天津地区鸡源沙门氏菌的基因分型研究

目的 研究并评估几种分子分型方法对亲缘关系相近沙门氏菌的分辨能力。方法 针对2015-2016年从天津市大型市场和超市中分离的106株沙门氏菌及其全基因组测序结果,分析了沙门氏菌的血清型、STs,并通过PFGE、cgMLST以及一种基于59个基因的分型方法对沙门氏菌进行分子分型研究。结果 106株沙门氏菌共分为8种血清型(肠炎沙门氏菌(n=94)、印第安纳沙门氏菌(n=4)、肯塔基沙门氏菌(n=2)、哈达尔沙门氏菌(n=2)、汤普森沙门氏菌(n=1)、鼠伤寒沙门氏菌(n=1)、田纳西沙门氏菌(n=1)和阿哥纳沙门氏菌(n=1))和8个ST型;PFGE分型方法将沙门氏菌分为7个集群,cgMLST分为8个集群,59个基因的分型方法将亲缘关系相近的分离株分为9个集群。结论 血清型分析表明肠炎沙门氏菌为这些沙门氏菌中的优势亚型,并与ST型结果一致;PFGE显示7个集群中包含一个优势集群,多为肠炎亚型;cgMLST具有最高的分辨率,将106株沙门氏菌分为8个集群;建立的基于59个基因的分子分型方法将沙门氏菌分为9个集群,分型结果表明此方法可以满足对亲缘关系相近沙门氏菌的分型研究。     

Wine yeast molecular typing using a simplified method for simultaneously extracting mtDNA,nuclear DNA and virus dsRNA

Quick and accurate methods are required for the identification of industrial, environmental, and clinical yeast strains. We propose a rapid method for the simultaneous extraction of yeast mtDNA, nuclear DNA, and virus dsRNA. It is simpler, cheaper, and faster than the previously reported methods. It allows one to choose among a broad range of molecular analysis approaches for yeast typing, avoiding the need to use of several different methods for the separate extraction of each nucleic acid type. The application of this method followed by the combined analysis of mtDNA and dsRNA (ScV-M and W) is a highly attractive option for fast and efficient wine yeast typing.     

空肠弯曲菌分离株ERIC-PCR分型和生化分型的比较研究

建立空肠弯曲菌(Campylobacter jejuni)的ERIC-PCR分子生物学分型技术,比较ERIC-PCR分型和生化分型的分型效果。从菌株TY1273出发,运用L16(54)正交试验,对Mg2+、dNTPs、引物和TaqDNA聚合酶浓度等因素在较大范围水平内进行反应体系条件摸索,得到一个初步的优化体系;在此基础之上进行单因素的进一步小范围水平内的微调优化,得到最终的优化体系;最后以优化的ERIC-PCR方法对24株C.jejuni分离株分型;同时根据API Campy生化反应结果进行生化分型,比较ERIC-PCR分子分型方法和生化分型方法。结果显示ERIC-PCR方法将24株菌扩增均得到大小在100 bp-3000 bp之间的条带,并可将其分为22个基因型,分辨系数为0.92,具有较高的分辨力。生化分型将24株菌分为19个生化型,显示了菌株基因的多样性。表明ERIC-PCR技术比生化分型能更好的体现菌株的遗传多样性,且具有简便和分辨力搞等优点,可用于C.jejuni的多样性研究。     

河北地区食源性单核细胞增生李斯特菌脂肪酸的分型研究

对脂肪酸分型方法在单核细胞增生李斯特菌(LM)菌株鉴定、菌株相似性分析等方面的应用价值进行评价。本研究选取2005~2007年从河北地区六大类食品中分离到的90株LM菌,提取脂肪酸,利用MIDI公司Sherlock系统进行菌体脂肪酸成分分析,使用SPSS 19.0软件对获得的数据资料进行统计分析及聚类分型,并将脂肪酸分型与传统的血清分型和分型金标准PFGE分型进行比较。结果表明,脂肪酸分析法判定LM菌的符合率为96.67%,所有菌株共检出20种脂肪酸成分,主要脂肪酸成分有3种,分别为脂肪酸15:0anteiso、17:0 anteiso和15:0 iso。各血清型间脂肪酸含量存在一定差异,血清1/2c型菌株与血清1/2a、1/2b和4b型菌株相比,有2种主要脂肪酸含量差异有统计学意义(P0.01)。与PFGE分型相比,在对结构简单的小样本资料的菌株亲缘关系鉴定中脂肪酸分型更具优势。将脂肪酸分型与血清学分型和PFGE分型相结合能够更好的分析LM菌菌株之间的相关性。     

Application of multiple locus variable number of tandem repeat analysis (MLVA), phage typing and antimicrobial susceptibility testing to subtype Salmonella enterica serovar Typhimurium isolated from pig farms, pork slaughterhouses and meat producing plants in Ireland

Salmonella enterica subsp. enterica serovar Typhimurium is a common zoonotic pathogen encountered in Irish pigs and the pork industry and its characterisation using highly discriminatory typing methods is necessary for epidemiological studies, outbreak investigation and control. Multiple locus variable number of tandem repeat analysis (MLVA), phage typing and antimicrobial susceptibility testing were applied to characterise 301 S. typhimurium isolates of porcine origin isolated from farms, slaughterhouses and pork meat producing plants in Ireland over a four-year period. 154 MLVA patterns were obtained compared to 19 phage types and 38 AMR patterns, and MLVA was particularly useful for discriminating isolates of the same phage type, e.g. DT104 and DT104b, or isolates that were Untypable or in the category of "react with phage but does not conform to a recognised phage type" (RDNC) by the phage typing method. Cluster analysis of MLVA profiles using a minimum spanning tree (MST) demonstrated two major clusters (I and II), which showed to have a clear association with phage types, cluster I associated to phage types DT104, U302 and DT120 and cluster II associated to DT193 and U288. The results of this present study showed that MLVA is highly discriminatory and permitted the identification of identical profiles among isolates obtained at different points of the pork food chain. The same MLVA profile was observed in some cases among isolates with different phage types. While this can be explained by the fact that some phage types are closely related, it also indicates that combining phage typing and MLVA enhances strain typing of S. typhimurium.     

阪崎克罗诺杆菌鉴定分型方法的比较及耐药特征分析

目的 开展乳粉原料中分离的阪崎克罗诺杆菌(Cronobacter sakazakii, C. sakazakii)鉴定分型比较研究及抗生素耐药基因特征分析。方法 采用形态学观察、生理生化特征分析、基质辅助激光解吸/电离飞行时间质谱法、16S rDNA测序分析,和基于全基因组测序技术的平均核苷酸一致性分析、多位点序列分型和基于全基因组的多位点序列分型技术,建立了对分离的2株C. sakazakii的鉴定分型方法,并对不同的方法进行比较,同时预测O-血清型和抗生素抗性基因。结果 本研究中分离菌株16-26、31-3经形态学、生理生化反应、16S rDNA、质谱和平均核苷酸一致性分析,均鉴定为C. sakazakii,可信度均在95%以上; MLST预测16-26为ST新型、31-3为ST4型, O血清型均为gnd 3型、galF 2型,均含有9种抗性基因, 2株C. sakazakii分离株的抗性基因呈现出多样性。结论 通过对分离的C. sakazakii进行鉴定分型比较研究,建立了一种基于表型和分子分型的食源性致病菌鉴定分型方法,为食源性致病菌的有效防控提供了有力的技术支撑和监管依据。     

多位点可变数量串联重复序列分析在细菌分子分型中的应用

多位点可变数量串联重复序列分析(multiple-locus variable number tandem repeat analysis,MLVA)是通过基因组中可变数量串联重复序列(variable number tandem repeat,VNTR)的特征来实现分型的分子分型技术,其特征是简单、快速、通量高、分辨力强,目前已广泛用于多种细菌分子分型.本文就MLVA技术的原理、在细菌分子分型中的应用及与其他分型方法的比较进行综述.     

ERIC-PCR及全自动核糖体分型法鉴定不同来源的解朊金黄杆菌

目的:为了建立一种高效分离筛选高产蛋白质谷氨酰胺酶的解朊金黄杆菌的筛选方法,采用肠道基因间重复序列扩增(ERIC-PCR)和全自动核糖体分型方法对来自不同环境的33株解朊金黄杆菌(Chryseobacterium proteolyticum)进行分子分型研究。方法:采用ERIC国际通用引物对33株解朊金黄杆菌进行PCR扩增和琼脂糖凝胶电泳检测,使用NTsys软件对电泳图进行聚类分析。同时,采用全自动核糖体分型方法对33株解朊金黄杆菌进行核糖体分型,采用Bionumeric软件对菌株进行聚类分析。结果:两种方法均可得到清晰的指纹图谱,可对33株解朊金黄杆菌进行分子分型。ERIC-PCR可扩增出3~9个100~10000 bp之间的条带,将菌株分为2个族群。全自动核糖体分型方法可将菌株分为2个亚型,每种亚型间菌株仍有细微差异。结论:同种菌株之间同源性达到99%以上,但仍在遗传进化关系上存在差异。来自同一地区的分离株有聚类成一类的趋势,且与菌株的产酶能力存在密切关联。研究结果表明聚类于族群Ⅱ的菌株基本都来自于河南,且该类群菌株的产酶能力明显高于族群Ⅰ。     

应用DiversiLab分型系统对沙门氏菌进行同源性分析

目的:为研究食品污染中沙门氏菌间的同源性关系,建立起沙门氏菌基于重复序列的分型技术。通过建立DiversiLab基因图谱数据库,以便对将来不同来源的沙门氏菌的基因图谱进行即时比较,确定其同源性,进而追溯污染来源,切断传播途径,为预测预警保障食品安全提供科学依据,为防止食源性疾病的发生提供技术支持。同时进行血清分型,比较分析2种方法的优劣和之间的关系。方法:对2002～2010年福建省出入境检验检疫局从各类食品及饲料中分离出的沙门氏菌先进行血清分型,然后进行DiversiLab分型,其中包括:DNA提取,rep-PCR和微电泳芯片分离检测。rep-PCR条件:94℃预变性2min;94℃变性30s,50℃退火30s,70℃延伸90s,35个循环,最后70℃延伸3min。结果:23株沙门氏菌被分成6个血清型,DiversiLab分型能将相同血清型的菌株分为不同的亚型。同一企业来源的菌株具有同源性。结论:DiversiLab分型系统是一种快速、易于操作、高重复性、高分辨率的基因分型方法,可作为食源性疾病同源性分型工具。结论:DiversiLab分型的分辨率高于血清型,2种分型方法密切相关。     

不同测定方法对大豆分离蛋白乳化性测定结果的影响

采用离心法、分光光度法、电导法对几种不同的大豆分离蛋白的乳化性进行测定，测定结果表明，采用不同方法测定四种大豆分离蛋白的乳化性，其总的趋势基本相同，说明这几种方法都可用于测定大豆分离蛋白的乳化性。相对而言，离心法简单可行，是一种比较适用的方法，其它两种方法仪器设备要求较高，且操作步骤比较繁琐。     

Strain typing of acetic acid bacteria responsible for vinegar production by the submerged elaboration method

Strain typing of 103 acetic acid bacteria isolates from vinegars elaborated by the submerged method from ciders, wines and spirit ethanol, was carried on in this study. Two different molecular methods were utilised: pulsed field gel electrophoresis (PFGE) of total DNA digests with a number of restriction enzymes, and enterobacterial repetitive intergenic consensus (ERIC) – PCR analysis. The comparative study of both methods showed that restriction fragment PFGE of SpeI digests of total DNA was a suitable method for strain typing and for determining which strains were present in vinegar fermentations. Results showed that strains of the species Gluconacetobacter europaeus were the most frequent leader strains of fermentations by the submerged method in the studied vinegars, and among them strain R1 was the predominant one. Results showed as well that mixed populations (at least two different strains) occurred in vinegars from cider and wine, whereas unique strains were found in spirit vinegars, which offered the most stressing conditions for bacterial growth.     

Molecular typing of Vibrio parahaemolyticus isolates from the middle-east coastline of China

The occurrence of outbreaks of Vibrio parahaemolyticus gastroenteritis in China highlights the need for strain characterization and subtyping of this pathogenic species. A total of 56 epidemiologically-unrelated strains of V. parahaemolyticus were isolated from clinical samples, seafood and various environmental sites in the middle-east coastline of China from 2006 to 2008. The isolates were characterized using four molecular typing methods, including ribotyping, enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR), pulsed-field gel electrophoresis (PFGE), and sequence analysis of the gyrB gene. Genetic profiles of cluster analysis from these molecular typing tests clearly showed that there were differences in potential pathogenicity among isolates from seafood and its environments. Genetic characterization of two isolates (F13 and QS2) that originated from seafood demonstrated that they were potentially pathogenic. Discriminatory indices of four typing methods for the 56 V. parahaemolyticus isolates were differentiated by Simpson's Index of Diversity. The discriminatory index of ERIC-PCR typing was maximal (D = 0.942), while that of sequence analysis of the gyrB gene was minimal (D = 0.702). The discriminatory ability was greatly enhanced (D = 0.966) when ERIC-PCR was coupled with sequence analysis of the gyrB gene. These results suggest that ERIC-PCR combined with sequence analysis of gyrB gene may be a reliable, rapid typing strategy for V. parahaemolyticus strains.     

Rapid discrimination of Salmonella isolates by single-strand conformation polymorphism analysis

A molecular typing technique was developed for the differentiation of Salmonella isolates based on single-strand conformation polymorphism (SSCP) analysis of amplicons generated by PCR. Amplicons from parts of the fimA (both the 5' and 3' ends), mdh, invA, and atpD genes were generated separately from a panel of Salmonella strains representing Salmonella bongori, and four subspecies and 17 serovars of Salmonella enterica. These amplicons were subjected to SSCP analysis for differentiation of the salmonellae on the basis of different conformational forms arising due to nucleotide sequence variations in the target genes. Several distinct SSCP banding patterns (a maximum of 14 each for atpD and fimA 3' end) were observed with this panel of Salmonella strains for amplicons generated from each target gene. The best discrimination of Salmonella subspecies and serovar was achieved from the SSCP analysis of a combination of at least three gene targets: atpD, invA, and either mdh or fimA 3' end. This demonstrates the applicability of SSCP analysis as an important additional method to classical typing approaches for the differentiation of foodborne Salmonella isolates. SSCP is simple to perform and should be readily transferable to food microbiology laboratories with basic PCR capability.     

High-resolution genotyping of Listeria monocytogenes by fluorescent amplified fragment length polymorphism analysis compared to pulsed-field gel electrophoresis, random amplified polymorphic DNA analysis, ribotyping, and PCR-restriction fragment length polymorphism analysis

The purpose of this study was to evaluate fluorescent amplified fragment length polymorphism (AFLP) analysis for the inter- and intraspecies differentiation of a collection of 96 strains of Listeria monocytogenes and 10 non-L. monocytogenes strains representing six other Listeria species of different origin. The AFLP technique was compared with three other molecular typing methods--ribotyping, random amplified polymorphic DNA analysis (RAPD), and pulsed-field gel electrophoresis (PFGE)--in terms of discriminatory ability. PCR-restriction fragment length polymorphism was included for virulence gene allele characterization. The 96 L. monocytogenes strains were divided into two major clusters by AFLP fingerprinting at a similarity level of 82% in concordance with the results of PFGE, RAPD, and ribotyping. One main cluster consisted of all of the 24 L. monocytogenes hly allele 1 strains, while another main cluster consisted of all of the 72 L. monocytogenes hly allele 2 strains. This indicates the existence of two distinct phylogenetic divisions. Isolates of the remaining Listeria species were not included in the clusters. AFLP, PFGE, and RAPD typing were highly discriminatory methods, with discrimination (D) indices of 0.974, 0.969, and 0.954, respectively, whereas ribotyping had a lower D index of 0.874. AFLP, PFGE, and RAPD typing showed some level of agreement in terms of strain grouping and differentiation. However, all three methods subdivided types of strains grouped by the other methods. Isolates with identical DNA profiles were distributed across the spectrum of origin. It was not possible to associate certain types with specific food sectors or clinical cases, which is indicative of the spread of L. monocytogenes clones across species. Overall, AFLP fingerprinting was suitable for the high-resolution genotyping of L. monocytogenes and had an equally high or higher differentiation power compared to PFGE or RAPD typing.     

海水提取硝酸钾新工艺过程中硝酸根的测定

目前用于测硝酸根的方法较多,但对于工业生产而言,快速、简便、而又比较准确的方法很少。为了满足海水提取硝酸钾新工艺的要求,文章选择了离子选择电极法来测定硝酸根离子,并对存在的相关问题进行讨论。     

傅立叶变换红外光谱技术对6种致病性大肠埃希氏菌快速分型的研究

目的建立肠致病性大肠埃希氏菌(Enteropathogenic E.coli,EPEC)、肠产毒性大肠埃希氏菌(Enterotoxigenic E.coli,ETEC)、肠侵袭性大肠埃希氏菌(Enteroinvasive E.coli,EIEC)、肠黏附性大肠埃希氏菌(Enteroadhesive E.coli,EAEC)、肠出血性大肠埃希氏菌(Enterohmorrhagic E.coli,EHEC)、弥散粘附性大肠埃希氏菌(Diffusely adherent E.coli,DAEC)6种致病性大肠埃希氏菌的傅立叶变换红外光谱(Fourier transform infrared spectroscopy,FT-IR)数据库及FT-IR分型方法。方法应用FT-IR技术对6种致病性大肠埃希氏菌进行指纹图谱数据采集并对其进行基线校正、归一化等处理,应用化学计量学方法对光谱数据进行分析。结果本研究建立了6种致病性大肠埃希氏菌的FT-IR光谱数据库,实现了对6种可疑目标大肠埃希氏菌鉴定;建立了主成分分析(principal component analysis,PCA)和分级聚类分析(hierarchical cluster analysis,HCA)2种模型,成功实现了对6种致病性大肠埃希氏菌的快速分型。结论 FT-IR分析方法快速、简便、易操作,结果重现性好,是一种鉴定6种致病性大肠埃希氏菌的有效方法。     

The PhenePlate system for studies of the diversity of enterococcal populations from the food chain and the environment

The growing interest in ecological investigations, such as studies of the "flow" of bacteria through the food chain, has resulted in a great need for simple typing techniques for bacteria that can be used when a large number of isolates need to be analysed. The present study describes a simple method for biochemical fingerprinting of enterococci, the PhenePlate RF (PhP-RF) system. The system is based on a 96-well microplate containing eight sets of 11 dehydrated reagents, selected to have a high discriminatory power among enterococcal isolates. The PhP plates are inoculated easily by picking single colonies directly from the primary agar culture and suspending them in the first well of each row in the microplate. The kinetics of each reaction is evaluated by measuring the absorbance value of each well three times during 64 h, whereupon a biochemical fingerprint is calculated as the mean value for each reagent over the three readings. The PhP-RF method was shown to be highly reproducible, even when results were compared between different laboratories. The discriminatory power, measured as Simpson's diversity index (Di), was as high as 0.96 for all enterococci. The PhP-RF method could also be used as a preliminary species identification method, by comparing the biochemical fingerprints of unknown strains to those of a set of reference strains of known species. Most strains of Enterococcus faecalis, Enterococcus faecium and Enterococcus hirae were correctly identified using this method. We conclude that the PhenePlate RF system is useful for rapid typing of enterococcal populations, and it is especially useful as a first screening method for ecological studies, when many isolates per sample need to be analysed.     

蜡样芽孢杆菌ERIC-PCR分子分型方法的建立

为建立简单快速的蜡状芽孢杆菌(Bacillus cereus)基因间重复共有序列PCR(ERIC-PCR)的分子分型方法,该研究以B.cereusCMCC 63303的基因组DNA为模板,并采用正交设计L16(45)对影响ERIC-PCR反应体系的五个因素(模板DNA、Mg2+、dNTP、TaqDNA聚合酶、引物)在四个浓度水平上进行优化,并通过单因素试验确定最佳退火温度,最后以优化后的反应体系对50株B.cereus分离株进行ERIC-PCR分子分型和聚类分析验证其稳定性和分型效果。结果显示应用建立的ERIC-PCR反应体系对50株分离株扩增均得到了9-17条、大小在200-4000 bp之间的条带,并可将其分为47个型,且分辨力达到0.996,具有较高稳定性和分辨能力。表明ERIC-PCR技术对B.cereus分型,具有简便和分辨力高等优点,可用于食源性B.cereus分离株的多样性研究。     

Free Amino Acids in Cheddar Cheese: Comparison of Quantitation Methods

Two reported methods were compared with a more rapid and accurate flow injection analysis (FIA) technique. A trinitrobenzenesulfonic acid (TNBS) method provided absolute values, was tedious, and the reagent was light-sensitive and required heating. An o-phthaldialdehyde (OPA) method was faster and less variable than the TNBS, but reaction time had to be carefully controlled. The results with the OPA correlated well with the TNBS but were overestimated due to reading small peptides and ammonium ions. The FIA method was simple and reliable, yielded values which correlated closely with amino acids and gave information about degree of proteolysis.     

Molecular typing of Streptococcus uberis strains isolated from cases of bovine mastitis

The discriminatory power of two polymerase chain reaction-based DNA fingerprinting methods, random amplified polymorphic DNA and repetitive extragenic palindrome were compared by subtyping 128 isolates of Streptococcus uberis cultured from cows in six different dairy herds in New Zealand. The typing results demonstrated that the majority of isolates possessed unique fingerprint profiles except on occasions where multiple isolates were obtained from individual cows. On these occasions, individual quarters of the mammary gland were generally, but not exclusively, infected by the same strain of bacteria. Both random amplified polymorphic DNA and repetitive extragenic palindromic typing assays were simple to perform, relatively inexpensive ($11.00 per reaction), and provided reliable and reproducible results. Furthermore, when these assays were used in conjunction with each other, they provided a means of confirmation of the specific DNA fingerprint patterns obtained.