J].J Clin Microbiol,2010,48(5):1690-1695.
[14] BANNERMAN T L,HANCOCK G A,TENOVER F C,et al.Pulsed-field gel electrophoresis as a replacement for bacteriophage typing of Staphylococcus aureus[J].J Clin Microbiol,1995,33(3):551-555.
[15] DE BAETS L,VAN IWAARDEN P,MEEUS N,et al.First certified reference materials for molecular fingerprinting of two approved probiotic Bacillus strains[J].Int J Food Microbiol,2009,129(1):16-20.
[16] MARTEN P,SMALLA K,BERG G.Genotypic and phenotypic differentiation of an antifungal biocontrol strain belonging to Bacillus subtilis[J].J Appl Microbiol,2000,89(3):463-471.
[17] OUOBA L I,DIAWARA B,AMOA-AWUA W,et al.Genotyping of starter cultures of Bacillus subtilis and Bacillus pumilus for fermentation of African locust bean (Parkia biglobosa) to produce Soumbala[J].Int J Food Microbiol,2004,90(2):197-205.
[18] GATSON J W,BENZ B F,CHANDRASEKARAN C,et al.Bacillus tequilensis sp.nov.,isolated from a 2000-year-old Mexican shaft-tomb,is closely related to Bacillus subtilis[J].Int J Syst Evol Microbiol,2006,56(Pt 7):1475-1484.
[19] LIU P Y,KE S C,CHEN S L.Use of pulsed-field gel electrophoresis to investigate a pseudo-outbreak of Bacillus cereus in a pediatric unit[J].J Clin Microbiol,1997,35(6):1533-1535.
[20] HELGASON E,CAUGANT D A,OLSEN I,et al.Genetic structure of population of Bacillus cereus and B.thuringiensis isolates associated with periodontitis and other human infections[J].J Clin Microbiol,2000,38(4):1615-1622.
[21] GARDE S,GAYA P,ARIAS R,et al.Enhanced PFGE protocol to study the genomic diversity of Clostridium spp.isolated from Manchego cheeses with late blowing defect[J].Food Control,2012,28(2):392-399.
[22] REDDY N R,MARSHALL K M,MORRISSEY T R,et al.Combined high pressure and thermal processing on inactivation of type A and proteolytic type B spores of Clostridium botulinum[J].J Food Prot,2013,76(8):1384-1392.
[23] SCHILL K M,WANG Y,BUTLER R R,et al.Geneticdiversity of Clostridium sporogenes PA 3679 isolates obtained from different sources as resolved by pulsed-field gel electrophoresis and high-throughput sequencing[J].Appl Environ Microbiol,2016,82(1):384-393.
[24] PARK J H,SONG J C,KIM M H,et al.Determination of genome size and a preliminary physical map of an extreme alkaliphile,Micrococcus sp.Y-1,by pulsed-field gel electrophoresis[J].Microbiology,1994,140 ( Pt 9):2247-2250.
[25] O'FARRELL B,HAASE J K,VELAYUDHAN V,et al.Transforming microbial genotyping:a robotic pipeline for genotyping bacterial strains[J].PLoS One,2012,7(10):e48022.
[26] CURRAN B,JONAS D,GRUNDMANN H,et al.Development of a multilocus sequence typing scheme for the opportunistic pathogen Pseudomonas aeruginosa[J].J Clin Microbiol,2004,42(12):5644-5649.
[27] WIRTH T,FALUSH D,LAN R,et al.Sex and virulence in Escherichia coli:an evolutionary perspective[J].Mol Microbiol,2006,60(5):1136-1151.
[28] SHARMA P,DAHIYA S,BALAJI V,et al.Typhoidal salmonellae:Use of Multi-locus sequence typing to determine population structure[J].PLoS One,2016,11(9):e0162530.
[29] ENRIGHT M C,DAY N P,DAVIES C E,et al.Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus[J].J Clin Microbiol,2000,38(3):1008-1015.
[30] KABORE D,GAGNON M,ROY D,et al.Rapid screening of starter cultures for maari based on antifungal properties[J].Microbiol Res,2018,207:66-74.
[31] DENG S P,HUANG D S.An integrated strategy for functional analysis of microbial communities based on gene ontology and 16S rRNA gene[J].Int J Data Min Bioinform,2015,13(1):63-74.
[32] XIA L P,BIAN L Y,XU M,et al.16S rRNA gene sequencing is a non-culture method of defining the specific bacterial etiology of ventilator-associated pneumonia[J].Int J Clin Exp Med,2015,8(10):18560-18570.
[33] 张国林,苏远科,沈海英,等.16S rRNA/ITS基因序列分析与微生物分类鉴定及其在药品微生物质量控制中的应用[J].中国现代应用药学,2017,34(10):1489-1495.
[34] 韩辉.伤寒和甲型副伤寒沙门菌遗传稳定性的试验室微进化研究[D].北京:中国疾病预防控制中心,2010.
[35] 王中强,邱少富,王勇,等.多位点序列分型技术及其研究进展[J].军事医学科学院院刊,2010(1):76-79.
[36] 上海市医学会检验分会临床微生物学组,上海市微生物学会临床微生物专委会,上海市微生物学会微生物耐药防控专委会.MALDI-TOF MS病原体鉴定质量保证专家共识[J].中华检验医学杂志,2018,41(8):567-570.
[37] 张仁峰,张炳昌,邵春红,等.MALDI-TOF MS用于碳青霉烯耐药肺炎克雷伯菌同源性分析的初步研究[J].中华检验医学杂志,2018,41(8):589-595.